From 314059e764433825e2b6cc032ca988e59431aca9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Sat, 25 May 2024 09:40:51 +0200 Subject: [PATCH] Results --- revdep/README.md | 64 +- revdep/cran.md | 227 +- revdep/failures.md | 188 - revdep/problems.md | 8553 +++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 8837 insertions(+), 195 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 598c4babd8..a0439223f9 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,10 +1,70 @@ # Revdeps -## Failed to check (3) +## Failed to check (2) |package |version |error |warning |note | |:---------|:-------|:-----|:-------|:----| |multinma |0.6.1 |1 | | | -|Seurat |? | | | | |streamDAG |? | | | | +## New problems (56) + +|package |version |error |warning |note | +|:------------|:-------|:--------|:-------|:--------| +|[akc](problems.md#akc)|0.9.9 |1 __+1__ | | | +|[archeofrag](problems.md#archeofrag)|0.8.2 |__+3__ | |__+1__ | +|[arulesViz](problems.md#arulesviz)|1.5-2 |__+1__ | | | +|[bigergm](problems.md#bigergm)|1.1.0 |__+3__ | |1 __+1__ | +|[bioregion](problems.md#bioregion)|1.1.0 |__+1__ | |1 | +|[bnviewer](problems.md#bnviewer)|0.1.6 |__+2__ | |2 | +|[causaloptim](problems.md#causaloptim)|0.9.8 |__+1__ | |1 | +|[cglasso](problems.md#cglasso)|2.0.7 |__+1__ | | | +|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | +|[cppRouting](problems.md#cpprouting)|3.1 |__+1__ | |4 | +|[cranly](problems.md#cranly)|0.6.0 |__+1__ | |1 __+1__ | +|[criticalpath](problems.md#criticalpath)|0.2.1 |__+3__ | |__+1__ | +|[dartR](problems.md#dartr)|2.9.7 | |1 |__+1__ | +|[debkeepr](problems.md#debkeepr)|0.1.1 |1 | |1 __+1__ | +|[DiagrammeR](problems.md#diagrammer)|1.0.11 |__+2__ | |1 | +|[dyndimred](problems.md#dyndimred)|1.0.4 |__+1__ | |2 | +|[dynwrap](problems.md#dynwrap)|1.2.4 |1 __+1__ | | | +|[egor](problems.md#egor)|1.24.2 |__+3__ | |__+1__ | +|[epicontacts](problems.md#epicontacts)|1.1.3 |__+2__ | |1 __+1__ | +|[erah](problems.md#erah)|2.0.1 |__+1__ | | | +|[fastRG](problems.md#fastrg)|0.3.2 |__+1__ | | | +|[fbnet](problems.md#fbnet)|1.0.3 |__+1__ | |1 | +|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | +|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | |1 __+1__ | +|[grainscape](problems.md#grainscape)|0.4.4 |__+3__ | |2 | +|[graphlayouts](problems.md#graphlayouts)|1.1.1 |1 __+2__ | |2 | +|[intergraph](problems.md#intergraph)|2.0-4 |__+3__ | |__+1__ | +|[interplex](problems.md#interplex)|0.1.2 |__+1__ | | | +|[LTFHPlus](problems.md#ltfhplus)|2.1.1 |__+1__ | | | +|[manynet](problems.md#manynet)|0.4.4 |__+2__ | |2 | +|[massiveGST](problems.md#massivegst)|1.2.3 |__+2__ | |__+1__ | +|[MEGENA](problems.md#megena)|1.3.7 |__+1__ | |1 __+1__ | +|[morph](problems.md#morph)|1.1.0 |__+1__ | | | +|[motifr](problems.md#motifr)|1.0.0 |__+1__ | | | +|[mstknnclust](problems.md#mstknnclust)|0.3.2 |__+2__ | |__+1__ | +|[multinet](problems.md#multinet)|4.1.2 |__+1__ | |2 | +|[nda](problems.md#nda)|0.1.13 |__+1__ | | | +|[Neighboot](problems.md#neighboot)|1.0.1 |__+1__ | | | +|[PCGII](problems.md#pcgii)|1.1.2 |__+1__ | | | +|[pmd](problems.md#pmd)|0.2.1 |__+2__ | |2 __+1__ | +|[polymapR](problems.md#polymapr)|1.1.5 |__+2__ | |1 __+1__ | +|[ptools](problems.md#ptools)|2.0.0 |__+2__ | | | +|[RavenR](problems.md#ravenr)|2.2.0 |__+2__ | |1 __+1__ | +|[rdracor](problems.md#rdracor)|1.0.3 |__+1__ | | | +|[ReDaMoR](problems.md#redamor)|0.7.4 |__+2__ | |__+1__ | +|[rgexf](problems.md#rgexf)|0.16.2 |__+1__ | | | +|[RNewsflow](problems.md#rnewsflow)|1.2.8 |__+1__ |1 |1 | +|[rsetse](problems.md#rsetse)|0.5.0 |__+2__ | |__+1__ | +|[rTwig](problems.md#rtwig)|1.0.2 |__+2__ | |__+1__ | +|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 | +|[SOMbrero](problems.md#sombrero)|1.4-2 |__+1__ | | | +|[TDApplied](problems.md#tdapplied)|3.0.3 |__+2__ | |1 __+1__ | +|[textrank](problems.md#textrank)|0.3.1 |__+2__ | |__+1__ | +|[tidygraph](problems.md#tidygraph)|1.3.1 |__+1__ | | | +|[timeordered](problems.md#timeordered)|1.0.0 |__+1__ | | | +|[wikkitidy](problems.md#wikkitidy)|0.1.12 |__+1__ | | | + diff --git a/revdep/cran.md b/revdep/cran.md index f2f6a1bdd3..43e2e5aa69 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,14 +1,233 @@ ## revdepcheck results -We checked 833 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 836 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems - * We failed to check 3 packages + * We saw 56 new problems + * We failed to check 2 packages Issues with CRAN packages are summarised below. +### New problems +(This reports the first line of each new failure) + +* akc + checking examples ... ERROR + +* archeofrag + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* arulesViz + checking examples ... ERROR + +* bigergm + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* bioregion + checking examples ... ERROR + +* bnviewer + checking examples ... ERROR + checking tests ... ERROR + +* causaloptim + checking tests ... ERROR + +* cglasso + checking examples ... ERROR + +* corrViz + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* cppRouting + checking examples ... ERROR + +* cranly + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* criticalpath + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* dartR + checking installed package size ... NOTE + +* debkeepr + checking re-building of vignette outputs ... NOTE + +* DiagrammeR + checking examples ... ERROR + checking tests ... ERROR + +* dyndimred + checking tests ... ERROR + +* dynwrap + checking examples ... ERROR + +* egor + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* epicontacts + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* erah + checking tests ... ERROR + +* fastRG + checking tests ... ERROR + +* fbnet + checking examples ... ERROR + +* GGally + checking tests ... ERROR + +* ggraph + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* grainscape + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + +* graphlayouts + checking examples ... ERROR + checking tests ... ERROR + +* intergraph + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* interplex + checking examples ... ERROR + +* LTFHPlus + checking examples ... ERROR + +* manynet + checking examples ... ERROR + checking tests ... ERROR + +* massiveGST + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MEGENA + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* morph + checking examples ... ERROR + +* motifr + checking examples ... ERROR + +* mstknnclust + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* multinet + checking examples ... ERROR + +* nda + checking examples ... ERROR + +* Neighboot + checking examples ... ERROR + +* PCGII + checking running R code from vignettes ... ERROR + +* pmd + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* polymapR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ptools + checking examples ... ERROR + checking tests ... ERROR + +* RavenR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rdracor + checking tests ... ERROR + +* ReDaMoR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rgexf + checking tests ... ERROR + +* RNewsflow + checking examples ... ERROR + +* rsetse + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rTwig + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* skynet + checking tests ... ERROR + +* SOMbrero + checking examples ... ERROR + +* TDApplied + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* textrank + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* tidygraph + checking tests ... ERROR + +* timeordered + checking examples ... ERROR + +* wikkitidy + checking examples ... ERROR + ### Failed to check * multinma (NA) -* Seurat (NA) * streamDAG (NA) diff --git a/revdep/failures.md b/revdep/failures.md index bf7d966d7d..b93704ab94 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -172613,194 +172613,6 @@ ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ -``` -# Seurat - -
- -* Version: 5.0.3 -* GitHub: https://github.com/satijalab/seurat -* Source code: https://github.com/cran/Seurat -* Date/Publication: 2024-03-18 23:40:02 UTC -* Number of recursive dependencies: 265 - -Run `revdepcheck::cloud_details(, "Seurat")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK -* this is package ‘Seurat’ version ‘5.0.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE -Package suggested but not available for checking: ‘monocle’ -* checking if this is a source package ... OK -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Seurat’ can be installed ... OK -* used C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -* checking C++ specification ... OK - Not all R platforms support C++17 -* checking installed package size ... NOTE - installed size is 17.6Mb - sub-directories of 1Mb or more: - R 1.9Mb - libs 14.5Mb -* checking package directory ... OK -* checking DESCRIPTION meta-information ... OK -* checking top-level files ... OK -* checking for left-over files ... OK -* checking index information ... OK -* checking package subdirectories ... OK -* checking R files for non-ASCII characters ... OK -* checking R files for syntax errors ... OK -* checking whether the package can be loaded ... OK -* checking whether the package can be loaded with stated dependencies ... OK -* checking whether the package can be unloaded cleanly ... OK -* checking whether the namespace can be loaded with stated dependencies ... OK -* checking whether the namespace can be unloaded cleanly ... OK -* checking loading without being on the library search path ... OK -* checking startup messages can be suppressed ... OK -* checking dependencies in R code ... OK -* checking S3 generic/method consistency ... OK -* checking replacement functions ... OK -* checking foreign function calls ... OK -* checking R code for possible problems ... OK -* checking Rd files ... OK -* checking Rd metadata ... OK -* checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘Signac’ -* checking for missing documentation entries ... OK -* checking for code/documentation mismatches ... OK -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking line endings in C/C++/Fortran sources/headers ... OK -* checking line endings in Makefiles ... OK -* checking compilation flags in Makevars ... OK -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 3 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ -* using R version 4.3.1 (2023-06-16) -* using platform: x86_64-pc-linux-gnu (64-bit) -* R was compiled by - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 -* running under: Ubuntu 20.04.6 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Seurat/DESCRIPTION’ ... OK -* this is package ‘Seurat’ version ‘5.0.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE -Package suggested but not available for checking: ‘monocle’ -* checking if this is a source package ... OK -* checking if there is a namespace ... OK -* checking for executable files ... OK -* checking for hidden files and directories ... OK -* checking for portable file names ... OK -* checking for sufficient/correct file permissions ... OK -* checking whether package ‘Seurat’ can be installed ... OK -* used C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ -* checking C++ specification ... OK - Not all R platforms support C++17 -* checking installed package size ... NOTE - installed size is 17.6Mb - sub-directories of 1Mb or more: - R 1.9Mb - libs 14.5Mb -* checking package directory ... OK -* checking DESCRIPTION meta-information ... OK -* checking top-level files ... OK -* checking for left-over files ... OK -* checking index information ... OK -* checking package subdirectories ... OK -* checking R files for non-ASCII characters ... OK -* checking R files for syntax errors ... OK -* checking whether the package can be loaded ... OK -* checking whether the package can be loaded with stated dependencies ... OK -* checking whether the package can be unloaded cleanly ... OK -* checking whether the namespace can be loaded with stated dependencies ... OK -* checking whether the namespace can be unloaded cleanly ... OK -* checking loading without being on the library search path ... OK -* checking startup messages can be suppressed ... OK -* checking dependencies in R code ... OK -* checking S3 generic/method consistency ... OK -* checking replacement functions ... OK -* checking foreign function calls ... OK -* checking R code for possible problems ... OK -* checking Rd files ... OK -* checking Rd metadata ... OK -* checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘Signac’ -* checking for missing documentation entries ... OK -* checking for code/documentation mismatches ... OK -* checking Rd \usage sections ... OK -* checking Rd contents ... OK -* checking for unstated dependencies in examples ... OK -* checking contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... OK -* checking LazyData ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking line endings in C/C++/Fortran sources/headers ... OK -* checking line endings in Makefiles ... OK -* checking compilation flags in Makevars ... OK -* checking for GNU extensions in Makefiles ... OK -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK -* checking use of PKG_*FLAGS in Makefiles ... OK -* checking compiled code ... OK -* checking examples ... OK -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 3 NOTEs - - - - - ``` # streamDAG diff --git a/revdep/problems.md b/revdep/problems.md index 9a20736339..df254a6d66 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1 +1,8552 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# akc + +
+ +* Version: 0.9.9 +* GitHub: https://github.com/hope-data-science/akc +* Source code: https://github.com/cran/akc +* Date/Publication: 2023-01-06 08:00:02 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "akc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘akc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: doc_group + > ### Title: Construct network of documents based on keyword co-occurrence + > ### Aliases: doc_group + > + > ### ** Examples + > + > library(akc) + > bibli_data_table %>% + + keyword_clean(id = "id",keyword = "keyword") %>% + + doc_group(id = "id",keyword = "keyword") -> grouped_doc + Error in `rename()`: + ! Can't rename columns that don't exist. + ✖ Column `name` doesn't exist. + Backtrace: + ▆ + 1. ├─... %>% doc_group(id = "id", keyword = "keyword") + 2. ├─akc::doc_group(., id = "id", keyword = "keyword") + 3. │ └─... %>% rename(id = name) + 4. ├─dplyr::rename(., id = name) + 5. ├─tidygraph:::rename.tbl_graph(., id = name) + 6. │ ├─dplyr::rename(d_tmp, ...) + 7. │ └─dplyr:::rename.data.frame(d_tmp, ...) + 8. │ └─tidyselect::eval_rename(expr(c(...)), .data) + 9. │ └─tidyselect:::rename_impl(...) + 10. │ └─tidyselect:::eval_select_impl(...) + 11. │ ├─tidyselect:::with_subscript_errors(...) + 12. │ │ └─base::withCallingHandlers(...) + 13. │ └─tidyselect:::vars_select_eval(...) + 14. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) + 15. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) + 16. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) + 17. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) + 18. │ └─tidyselect:::as_indices_sel_impl(...) + 19. │ └─tidyselect:::as_indices_impl(...) + 20. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg) + 21. │ └─vctrs::vec_as_location(...) + 22. └─vctrs (local) ``() + 23. └─vctrs:::stop_subscript_oob(...) + 24. └─vctrs:::stop_subscript(...) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Benchmarking.Rmd’ + ... + + keyword_merge() + + > topn_sample <- 100:300 + + > com_detect_fun_list <- ls("package:akc") %>% str_extract("^group.+") %>% + + na.omit() %>% setdiff(c("group_biconnected_component", "group_compon ..." ... [TRUNCATED] + + When sourcing ‘Benchmarking.R’: + Error: could not find function "str_extract" + Execution halted + + ‘Benchmarking.Rmd’ using ‘UTF-8’... failed + ‘akc_vignette.Rmd’ using ‘UTF-8’... OK + ‘tutorial_raw_text.Rmd’ using ‘UTF-8’... OK + ``` + +# archeofrag + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/sebastien-plutniak/archeofrag +* Source code: https://github.com/cran/archeofrag +* Date/Publication: 2022-09-11 22:02:59 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "archeofrag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘archeofrag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_cr_graph + > ### Title: Make a "connection" relationships graph. + > ### Aliases: make_cr_graph make_cr_graph-methods + > ### Keywords: build data + > + > ### ** Examples + > + > cr.df <- matrix(c(1,2, 1,3, 2,3, 4,5, 4,6, 7,8), ncol=2, byrow=TRUE) + > sr.df <- matrix( c(1,1, 9,1, 10,1, 11,2, 12,2, 13,2), ncol=2, byrow=TRUE) + > fragments.df <- data.frame(1:13, letters[1:13]) + > + > cr_g <- make_frag_object(cr=cr.df, fragments=fragments.df) + > crsr_g <- make_frag_object(cr=cr.df, sr=sr.df, fragments=fragments.df) + > + > make_cr_graph(cr_g) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 8, the number of target vertices, not 13 + Calls: make_cr_graph ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(archeofrag) + > + > test_check("archeofrag") + H1 != H2? p.value Obs. value/H1 Obs. value/H2 + edges TRUE 0.02 lower within + weightsum FALSE 0.06 lower within + balance FALSE 0.45 higher higher + disturbance FALSE 0.9 lower lower + admixture FALSE 0.98 within within + cohesion1 FALSE 0.05 within higher + cohesion2 FALSE 0.07 within lower + [ FAIL 3 | WARN 2 | SKIP 0 | PASS 57 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-frag.diameters.R:6:3'): frag.diameters ───────────────────────── + Error in `data.frame(..., check.names = FALSE)`: arguments imply differing number of rows: 78, 177 + Backtrace: + ▆ + 1. ├─archeofrag::make_cr_graph(abu.frag) at test-frag.diameters.R:6:3 + 2. └─archeofrag::make_cr_graph(abu.frag) + 3. └─igraph::graph_from_data_frame(...) + 4. └─base::cbind(data.frame(name = names), vertices) + 5. └─base::cbind(deparse.level, ...) + 6. └─base::data.frame(..., check.names = FALSE) + ── Error ('test-frag.diameters.R:13:3'): frag.diameters (with cumulative) ────── + Error in `data.frame(..., check.names = FALSE)`: arguments imply differing number of rows: 78, 177 + Backtrace: + ▆ + 1. ├─archeofrag::make_cr_graph(abu.frag) at test-frag.diameters.R:13:3 + 2. └─archeofrag::make_cr_graph(abu.frag) + 3. └─igraph::graph_from_data_frame(...) + 4. └─base::cbind(data.frame(name = names), vertices) + 5. └─base::cbind(deparse.level, ...) + 6. └─base::data.frame(..., check.names = FALSE) + ── Error ('test-make_frag_object.R:42:3'): make_crsr_graph works ─────────────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 8, the number of target vertices, not 13 + Backtrace: + ▆ + 1. ├─archeofrag::make_crsr_graph(f.obj) at test-make_frag_object.R:42:3 + 2. └─archeofrag::make_crsr_graph(f.obj) + 3. ├─archeofrag::make_cr_graph(object) + 4. └─archeofrag::make_cr_graph(object) + 5. └─igraph::graph_from_data_frame(...) + 6. └─igraph::add_vertices(g, length(names), attr = vattrs) + 7. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 8. └─igraph:::i_set_vertex_attr(...) + + [ FAIL 3 | WARN 2 | SKIP 0 | PASS 57 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘archeofrag-vignette.Rmd’ + ... + + > data(LiangAbu) + + > abu.frag <- make_frag_object(cr = df.cr, fragments = fragments.info) + + > abu.g <- make_cr_graph(abu.frag) + + When sourcing ‘archeofrag-vignette.R’: + Error: arguments imply differing number of rows: 78, 177 + Execution halted + + ‘archeofrag-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘archeofrag-vignette.Rmd’ using rmarkdown + + Quitting from lines at lines 61-65 [make-empirical-graph] (archeofrag-vignette.Rmd) + Error: processing vignette 'archeofrag-vignette.Rmd' failed with diagnostics: + arguments imply differing number of rows: 78, 177 + --- failed re-building ‘archeofrag-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘archeofrag-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# arulesViz + +
+ +* Version: 1.5-2 +* GitHub: https://github.com/mhahsler/arulesViz +* Source code: https://github.com/cran/arulesViz +* Date/Publication: 2023-03-07 16:50:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "arulesViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘arulesViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: associations2igraph + > ### Title: Convert rules or itemsets into a graph + > ### Aliases: saveAsGraph associations2igraph igraph tidygraph + > ### Keywords: file + > + > ### ** Examples + > + > data("Groceries") + > rules <- apriori(Groceries, parameter=list(support = 0.01, confidence = 0.5)) + Apriori + + Parameter specification: + confidence minval smax arem aval originalSupport maxtime support minlen + 0.5 0.1 1 none FALSE TRUE 5 0.01 1 + maxlen target ext + 10 rules TRUE + + Algorithmic control: + filter tree heap memopt load sort verbose + 0.1 TRUE TRUE FALSE TRUE 2 TRUE + + Absolute minimum support count: 98 + + set item appearances ...[0 item(s)] done [0.00s]. + set transactions ...[169 item(s), 9835 transaction(s)] done [0.01s]. + sorting and recoding items ... [88 item(s)] done [0.00s]. + creating transaction tree ... done [0.00s]. + checking subsets of size 1 2 3 4 done [0.00s]. + writing ... [15 rule(s)] done [0.00s]. + creating S4 object ... done [0.00s]. + > + > # convert rules into a graph with rules as nodes + > library("igraph") + + Attaching package: ‘igraph’ + + The following object is masked from ‘package:arules’: + + union + + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + > g <- associations2igraph(rules) + > g + IGRAPH d334f71 DN-B 27 45 -- + + attr: name (v/c), label (v/c), index (v/n), type (v/n), support + | (v/n), confidence (v/n), coverage (v/n), lift (v/n), count (v/n) + + edges from d334f71 (vertex names): + [1] 27 ->assoc1 30 ->assoc1 23 ->assoc2 26 ->assoc2 + [5] 23 ->assoc3 55 ->assoc3 30 ->assoc4 31 ->assoc4 + [9] 23 ->assoc5 31 ->assoc5 16 ->assoc6 23 ->assoc6 + [13] 14 ->assoc7 20 ->assoc7 15 ->assoc8 20 ->assoc8 + [17] 15 ->assoc9 20 ->assoc9 15 ->assoc10 30 ->assoc10 + [21] 20 ->assoc11 30 ->assoc11 20 ->assoc12 30 ->assoc12 + [25] 20 ->assoc13 56 ->assoc13 20 ->assoc14 56 ->assoc14 + + ... omitted several edges + > + > plot(g) + > + > # convert the graph into a tidygraph + > library("tidygraph") + + Attaching package: ‘tidygraph’ + + The following object is masked from ‘package:igraph’: + + groups + + The following object is masked from ‘package:stats’: + + filter + + > as_tbl_graph(g) + # A tbl_graph: 27 nodes and 45 edges + # + # A directed acyclic simple graph with 1 component + # + # Node Data: 27 × 9 (active) + name label index type support confidence coverage lift count + + 1 14 citrus fruit 14 1 NA NA NA NA NA + 2 15 tropical fruit 15 1 NA NA NA NA NA + 3 16 pip fruit 16 1 NA NA NA NA NA + 4 20 root vegetables 20 1 NA NA NA NA NA + 5 23 other vegetables 23 1 NA NA NA NA NA + 6 25 whole milk 25 1 NA NA NA NA NA + 7 26 butter 26 1 NA NA NA NA NA + 8 27 curd 27 1 NA NA NA NA NA + 9 30 yogurt 30 1 NA NA NA NA NA + 10 31 whipped/sour cream 31 1 NA NA NA NA NA + # ℹ 17 more rows + # + # Edge Data: 45 × 2 + from to + + 1 8 13 + 2 9 13 + 3 5 14 + # ℹ 42 more rows + > + > # convert the generating itemsets of the rules into a graph with itemsets as edges + > itemsets <- generatingItemsets(rules) + > itemsets + set of 15 itemsets + > g <- associations2igraph(itemsets, associationsAsNodes = FALSE) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 56, the number of target vertices, not 12 + Calls: associations2igraph ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +# bigergm + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/bigergm +* Date/Publication: 2024-02-16 15:10:10 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "bigergm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bigergm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hergm + > ### Title: Hierarchical exponential-family random graph models (HERGMs) + > ### with local dependence + > ### Aliases: hergm + > + > ### ** Examples + > + > # Load an embedded network object. + > data(toyNet) + > + > # Specify the model that you would like to estimate. + > model_formula <- toyNet ~ edges + nodematch("x") + nodematch("y") + triangle + > # Estimate the model + > hergm_res <- bigergm::hergm( + + object = model_formula, + + # The model you would like to estimate + + n_clusters = 4, + + # The number of blocks + + n_MM_step_max = 10, + + # The maximum number of MM algorithm steps + + estimate_parameters = TRUE, + + # Perform parameter estimation after the block recovery step + + clustering_with_features = TRUE, + + # Indicate that clustering must take into account nodematch on characteristics + + check_block_membership = FALSE) + Error in igraph::delete_vertex_attr(rval, "name") : + No such vertex attribute: name + Calls: ... asIgraph.network -> asIgraph -> asIgraph.data.frame -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bigergm) + Loading required package: ergm + Loading required package: network + + 'network' 1.18.2 (2023-12-04), part of the Statnet Project + * 'news(package="network")' for changes since last version + * 'citation("network")' for citation information + * 'https://statnet.org' for help, support, and other information + + + 'ergm' 4.6.0 (2023-12-17), part of the Statnet Project + * 'news(package="ergm")' for changes since last version + * 'citation("ergm")' for citation information + * 'https://statnet.org' for help, support, and other information + + 'ergm' 4 is a major update that introduces some backwards-incompatible + changes. Please type 'news(package="ergm")' for a list of major + changes. + + Loading required package: Rcpp + > + > test_check("bigergm") + Compute pi for pi_s0v0w0 + [1] 1 + Compute pi for pi_s1v0w0 + [1] 2 + Compute pi for pi_s0v1w0 + [1] 3 + Compute pi for pi_s1v1w0 + [1] 4 + Compute pi for pi_s0v0w1 + [1] 5 + Compute pi for pi_s1v0w1 + [1] 6 + Compute pi for pi_s0v1w1 + [1] 7 + Compute pi for pi_s1v1w1 + [1] 8 + Compute pi for pi_s0v0w0 + [1] 1 + Compute pi for pi_s1v0w0 + [1] 2 + Compute pi for pi_s0v1w0 + [1] 3 + Compute pi for pi_s1v1w0 + [1] 4 + Compute pi for pi_s0v0w1 + [1] 5 + Compute pi for pi_s1v0w1 + [1] 6 + Compute pi for pi_s0v1w1 + [1] 7 + Compute pi for pi_s1v1w1 + [1] 8 + Compute pi for pi_s0v0w0 + [1] 1 + Compute pi for pi_s1v0w0 + [1] 2 + Compute pi for pi_s0v1w0 + [1] 3 + Compute pi for pi_s1v1w0 + [1] 4 + Compute pi for pi_s0v0w1 + [1] 5 + Compute pi for pi_s1v0w1 + [1] 6 + Compute pi for pi_s0v1w1 + [1] 7 + Compute pi for pi_s1v1w1 + [1] 8 + edges nodematch('x') nodematch('y') triangle kstar(2) + -3.00 1.00 1.00 0.76 0.08 + edges nodematch('x') nodematch('y') + -5 2 2 + edges nodematch('x') nodematch('y') triangle kstar(2) + -3.00 1.00 1.00 0.76 0.08 + edges nodematch('x') nodematch('y') + -5 2 2 + [ FAIL 6 | WARN 2 | SKIP 2 | PASS 91 ] + + ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ + • On CRAN (2): 'test-EM-checkpoint.R:2:3', 'test-cache.R:49:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-estimate_within_param.R:185:3'): control.ergm settings can be passed to the within estimation from hergm function ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. └─bigergm::hergm(...) at test-estimate_within_param.R:185:3 + 2. └─bigergm:::MM_wrapper(...) + 3. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 4. │ └─igraph:::ensure_igraph(graph) + 5. ├─intergraph::asIgraph(network) + 6. └─intergraph:::asIgraph.network(network) + 7. ├─intergraph::asIgraph(...) + 8. └─intergraph:::asIgraph.data.frame(...) + 9. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-gof.R:35:3'): (code run outside of `test_that()`) ────────────── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. └─bigergm (local) get_dummy_net(50, 2) at test-gof.R:55:1 + 2. └─bigergm::hergm(...) at test-gof.R:35:3 + 3. └─bigergm:::MM_wrapper(...) + 4. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 5. │ └─igraph:::ensure_igraph(graph) + 6. ├─intergraph::asIgraph(network) + 7. └─intergraph:::asIgraph.network(network) + 8. ├─intergraph::asIgraph(...) + 9. └─intergraph:::asIgraph.data.frame(...) + 10. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-include-covariates.R:21:3'): Check if algorithm automatically checks if covariates are specified ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─testthat::expect_warning(...) at test-include-covariates.R:21:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─bigergm::hergm(...) + 7. └─bigergm:::MM_wrapper(...) + 8. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─intergraph::asIgraph(network) + 11. └─intergraph:::asIgraph.network(network) + 12. ├─intergraph::asIgraph(...) + 13. └─intergraph:::asIgraph.data.frame(...) + 14. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-simulate_hergm.R:545:3'): Setting output = 'edgelist' returns a single edgelist for the full + simulated network ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. └─bigergm::hergm(...) at test-simulate_hergm.R:545:3 + 2. └─bigergm:::MM_wrapper(...) + 3. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 4. │ └─igraph:::ensure_igraph(graph) + 5. ├─intergraph::asIgraph(network) + 6. └─intergraph:::asIgraph.network(network) + 7. ├─intergraph::asIgraph(...) + 8. └─intergraph:::asIgraph.data.frame(...) + 9. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-simulate_hergm.R:601:3'): Setting output = 'edgelist' returns a list of full-network edgelists ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. └─bigergm::hergm(...) at test-simulate_hergm.R:601:3 + 2. └─bigergm:::MM_wrapper(...) + 3. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 4. │ └─igraph:::ensure_igraph(graph) + 5. ├─intergraph::asIgraph(network) + 6. └─intergraph:::asIgraph.network(network) + 7. ├─intergraph::asIgraph(...) + 8. └─intergraph:::asIgraph.data.frame(...) + 9. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-unique-names.R:24:3'): Check if algorithm works even if vertex.names are nonunique ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─testthat::expect_warning(...) at test-unique-names.R:24:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─bigergm::hergm(...) + 7. └─bigergm:::MM_wrapper(...) + 8. ├─igraph::cluster_infomap(intergraph::asIgraph(network)) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─intergraph::asIgraph(network) + 11. └─intergraph:::asIgraph.network(network) + 12. ├─intergraph::asIgraph(...) + 13. └─intergraph:::asIgraph.data.frame(...) + 14. └─igraph::delete_vertex_attr(rval, "name") + + [ FAIL 6 | WARN 2 | SKIP 2 | PASS 91 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘intro-bigergm.Rmd’ + ... + > model_formula <- toyNet ~ edges + nodematch("x") + + + nodematch("y") + triangle + + > hergm_res <- bigergm::hergm(object = model_formula, + + n_clusters = 4, n_MM_step_max = 100, estimate_parameters = TRUE, + + clustering_with_f .... [TRUNCATED] + + When sourcing ‘intro-bigergm.R’: + Error: No such vertex attribute: name + Execution halted + + ‘intro-bigergm.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘intro-bigergm.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 17.3Mb + sub-directories of 1Mb or more: + libs 16.8Mb + ``` + +# bioregion + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/bioRgeo/bioregion +* Source code: https://github.com/cran/bioregion +* Date/Publication: 2024-03-19 16:30:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "bioregion")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bioregion-Ex.R’ failed + The error most likely occurred in: + + > ### Name: map_clusters + > ### Title: Create a map of bioregions + > ### Aliases: map_clusters + > + > ### ** Examples + > + > data(fishmat) + > data(fishsf) + > + > net <- similarity(fishmat, metric = "Simpson") + > clu <- netclu_greedy(net) + Error in comtemp[, 2] : subscript out of bounds + Calls: netclu_greedy + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + data 3.6Mb + help 2.6Mb + libs 1.1Mb + ``` + +# bnviewer + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/bnviewer +* Date/Publication: 2020-09-14 06:00:03 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "bnviewer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bnviewer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: viewer + > ### Title: Interactive Bayesian Network Viewer + > ### Aliases: viewer + > + > ### ** Examples + > + > + > library(bnlearn) + > library(bnviewer) + > + > data("alarm") + > bayesianNetwork = hc(alarm) + > + > viewer(bayesianNetwork, + + bayesianNetwork.background = "-webkit-radial-gradient(center, ellipse cover, + + rgba(255,255,255,1) 0%, + + rgba(246,246,246,1) 47%, + + rgba(237,237,237,1) 100%)", + + bayesianNetwork.width = "100%", + + bayesianNetwork.height = "100vh", + + bayesianNetwork.layout = "layout_components", + + bayesianNetwork.title="
Discrete Bayesian Network - Alarm", + + bayesianNetwork.subtitle = "Monitoring of emergency care patients", + + + + node.colors = list(background = "white", + + border = "black", + + highlight = list(background = "#e91eba", + + border = "black")), + + node.font = list(color = "black", face="Arial"), + + + + clusters.legend.title = list(text = "Legend
Variable Categories", + + style = "font-size:18px; + + font-family:Arial; + + color:black; + + text-align:center;"), + + clusters.legend.options = list( + + list(label = "Pressure", + + shape = "icon", + + icon = list(code = "f1ce", + + size = 50, + + color = "#e91e63")), + + list(label = "Volume", + + shape = "icon", + + icon = list(code = "f140", + + size = 50, + + color = "#03a9f4")), + + list(label = "Ventilation", + + shape = "icon", + + icon = list(code = "f192", + + size = 50, + + color = "#4caf50")), + + list(label = "Saturation", + + shape = "icon", + + icon = list(code = "f10c", + + size = 50, + + color = "#ffc107")) + + ), + + + + clusters = list( + + list(label = "Pressure", + + shape = "icon", + + icon = list(code = "f1ce", color = "#e91e63"), + + nodes = list("CVP","BP","HRBP","PAP","PRSS")), + + list(label = "Volume", + + shape = "icon", + + icon = list(code = "f140", color = "#03a9f4"), + + nodes = list("MINV","MVS","LVV","STKV")), + + list(label = "Ventilation", + + shape = "icon", + + icon = list(code = "f192", color = "#4caf50"), + + nodes = list("VALV","VLNG","VTUB","VMCH")), + + list(label = "Saturation", + + shape = "icon", + + icon = list(code = "f10c", color = "#ffc107"), + + nodes = list("HRSA","SAO2","PVS")) + + ) + + ) + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 36, 37 + Calls: viewer ... -> -> cbind -> cbind -> data.frame + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘alarm.R’ + Running the tests in ‘tests/alarm.R’ failed. + Complete output: + > library(bnlearn) + > library(bnviewer) + > + > bn.learn.hc = hc(alarm) + > + > viewer(bn.learn.hc, + + bayesianNetwork.width = "100%", + + bayesianNetwork.height = "80vh", + + bayesianNetwork.layout = "layout_on_grid", + + bayesianNetwork.title="Discrete Bayesian Network - Coronary", + + bayesianNetwork.subtitle = "Coronary heart disease data set", + + bayesianNetwork.footer = "Fig. 1 - Layout on grid", + + edges.smooth = TRUE, + + edges.shadow = TRUE, + + edges.width = 1.5, + + node.colors = list(background = "#f4bafd", + + border = "#2b7ce9", + + highlight = "#97c2fc") + + + + ) + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 36, 37 + Calls: viewer ... -> -> cbind -> cbind -> data.frame + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘caret’ ‘e1071’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# causaloptim + +
+ +* Version: 0.9.8 +* GitHub: https://github.com/sachsmc/causaloptim +* Source code: https://github.com/cran/causaloptim +* Date/Publication: 2023-10-31 14:30:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "causaloptim")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(causaloptim) + Loading required package: igraph + + Attaching package: 'igraph' + + The following object is masked from 'package:testthat': + + compare + + The following objects are masked from 'package:stats': + + decompose, spectrum + + The following object is masked from 'package:base': + + union + + > library(shiny) + > + > test_check("causaloptim") + [ FAIL 6 | WARN 9 | SKIP 0 | PASS 68 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-server.R:132:9'): dag input 2 ────────────────────────────────── + Error in `warn_version(graph)`: This graph was created by a now unsupported old igraph version. + Call upgrade_graph() before using igraph functions on that object. + Backtrace: + ▆ + 1. ├─shiny::testServer(...) at test-server.R:76:5 + 2. │ ├─shiny:::withMockContext(...) + 3. │ │ ├─shiny::isolate(...) + 4. │ │ │ ├─shiny::..stacktraceoff..(...) + 5. │ │ │ └─ctx$run(...) + 6. │ │ │ ├─promises::with_promise_domain(...) + 7. │ │ │ │ └─domain$wrapSync(expr) + 8. │ │ │ ├─shiny::withReactiveDomain(...) + 9. │ │ │ │ └─promises::with_promise_domain(...) + 10. │ │ │ │ └─domain$wrapSync(expr) + 11. │ │ │ │ └─base::force(expr) + 12. │ │ │ └─env$runWith(self, func) + 13. │ │ │ └─shiny (local) contextFunc() + 14. │ │ │ └─shiny::..stacktraceon..(expr) + 15. │ │ ├─shiny::withReactiveDomain(...) + 16. │ │ │ └─promises::with_promise_domain(...) + 17. │ │ │ └─domain$wrapSync(expr) + 18. │ │ │ └─base::force(expr) + 19. │ │ └─withr::with_options(...) + 20. │ │ └─base::force(code) + 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) + 22. └─testthat::expect_equal(returned_igraphobject, graphres) at test-server.R:132:9 + 23. └─testthat:::expect_waldo_equal("equal", act, exp, info, ..., tolerance = tolerance) + 24. └─testthat:::waldo_compare(...) + 25. └─waldo::compare(x, y, ..., x_arg = x_arg, y_arg = y_arg) + 26. └─waldo:::compare_structure(x, y, paths = c(x_arg, y_arg), opts = opts) + 27. ├─base::length(x) + 28. └─igraph:::length.igraph(x) + 29. └─igraph::vcount(x) + 30. └─igraph:::vcount_impl(graph) + 31. └─igraph:::ensure_igraph(graph) + 32. └─igraph::is_igraph(graph) + 33. └─igraph:::warn_version(graph) + ── Failure ('test-server.R:307:5'): graphres_from_edges works ────────────────── + `test0` (`actual`) not equal to TRUE (`expected`). + + `actual`: FALSE + `expected`: TRUE + ── Failure ('test-server.R:884:17'): Classic Balke-Pearl works 1 ─────────────── + igraph::identical_graphs(graphres_object, graphres_expected) is not TRUE + + `actual`: FALSE + `expected`: TRUE + Backtrace: + ▆ + 1. ├─shiny::testServer(...) at test-server.R:867:9 + 2. │ ├─shiny:::withMockContext(...) + 3. │ │ ├─shiny::isolate(...) + 4. │ │ │ ├─shiny::..stacktraceoff..(...) + 5. │ │ │ └─ctx$run(...) + 6. │ │ │ ├─promises::with_promise_domain(...) + 7. │ │ │ │ └─domain$wrapSync(expr) + 8. │ │ │ ├─shiny::withReactiveDomain(...) + 9. │ │ │ │ └─promises::with_promise_domain(...) + 10. │ │ │ │ └─domain$wrapSync(expr) + 11. │ │ │ │ └─base::force(expr) + 12. │ │ │ └─env$runWith(self, func) + 13. │ │ │ └─shiny (local) contextFunc() + 14. │ │ │ └─shiny::..stacktraceon..(expr) + 15. │ │ ├─shiny::withReactiveDomain(...) + 16. │ │ │ └─promises::with_promise_domain(...) + 17. │ │ │ └─domain$wrapSync(expr) + 18. │ │ │ └─base::force(expr) + 19. │ │ └─withr::with_options(...) + 20. │ │ └─base::force(code) + 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) + 22. └─testthat::expect_true(...) at test-server.R:884:17 + ── Failure ('test-server.R:918:17'): Classic Balke-Pearl works 2 ─────────────── + igraph::identical_graphs(graphres_object, graphres_expected) is not TRUE + + `actual`: FALSE + `expected`: TRUE + Backtrace: + ▆ + 1. ├─shiny::testServer(...) at test-server.R:897:9 + 2. │ ├─shiny:::withMockContext(...) + 3. │ │ ├─shiny::isolate(...) + 4. │ │ │ ├─shiny::..stacktraceoff..(...) + 5. │ │ │ └─ctx$run(...) + 6. │ │ │ ├─promises::with_promise_domain(...) + 7. │ │ │ │ └─domain$wrapSync(expr) + 8. │ │ │ ├─shiny::withReactiveDomain(...) + 9. │ │ │ │ └─promises::with_promise_domain(...) + 10. │ │ │ │ └─domain$wrapSync(expr) + 11. │ │ │ │ └─base::force(expr) + 12. │ │ │ └─env$runWith(self, func) + 13. │ │ │ └─shiny (local) contextFunc() + 14. │ │ │ └─shiny::..stacktraceon..(expr) + 15. │ │ ├─shiny::withReactiveDomain(...) + 16. │ │ │ └─promises::with_promise_domain(...) + 17. │ │ │ └─domain$wrapSync(expr) + 18. │ │ │ └─base::force(expr) + 19. │ │ └─withr::with_options(...) + 20. │ │ └─base::force(code) + 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) + 22. └─testthat::expect_true(...) at test-server.R:918:17 + ── Failure ('test-server.R:1197:17'): Classic Balke-Pearl works with monotone IV ── + igraph::identical_graphs(g1 = graphres_object, g2 = graphres_expected) is not TRUE + + `actual`: FALSE + `expected`: TRUE + Backtrace: + ▆ + 1. ├─shiny::testServer(...) at test-server.R:1176:9 + 2. │ ├─shiny:::withMockContext(...) + 3. │ │ ├─shiny::isolate(...) + 4. │ │ │ ├─shiny::..stacktraceoff..(...) + 5. │ │ │ └─ctx$run(...) + 6. │ │ │ ├─promises::with_promise_domain(...) + 7. │ │ │ │ └─domain$wrapSync(expr) + 8. │ │ │ ├─shiny::withReactiveDomain(...) + 9. │ │ │ │ └─promises::with_promise_domain(...) + 10. │ │ │ │ └─domain$wrapSync(expr) + 11. │ │ │ │ └─base::force(expr) + 12. │ │ │ └─env$runWith(self, func) + 13. │ │ │ └─shiny (local) contextFunc() + 14. │ │ │ └─shiny::..stacktraceon..(expr) + 15. │ │ ├─shiny::withReactiveDomain(...) + 16. │ │ │ └─promises::with_promise_domain(...) + 17. │ │ │ └─domain$wrapSync(expr) + 18. │ │ │ └─base::force(expr) + 19. │ │ └─withr::with_options(...) + 20. │ │ └─base::force(code) + 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) + 22. └─testthat::expect_true(...) at test-server.R:1197:17 + ── Failure ('test-server.R:1878:17'): Natural direct effect works ────────────── + igraph::identical_graphs(g1 = graphres_object, g2 = graphres_expected) is not TRUE + + `actual`: FALSE + `expected`: TRUE + Backtrace: + ▆ + 1. ├─shiny::testServer(...) at test-server.R:1857:9 + 2. │ ├─shiny:::withMockContext(...) + 3. │ │ ├─shiny::isolate(...) + 4. │ │ │ ├─shiny::..stacktraceoff..(...) + 5. │ │ │ └─ctx$run(...) + 6. │ │ │ ├─promises::with_promise_domain(...) + 7. │ │ │ │ └─domain$wrapSync(expr) + 8. │ │ │ ├─shiny::withReactiveDomain(...) + 9. │ │ │ │ └─promises::with_promise_domain(...) + 10. │ │ │ │ └─domain$wrapSync(expr) + 11. │ │ │ │ └─base::force(expr) + 12. │ │ │ └─env$runWith(self, func) + 13. │ │ │ └─shiny (local) contextFunc() + 14. │ │ │ └─shiny::..stacktraceon..(expr) + 15. │ │ ├─shiny::withReactiveDomain(...) + 16. │ │ │ └─promises::with_promise_domain(...) + 17. │ │ │ └─domain$wrapSync(expr) + 18. │ │ │ └─base::force(expr) + 19. │ │ └─withr::with_options(...) + 20. │ │ └─base::force(code) + 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) + 22. └─testthat::expect_true(...) at test-server.R:1878:17 + + [ FAIL 6 | WARN 9 | SKIP 0 | PASS 68 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + libs 3.1Mb + shiny 1.0Mb + ``` + +# cglasso + +
+ +* Version: 2.0.7 +* GitHub: NA +* Source code: https://github.com/cran/cglasso +* Date/Publication: 2024-02-12 08:40:02 UTC +* Number of recursive dependencies: 11 + +Run `revdepcheck::cloud_details(, "cglasso")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cglasso-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cggm + > ### Title: Post-Hoc Maximum Likelihood Refitting of a Conditional Graphical + > ### Lasso + > ### Aliases: cggm + > ### Keywords: regression + > + > ### ** Examples + > + > set.seed(123) + > # Y ~ N(XB, Sigma) and + > # 1. probability of left/right censored values equal to 0.05 + > # 2. probability of missing-at-random values equal to 0.05 + > n <- 100L + > p <- 3L + > q <- 2L + > b0 <- runif(p) + > B <- matrix(runif(q * p), nrow = q, ncol = p) + > X <- matrix(rnorm(n * q), nrow = n, ncol = q) + > rho <- 0.3 + > Sigma <- outer(1L:p, 1L:p, function(i, j) rho^abs(i - j)) + > Z <- rcggm(n = n, b0 = b0, X = X, B = B, Sigma = Sigma, probl = 0.05, probr = 0.5, probna = 0.05) + > out <- cglasso(. ~ ., data = Z) + > + > # MLE of the censored Gaussian graphical model identified by 'BIC' + > out.mle <- cggm(out, GoF = BIC) + > out.mle + + Call: cggm(object = out, GoF = BIC) + + df N. Comp. + 15 (100.000%) 1 + + > + > # accessor functions + > coef(out.mle, drop = TRUE) + $B + response + coef Y1 Y2 Y3 + Int. 0.05320545 0.78327450 0.2701906 + X1 0.69498839 -0.05066828 0.8049508 + X2 0.79525227 0.50210278 0.5624755 + + $Sigma + response + response Y1 Y2 Y3 + Y1 0.7318983 0.2609506 0.1155406 + Y2 0.2609506 0.7294057 0.2144929 + Y3 0.1155406 0.2144929 0.8345455 + + $Theta + response + response Y1 Y2 Y3 + Y1 1.57087061 -0.5387564 -0.07901192 + Y2 -0.53875640 1.6678453 -0.35407638 + Y3 -0.07901192 -0.3540764 1.30019989 + + > fitted(out.mle, drop = TRUE) + response + Y1 Y2 Y3 + 1 -0.774529441 0.31399823 -0.349408622 + 2 -0.557269121 0.45522189 -0.198335769 + 3 0.539923779 1.00096363 0.671818975 + 4 1.362159388 0.98292668 1.597317614 + 5 -1.330344138 0.75517703 -1.249694121 + 6 2.339170664 1.39928757 2.416724043 + 7 1.805898324 1.64328227 1.667746442 + 8 2.196545572 0.89898982 2.578515884 + 9 0.223491811 0.62202445 0.562714752 + 10 0.339329954 0.84732915 0.547217924 + 11 0.418988974 1.52761972 0.200192551 + 12 0.809591893 0.62709459 1.210943853 + 13 -0.619751143 -0.04568822 0.052930605 + 14 -0.192838534 0.65518482 0.078714135 + 15 0.272950784 1.30594545 0.179796280 + 16 0.222491536 1.24918313 0.160051883 + 17 0.236230539 1.00449102 0.331992446 + 18 0.090796164 0.97093706 0.191819503 + 19 -0.227034457 1.13775169 -0.268269287 + 20 1.482086687 1.72724693 1.254055865 + 21 1.276701373 1.03173139 1.471079165 + 22 -0.657138853 0.40594586 -0.277795283 + 23 -1.250150724 0.53086300 -1.016934117 + 24 0.112747120 1.22150400 0.055788383 + 25 0.336795706 0.62707289 0.685424522 + 26 0.719453616 1.36058427 0.641119699 + 27 0.084031382 1.44468405 -0.119025925 + 28 0.945847475 1.64035521 0.713637179 + 29 0.116747182 0.88673544 0.274576963 + 30 0.357297675 0.54124288 0.763167741 + 31 -0.046405401 0.79448596 0.152290467 + 32 -1.701617032 -0.48609925 -0.867627626 + 33 -2.966943580 0.45609418 -2.877350700 + 34 0.016689917 1.13798601 0.002490766 + 35 0.185440479 0.72650841 0.453521098 + 36 -0.491145173 1.03698509 -0.497321813 + 37 -0.514326882 0.21225048 0.004963726 + 38 0.008534657 0.36341036 0.489363560 + 39 -0.270665632 0.65902902 -0.010255348 + 40 0.318621903 0.34248433 0.847437136 + 41 -0.245719926 1.05189091 -0.234064888 + 42 -0.689067221 0.12191438 -0.131428141 + 43 1.269889270 1.35389458 1.257235727 + 44 0.154862040 1.28133941 0.064290093 + 45 -1.866495868 0.21679847 -1.500941995 + 46 0.739239738 1.20230158 0.764456513 + 47 -2.114602922 -0.37391331 -1.398508461 + 48 1.713523411 1.00442187 1.974111054 + 49 0.868857242 0.69699942 1.232061843 + 50 -1.662928848 -0.43535496 -0.857114110 + 51 -0.691183783 0.82672418 -0.585049510 + 52 -0.379319998 0.76513684 -0.198967007 + 53 -0.087500624 -0.10006778 0.679367476 + 54 -0.013155771 1.26513863 -0.112096029 + 55 0.657416663 0.33957263 1.225886307 + 56 0.733315020 1.33097814 0.675483168 + 57 -0.698636576 0.53774852 -0.408311099 + 58 -0.057816184 1.09152542 -0.050578624 + 59 0.093154951 -0.24381672 0.972212059 + 60 -2.316371332 -0.05969623 -1.823966532 + 61 1.489403840 1.44734275 1.441403501 + 62 0.462067980 0.43742974 0.946092880 + 63 1.265721966 1.23832842 1.326597159 + 64 0.324737432 0.75304187 0.591367051 + 65 0.892913869 0.92501206 1.112812119 + 66 1.546777159 1.80087900 1.278817672 + 67 -1.042655802 0.20341151 -0.576637181 + 68 -1.173385389 0.44974287 -0.879667356 + 69 -0.721083925 0.65417815 -0.507808715 + 70 -1.164634798 0.71316497 -1.038602022 + 71 0.733431125 0.90963351 0.945386638 + 72 1.516009868 1.70988718 1.302877866 + 73 -1.204224679 0.32499476 -0.834074047 + 74 1.605448866 1.90004744 1.280539194 + 75 -0.653545422 0.72016990 -0.474989321 + 76 0.287296049 1.31236693 0.191630174 + 77 -0.897210178 0.36665762 -0.519489761 + 78 -0.567340102 0.54780996 -0.268811478 + 79 0.736705544 1.17343832 0.780119937 + 80 -2.152691723 -0.23333248 -1.530855512 + 81 -0.415358928 0.79379712 -0.257376143 + 82 -0.894814932 0.62566415 -0.682661505 + 83 0.424811781 0.69302441 0.741031371 + 84 1.691075962 1.67040908 1.522747981 + 85 -0.539183715 0.37261457 -0.125342062 + 86 1.708327172 1.72726516 1.505520188 + 87 0.277207387 1.16401537 0.275401275 + 88 0.202246907 1.18473717 0.178811939 + 89 1.106735773 1.47141189 1.000640792 + 90 -0.292052011 0.48569122 0.076955808 + 91 0.311377857 0.31373725 0.857790969 + 92 -0.694473230 0.53810408 -0.403911017 + 93 0.894979119 1.16523561 0.961299749 + 94 -0.567891916 0.43223855 -0.195427915 + 95 -0.675975471 0.12202822 -0.116948987 + 96 2.069953194 1.96669514 1.754183122 + 97 0.419730497 0.14405427 1.086872528 + 98 0.232434200 0.87799063 0.408767082 + 99 0.770335452 0.66033197 1.146027729 + 100 -1.439124253 0.11443892 -0.960362356 + > residuals(out.mle, type = "working", drop = TRUE) + response + Y1 Y2 Y3 + 1 0.154469421 -0.66465697 -0.215224678 + 2 0.570599736 -1.10108641 -1.164366021 + 3 -0.876635559 -0.66058646 0.456546434 + 4 0.180132188 0.57054188 0.173084322 + 5 -0.719819672 0.59377366 0.324970209 + 6 0.013398836 0.35083718 0.025928509 + 7 0.073452013 0.24793111 0.152892410 + 8 -0.231215722 -0.74782884 -0.196742825 + 9 -0.205509141 0.73353624 -0.034184954 + 10 -0.817423018 0.51009158 0.594870651 + 11 0.423465480 -1.31120972 -0.385620785 + 12 0.284755253 -0.44069033 0.210595262 + 13 -1.760114077 -1.56607202 -0.868531202 + 14 0.964121536 -0.34557609 -0.499144728 + 15 -0.061449917 0.34170942 0.880011951 + 16 0.743419559 0.40799963 0.073864190 + 17 -0.210306511 -0.07607379 0.768863247 + 18 0.833292351 0.56117009 0.091687499 + 19 -0.685768560 0.29771568 -0.332855771 + 20 0.039734035 0.03513812 -1.021267264 + 21 0.207958031 0.54203522 0.212344462 + 22 -0.368902863 -0.06775732 1.190767730 + 23 1.023835759 1.03445764 1.370442032 + 24 -1.368155453 -0.95448178 -0.062848559 + 25 0.673266305 0.79716719 -0.002366995 + 26 0.450244027 0.36856380 0.595288634 + 27 -0.962051486 0.11670637 0.055823922 + 28 0.339180725 0.24878746 0.553530508 + 29 0.782772551 0.53871520 -0.683536813 + 30 0.593508589 0.74652914 -1.224228754 + 31 0.325305967 -0.79334374 -1.024765349 + 32 -1.163968429 -0.21868042 -0.712647985 + 33 -0.522763935 -0.93344870 -0.405683396 + 34 0.287974290 0.48793053 1.021612848 + 35 0.772195961 0.73058662 0.709603802 + 36 -0.069873991 -0.73621248 -0.278291670 + 37 -0.269385791 -1.64996374 0.995805644 + 38 -1.239846226 0.27474555 0.657669752 + 39 1.060397201 0.03105571 1.001333740 + 40 0.627812694 0.04005752 -0.878504579 + 41 -0.333677800 -0.41598969 -1.297942476 + 42 1.432422546 1.16660043 1.115842964 + 43 0.210201417 0.37188859 -0.004979215 + 44 -1.246287722 -2.64025592 -1.110917399 + 45 1.621223626 1.18842662 0.097622412 + 46 0.228409367 -1.10372522 0.365403819 + 47 0.503237101 0.11673455 -0.049329497 + 48 0.090879170 0.55798124 0.084438556 + 49 0.375257573 0.75020719 0.300875811 + 50 0.627704890 -1.02689479 0.454517953 + 51 -0.128993818 0.56042298 -0.357656392 + 52 0.369770196 0.72063687 0.410934239 + 53 0.136083186 0.22198086 0.574773431 + 54 0.909929608 0.41522614 1.101120252 + 55 0.325316793 -0.49735139 -1.955758037 + 56 0.344027864 0.18319216 -1.475399531 + 57 -0.742683936 0.73489643 0.070437391 + 58 0.942074867 0.50778246 1.055562702 + 59 -0.213062200 -0.49363702 0.316934459 + 60 0.822207037 1.39096663 1.530785164 + 61 0.143102089 0.32878416 0.222066379 + 62 -1.010582759 0.19583819 0.398615991 + 63 -0.958532164 -0.78312838 0.079523147 + 64 -0.147663166 0.57223168 -0.928570500 + 65 -1.290050008 -1.34820396 0.105500876 + 66 -0.100408811 -0.17317120 -2.301136217 + 67 1.728884501 1.09531344 0.267402084 + 68 0.089332687 0.89996017 0.534881286 + 69 -1.514860110 -0.95845278 -1.390243294 + 70 0.101021506 -0.75767901 -1.372305723 + 71 -0.708739886 0.47952568 0.368536816 + 72 0.135983925 0.22331698 0.272224268 + 73 -0.459998077 -0.07562232 -1.504707404 + 74 -0.218294197 -1.18474518 0.062173543 + 75 -1.386139775 0.55658386 0.272022060 + 76 0.704913199 0.39175081 0.882668006 + 77 -0.417797204 -1.17294082 -0.343012474 + 78 0.264055468 0.83004674 0.218884670 + 79 0.318047184 -0.38956928 -0.765921026 + 80 -0.819112631 -0.14644777 -0.966881060 + 81 -0.941741520 -0.99898978 -0.435457312 + 82 -1.828384903 -0.17560862 -0.801843191 + 83 -0.002161326 0.75277936 0.538552626 + 84 0.095224883 0.23772439 0.195254235 + 85 0.707304973 1.00870197 0.414350520 + 86 0.091693796 0.21722768 0.200693188 + 87 -0.729669522 -0.26198292 0.781294534 + 88 0.760877974 0.45698947 0.891565258 + 89 0.270657314 0.31803561 0.403384586 + 90 1.071314315 0.25398168 -1.898604385 + 91 -0.762084746 0.03734577 0.430031860 + 92 0.702412324 0.89591880 1.342377667 + 93 0.362768884 0.46756395 0.422677956 + 94 -0.124086360 -1.83332035 -0.018964132 + 95 0.683314782 0.51255185 -0.038258933 + 96 0.036220931 0.14305217 0.130477393 + 97 0.525273346 -0.38533090 0.276909069 + 98 0.665709310 -0.21806981 -0.297823012 + 99 -1.378849081 -0.53960720 0.186984634 + 100 -0.825099069 -0.52155698 -0.189316020 + > impute(out.mle, type = "both") + response + Y1 Y2 Y3 + 1 -0.620060019 -0.350658741 -0.564633300 + 2 0.013330616 -0.645864524 -1.362701790 + 3 -0.336711780 0.340377174 1.128365409 + 4 1.542291576 1.553468564 1.770401936 + 5 -2.050163810 1.348950691 -0.924723911 + 6 2.352569501 1.750124747 2.442652552 + 7 1.879350337 1.891213388 1.820638852 + 8 1.965329850 0.151160984 2.381773059 + 9 0.017982670 1.355560689 0.528529799 + 10 -0.478093064 1.357420736 1.142088575 + 11 0.842454453 0.216410007 -0.185428233 + 12 1.094347145 0.186404252 1.421539115 + 13 -2.379865220 -1.611760240 -0.815600597 + 14 0.771283002 0.309608729 -0.420430593 + 15 0.211500867 1.647654871 1.059808231 + 16 0.965911095 1.657182761 0.233916073 + 17 0.025924028 0.928417226 1.100855693 + 18 0.924088516 1.532107157 0.283507002 + 19 -0.912803016 1.435467370 -0.601125059 + 20 1.521820721 1.762385042 0.232788601 + 21 1.484659404 1.573766612 1.683423627 + 22 -1.026041715 0.338188541 0.912972447 + 23 -0.226314965 1.565320642 0.353507915 + 24 -1.255408333 0.267022224 -0.007060177 + 25 1.010062011 1.424240085 0.683057527 + 26 1.169697643 1.729148070 1.236408333 + 27 -0.878020105 1.561390417 -0.063202003 + 28 1.285028200 1.889142668 1.267167687 + 29 0.899519733 1.425450641 -0.408959850 + 30 0.950806264 1.287772017 -0.461061014 + 31 0.278900567 0.001142227 -0.872474882 + 32 -2.865585461 -0.704779679 -1.580275611 + 33 -3.489707515 -0.477354517 -3.283034096 + 34 0.304664207 1.625916541 1.024103614 + 35 0.957636440 1.457095030 1.163124900 + 36 -0.561019164 0.300772610 -0.775613483 + 37 -0.783712673 -1.437713260 1.000769370 + 38 -1.231311570 0.638155917 1.147033312 + 39 0.789731569 0.690084734 0.991078392 + 40 0.946434597 0.382541856 -0.031067443 + 41 -0.579397726 0.635901221 -1.532007364 + 42 0.743355325 1.288514812 0.984414823 + 43 1.480090688 1.725783175 1.252256512 + 44 -1.091425682 -1.358916509 -1.046627306 + 45 -0.245272243 1.405225096 -1.403319583 + 46 0.967649105 0.098576366 1.129860332 + 47 -1.611365821 -0.257178763 -1.447837959 + 48 1.804402580 1.562403111 2.058549610 + 49 1.244114815 1.447206612 1.532937654 + 50 -1.035223958 -1.462249757 -0.402596157 + 51 -0.820177601 1.387147168 -0.942705901 + 52 -0.009549801 1.485773709 0.211967231 + 53 0.048582562 0.121913082 1.254140908 + 54 0.896773838 1.680364771 0.989024223 + 55 0.982733456 -0.157778755 -0.729871731 + 56 1.077342884 1.514170306 -0.799916363 + 57 -1.441320513 1.272644954 -0.337873708 + 58 0.884258682 1.599307882 1.004984078 + 59 -0.119907249 -0.737453747 1.289146518 + 60 -1.494164295 1.331270404 -0.293181368 + 61 1.632505929 1.776126909 1.663469880 + 62 -0.548514779 0.633267935 1.344708871 + 63 0.307189802 0.455200043 1.406120305 + 64 0.177074266 1.325273544 -0.337203449 + 65 -0.397136139 -0.423191900 1.218312995 + 66 1.446368348 1.627707808 -1.022318545 + 67 0.686228699 1.298724951 -0.309235097 + 68 -1.084052702 1.349703043 -0.344786069 + 69 -2.235944035 -0.304274631 -1.898052009 + 70 -1.063613292 -0.044514036 -2.410907744 + 71 0.024691239 1.389159192 1.313923454 + 72 1.651993793 1.933204157 1.575102134 + 73 -1.664222755 0.249372438 -2.338781450 + 74 1.387154669 0.715302254 1.342712737 + 75 -2.039685197 1.276753752 -0.202967260 + 76 0.992209248 1.704117740 1.074298180 + 77 -1.315007382 -0.806283194 -0.862502235 + 78 -0.303284634 1.377856693 -0.049926808 + 79 1.054752728 0.783869037 0.014198911 + 80 -2.971804354 -0.379780249 -2.497736572 + 81 -1.357100448 -0.205192666 -0.692833455 + 82 -2.723199835 0.450055524 -1.484504696 + 83 0.422650455 1.445803765 1.279583997 + 84 1.786300845 1.908133474 1.718002217 + 85 0.168121258 1.381316545 0.289008458 + 86 1.800020968 1.944492832 1.706213376 + 87 -0.452462135 0.902032449 1.056695809 + 88 0.963124881 1.641726640 1.070377197 + 89 1.377393087 1.789447504 1.404025379 + 90 0.779262304 0.739672896 -1.821648577 + 91 -0.450706889 0.351083025 1.287822830 + 92 0.007939094 1.434022881 0.938466649 + 93 1.257748003 1.632799562 1.383977705 + 94 -0.691978277 -1.401081796 -0.214392047 + 95 0.007339311 0.634580071 -0.155207919 + 96 2.106174125 2.109747310 1.884660515 + 97 0.945003843 -0.241276629 1.363781597 + 98 0.898143509 0.659920815 0.110944071 + 99 -0.608513630 0.120724769 1.333012363 + 100 -2.264223322 -0.407118057 -1.149678377 + > + > # goodness-of-fit functions + > AIC(out.mle) + + Sequence of ‘AIC’ values of the fitted model + + Details: + lambda rho df AIC + 0.0888 8.59e-07 15 779 + + > BIC(out.mle) + + Sequence of ‘BIC’ values of the fitted model + + Details: + lambda rho df BIC + 0.0888 8.59e-07 15 818 + + > summary(out.mle) + + Call: cggm(object = out, GoF = BIC) + + lambda rho df.B df.Tht df (df%) BIC + 0.0888 8.59e-07 9 6 15 (100.000%) 818 + + =============================================================== + + Summary of the Selected Model + + nObs: 100 + nResp: 3 + nPred: 2 + lambda: 0.0888442 + lambda.id: 1 + rho: 8.593237e-07 + rho.id: 1 + BIC: 817.7793 + df.B: 9 + df.Tht: 6 + df: 15 + + =============================================================== + + > + > # network analysis + > out.graph <- plot(out.mle) + Error in rbind(deparse.level, ...) : + numbers of columns of arguments do not match + Calls: plot ... plot -> plot.cglasso2igraph -> getGraph -> rbind -> rbind + Execution halted + ``` + +# corrViz + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/corrViz +* Date/Publication: 2023-06-30 11:40:07 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "corrViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘corrViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: corrNetwork + > ### Title: corrNetwork + > ### Aliases: corrNetwork + > + > ### ** Examples + > + > ci <- cor(iris[1:4]) + > corrNetwork(mat = ci, threshold = 0.5) + > + > # Another example + > cm <- cor(mtcars) + > + > corrNetwork(mat = cm, + + threshold = 0.8, + + layout = 'layout_on_grid', + + physics = FALSE) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 8, the number of target vertices, not 11 + Calls: corrNetwork ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘corrViz.Rmd’ + ... + > corrHeatmap(mat = cm, display = "lower", reorder = FALSE) + + > corrNetwork(mat = cm, threshold = 0, layout = "layout_nicely", + + width = "100%", height = "400px", physics = FALSE) + + > corrNetwork(mat = cm, threshold = 0.8, physics = TRUE) + + When sourcing ‘corrViz.R’: + Error: Length of new attribute value must be 1 or 8, the number of target vertices, not 11 + Execution halted + + ‘corrViz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘corrViz.Rmd’ using rmarkdown + + Quitting from lines at lines 133-136 [network2] (corrViz.Rmd) + Error: processing vignette 'corrViz.Rmd' failed with diagnostics: + Length of new attribute value must be 1 or 8, the number of target vertices, not 11 + --- failed re-building ‘corrViz.Rmd’ + + SUMMARY: processing the following file failed: + ‘corrViz.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.2Mb + sub-directories of 1Mb or more: + doc 6.7Mb + ``` + +# cppRouting + +
+ +* Version: 3.1 +* GitHub: https://github.com/vlarmet/cppRouting +* Source code: https://github.com/cran/cppRouting +* Date/Publication: 2022-12-01 13:20:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "cppRouting")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cppRouting-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cpp_simplify + > ### Title: Reduce the number of edges by removing non-intersection nodes, + > ### duplicated edges and isolated loops in the graph. + > ### Aliases: cpp_simplify + > + > ### ** Examples + > + > #Simple directed graph + > edges<-data.frame(from=c(1,2,3,4,5,6,7,8), + + to=c(0,1,2,3,6,7,8,5), + + dist=c(1,1,1,1,1,1,1,1)) + > + > #Plot + > if(requireNamespace("igraph",quietly = TRUE)){ + + igr<-igraph::graph_from_data_frame(edges) + + plot(igr) + + } + Error in add_edges(g, edges, attr = eattrs) : + At vendor/cigraph/src/graph/type_indexededgelist.c:261 : Out-of-range vertex IDs when adding edges. Invalid vertex ID + Calls: -> add_edges + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 16.4Mb + sub-directories of 1Mb or more: + libs 16.2Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘RcppProgress’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# cranly + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/ikosmidis/cranly +* Source code: https://github.com/cran/cranly +* Date/Publication: 2022-08-26 22:14:41 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "cranly")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cranly.Rmd’ + ... + > attr(cran_db, "timestamp") + [1] "2022-08-26 13:43:43 UTC" + + > package_network <- build_network(cran_db) + + > package_summaries <- summary(package_network) + + When sourcing ‘cranly.R’: + Error: arguments imply differing number of rows: 18416, 19260 + Execution halted + when running code in ‘dependence_trees.Rmd’ + ... + 23 methods -3 + 24 rlang -3 + 25 cli -3 + + > tibble_tree <- build_dependence_tree(package_network, + + "tibble") + + When sourcing ‘dependence_trees.R’: + Error: arguments imply differing number of rows: 18416, 19260 + Execution halted + + ‘cranly.Rmd’ using ‘UTF-8’... failed + ‘dependence_trees.Rmd’ using ‘UTF-8’... failed + ‘extractors.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cranly.Rmd’ using rmarkdown + + Quitting from lines at lines 63-65 [unnamed-chunk-7] (cranly.Rmd) + Error: processing vignette 'cranly.Rmd' failed with diagnostics: + arguments imply differing number of rows: 18416, 19260 + --- failed re-building ‘cranly.Rmd’ + + --- re-building ‘dependence_trees.Rmd’ using rmarkdown + + Quitting from lines at lines 61-63 [unnamed-chunk-6] (dependence_trees.Rmd) + Error: processing vignette 'dependence_trees.Rmd' failed with diagnostics: + arguments imply differing number of rows: 18416, 19260 + --- failed re-building ‘dependence_trees.Rmd’ + + --- re-building ‘extractors.Rmd’ using rmarkdown + --- finished re-building ‘extractors.Rmd’ + + SUMMARY: processing the following files failed: + ‘cranly.Rmd’ ‘dependence_trees.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + doc 5.1Mb + ``` + +# criticalpath + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/rubens2005/criticalpath +* Source code: https://github.com/cran/criticalpath +* Date/Publication: 2022-03-13 22:40:10 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "criticalpath")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘criticalpath-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sch_add_activities + > ### Title: Add Activities + > ### Aliases: sch_add_activities + > + > ### ** Examples + > + > # Example #1 + > sch <- sch_new() %>% + + sch_add_activities( + + id = 1:17, + + name = paste("a", as.character(1:17), sep=""), + + duration = c(1L,2L,2L,4L,3L,3L,3L,2L,1L,1L,2L,1L,1L,1L,1L,2L,1L) + + ) %>% + + sch_plan() + Error in sch_plan(.) : + The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Calls: %>% -> sch_plan + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(criticalpath) + > + > test_check("criticalpath") + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 616 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-cpt-add_act_rel.R:126:3'): Does not return Inf!!! ────────────── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-add_act_rel.R:126:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-add_activity.R:11:3'): Add activities works, with duration equal zero! ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─sch %<>% sch_add_activity(2L, "2", 0L) %>% sch_plan() at test-cpt-add_activity.R:11:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-add_activity.R:36:3'): Add activities works, with duration ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─sch %<>% sch_add_activity(2L, "B", 2L) %>% sch_plan() at test-cpt-add_activity.R:36:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-add_activity.R:61:3'): Add activities works, with mean duration equal SIX ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─sch %<>% sch_add_activity(2L, "Task 2", 6L) %>% sch_plan() at test-cpt-add_activity.R:61:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-add_activity.R:98:3'): Add activities tibble. ────────────── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─sch_new() %>% sch_add_activities_tibble(atb) %>% sch_plan() at test-cpt-add_activity.R:98:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-add_relation.R:2:3'): Creating a sch step-by-step: first with activities and then with relations. ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-add_relation.R:2:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:11:3'): FS type | A_duration == B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:11:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:55:3'): FS type | A_duration == B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:55:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:99:3'): FS type | A_duration == B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:99:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:143:3'): FS type | A_duration < B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:143:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:187:3'): FS type | A_duration < B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:187:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:231:3'): FS type | A_duration < B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:231:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:275:3'): FS type | A_duration > B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:275:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:319:3'): FS type | A_duration > B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:319:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:363:3'): FS type | A_duration > B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:363:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:411:3'): FF type | A_duration == B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:411:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:455:3'): FF type | A_duration == B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:455:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:499:3'): FF type | A_duration == B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:499:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:543:3'): FF type | A_duration < B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:543:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:587:3'): FF type | A_duration < B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:587:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:631:3'): FF type | A_duration < B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:631:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:675:3'): FF type | A_duration > B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:675:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:719:3'): FF type | A_duration > B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:719:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:763:3'): FF type | A_duration > B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:763:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:811:3'): SS type | A_duration == B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:811:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:855:3'): SS type | A_duration == B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:855:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:899:3'): SS type | A_duration == B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:899:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:943:3'): SS type | A_duration < B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:943:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:987:3'): SS type | A_duration < B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:987:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1031:3'): SS type | A_duration < B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1031:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1075:3'): SS type | A_duration > B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1075:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1119:3'): SS type | A_duration > B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1119:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1163:3'): SS type | A_duration > B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1163:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1211:3'): SF type | A_duration == B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1211:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1255:3'): SF type | A_duration == B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1255:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1299:3'): SF type | A_duration == B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1299:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1343:3'): SF type | A_duration < B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1343:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1387:3'): SF type | A_duration < B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1387:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1431:3'): SF type | A_duration < B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1431:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1475:3'): SF type | A_duration > B_duration | lag == 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1475:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1519:3'): SF type | A_duration > B_duration | lag > 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1519:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-early_start_finish_by_relation_type.R:1563:3'): SF type | A_duration > B_duration | lag < 0 ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-early_start_finish_by_relation_type.R:1563:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-gantt_matrix.R:148:3'): There is no Gantt matrix for a sch with zero duration! ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-gantt_matrix.R:148:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-gantt_matrix.R:157:3'): A,B,C ────────────────────────────── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─criticalpath (local) s0() at test-cpt-gantt_matrix.R:157:3 + 2. │ └─... %>% sch_plan() at test-cpt-gantt_matrix.R:4:3 + 3. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-gantt_matrix.R:180:3'): A->B, C ──────────────────────────── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─criticalpath (local) s1() at test-cpt-gantt_matrix.R:180:3 + 2. │ └─... %>% sch_plan() at test-cpt-gantt_matrix.R:18:3 + 3. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-schedule_from_data_frame.R:77:3'): Creating a schedule only with activities list, without relations ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-schedule_from_data_frame.R:77:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-topological_indicators.R:61:3'): Topological Indicator with sch with TWO PARALLEL activities ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-topological_indicators.R:61:3 + 2. └─criticalpath::sch_plan(.) + ── Error ('test-cpt-topological_indicators.R:89:3'): Topological Indicator with sch with THREE PARALLEL activities ── + Error in `sch_plan(.)`: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Backtrace: + ▆ + 1. ├─... %>% sch_plan() at test-cpt-topological_indicators.R:89:3 + 2. └─criticalpath::sch_plan(.) + + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 616 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘criticalpath-introduction.Rmd’ + ... + + > sch <- sch_new() %>% sch_add_activity(1, "Task 1", + + 5) %>% sch_add_activity(2, "Task 2", 6) %>% sch_add_activity(3, + + "Task 3", 8) %>% sc .... [TRUNCATED] + + When sourcing ‘criticalpath-introduction.R’: + Error: The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Execution halted + + ‘criticalpath-introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘criticalpath-introduction.Rmd’ using rmarkdown + + Quitting from lines at lines 266-278 [unnamed-chunk-5] (criticalpath-introduction.Rmd) + Error: processing vignette 'criticalpath-introduction.Rmd' failed with diagnostics: + The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + --- failed re-building ‘criticalpath-introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘criticalpath-introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dartR + +
+ +* Version: 2.9.7 +* GitHub: NA +* Source code: https://github.com/cran/dartR +* Date/Publication: 2023-06-07 10:40:02 UTC +* Number of recursive dependencies: 286 + +Run `revdepcheck::cloud_details(, "dartR")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 7.6Mb + sub-directories of 1Mb or more: + R 3.5Mb + data 1.7Mb + help 1.6Mb + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘dartRTutorials.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2023) is older than remote repository (2024). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/bookmark.sty'' had status 1 + ! LaTeX Error: File `bookmark.sty' not found. + + ! Emergency stop. + + + Error: processing vignette 'dartRTutorials.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/dartR/new/dartR.Rcheck/vign_test/dartR/vignettes/dartRTutorials.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See dartRTutorials.log for more info. + --- failed re-building ‘dartRTutorials.Rmd’ + + SUMMARY: processing the following file failed: + ‘dartRTutorials.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# debkeepr + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/jessesadler/debkeepr +* Source code: https://github.com/cran/debkeepr +* Date/Publication: 2023-03-22 09:00:10 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "debkeepr")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘debkeepr.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘debkeepr.Rmd’ + ... + + When sourcing ‘debkeepr.R’: + Error: Incompatible `bases`. + ℹ `bases` must be compatible to combine , , or + vectors. + ✖ Cannot combine: `..1` vector with `bases` s = 20 and d = 12. + ✖ Cannot combine: `..2` vector with `bases` s = 30 and d = 18. + ℹ Use `deb_convert_bases()` to convert one or more of the vectors to compatible + `bases`. + Execution halted + when running code in ‘ledger.Rmd’ + ... + > ggraph(ledger_graph, layout = "kk") + geom_edge_fan(aes(alpha = val), + + width = 1, arrow = arrow(length = unit(2, "mm"), type = "closed"), + + .... [TRUNCATED] + + When sourcing ‘ledger.R’: + Error: Problem while computing aesthetics. + ℹ Error occurred in the 3rd layer. + Caused by error: + ! object 'name' not found + Execution halted + + ‘debkeepr.Rmd’ using ‘UTF-8’... failed + ‘ledger.Rmd’ using ‘UTF-8’... failed + ‘transactions.Rmd’ using ‘UTF-8’... OK + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 53 marked UTF-8 strings + ``` + +# DiagrammeR + +
+ +* Version: 1.0.11 +* GitHub: https://github.com/rich-iannone/DiagrammeR +* Source code: https://github.com/cran/DiagrammeR +* Date/Publication: 2024-02-02 23:30:03 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DiagrammeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: colorize_node_attrs + > ### Title: Apply colors based on node attribute values + > ### Aliases: colorize_node_attrs + > + > ### ** Examples + > + > # Create a graph with 8 + > # nodes and 7 edges + > graph <- + + create_graph() %>% + + add_path(n = 8) %>% + + set_node_attrs( + + node_attr = weight, + + values = c( + + 8.2, 3.7, 6.3, 9.2, + + 1.6, 2.5, 7.2, 5.4)) + > + > # Find group membership values for all nodes + > # in the graph through the Walktrap community + > # finding algorithm and join those group values + > # to the graph's internal node data frame (ndf) + > # with the `join_node_attrs()` function + > graph <- + + graph %>% + + join_node_attrs( + + df = get_cmty_walktrap(.)) + Error in data.frame(id = igraph::membership(cmty_walktrap_obj) %>% names() %>% : + arguments imply differing number of rows: 0, 8 + Calls: %>% ... colnames -> is.data.frame -> get_cmty_walktrap -> data.frame + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + > + > library(testthat) + > library(DiagrammeR) + > + > test_check("DiagrammeR") + The series of graph actions was not applied to the graph because of an error at action index 1. + [ FAIL 52 | WARN 0 | SKIP 23 | PASS 1423 ] + + ══ Skipped tests (23) ══════════════════════════════════════════════════════════ + • On CRAN (23): 'test-add_forward_reverse_edges.R:94:3', + 'test-add_graphs.R:41:3', 'test-add_graphs.R:262:3', + 'test-add_graphs.R:1787:3', 'test-add_nodes_edges_from_table.R:684:3', + 'test-colorize_nodes_edges.R:415:3', 'test-create_combine_nodes.R:88:3', + 'test-create_subgraph.R:73:3', 'test-delete_node_edge.R:286:3', + 'test-get_select_last_nodes_edges_created.R:135:3', + 'test-graph_series.R:361:3', 'test-graph_validation.R:17:3', + 'test-graph_validation.R:241:3', 'test-graph_validation.R:301:3', + 'test-render_graph.R:3:3', 'test-selections.R:163:3', + 'test-set_get_node_edge_attrs.R:332:3', 'test-similarity_measures.R:106:3', + 'test-similarity_measures.R:126:3', 'test-transform_graph.R:138:3', + 'test-transform_graph.R:308:3', 'test-trav_out_until.R:73:3', + 'test-traversals.R:148:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-cache_attrs.R:17:3'): Setting a cache is possible ────────────── + Error in `data.frame(id = closeness_values %>% names() %>% as.integer(), + closeness = closeness_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_closeness(graph) at test-cache_attrs.R:17:3 + 2. └─base::data.frame(...) + ── Error ('test-cache_attrs.R:114:3'): Getting a cache is possible ───────────── + Error in `data.frame(id = closeness_values %>% names() %>% as.integer(), + closeness = closeness_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_closeness(graph) at test-cache_attrs.R:114:3 + 2. └─base::data.frame(...) + ── Error ('test-colorize_nodes_edges.R:21:3'): Adding color based on node attributes is possible ── + Error in `data.frame(id = igraph::membership(cmty_walktrap_obj) %>% names() %>% + as.integer(), walktrap_group = as.vector(igraph::membership(cmty_walktrap_obj)), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 50 + Backtrace: + ▆ + 1. ├─graph %>% join_node_attrs(get_cmty_walktrap(.)) at test-colorize_nodes_edges.R:21:3 + 2. ├─DiagrammeR::join_node_attrs(., get_cmty_walktrap(.)) + 3. │ └─base::colnames(df) + 4. │ └─base::is.data.frame(x) + 5. └─DiagrammeR::get_cmty_walktrap(.) + 6. └─base::data.frame(...) + ── Error ('test-count_entities.R:137:3'): counting the number of strongly connected components is possible ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 0, the number of target vertices, not 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(graph %>% count_s_connected_cmpts(), 4) at test-count_entities.R:137:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph %>% count_s_connected_cmpts() + 5. └─DiagrammeR::count_s_connected_cmpts(.) + 6. └─DiagrammeR::to_igraph(graph) + 7. └─igraph::graph_from_data_frame(...) + 8. └─igraph::add_vertices(g, length(names), attr = vattrs) + 9. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 10. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-degree_total_in_out.R:15:3'): a degree data frame can be generated ── + Error in `data.frame(id = total_degree_values %>% names() %>% as.integer(), + total_degree = total_degree_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_degree_total(graph) at test-degree_total_in_out.R:15:3 + 2. └─base::data.frame(...) + ── Error ('test-get_aggregate_degree.R:18:3'): Getting aggregated indegree values is possible ── + Error in `data.frame(id = indegree_values %>% names() %>% as.integer(), + indegree = indegree_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-get_aggregate_degree.R:18:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─DiagrammeR::get_agg_degree_in(graph = graph, agg = "mean") + 5. └─DiagrammeR::get_degree_in(graph) + 6. └─base::data.frame(...) + ── Error ('test-get_aggregate_degree.R:135:3'): Getting aggregated outdegree values is possible ── + Error in `data.frame(id = outdegree_values %>% names() %>% as.integer(), + outdegree = outdegree_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-get_aggregate_degree.R:135:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─DiagrammeR::get_agg_degree_out(graph = graph, agg = "mean") + 5. └─DiagrammeR::get_degree_out(graph) + 6. └─base::data.frame(...) + ── Error ('test-get_aggregate_degree.R:257:3'): Getting aggregated total degree values is possible ── + Error in `data.frame(id = total_degree_values %>% names() %>% as.integer(), + total_degree = total_degree_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-get_aggregate_degree.R:257:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─DiagrammeR::get_agg_degree_total(graph = graph, agg = "mean") + 5. └─DiagrammeR::get_degree_total(graph) + 6. └─base::data.frame(...) + ── Error ('test-get_cmty.R:14:3'): the edge betweeness algorithm is functional ── + Error in `data.frame(id = igraph::membership(cmty_edge_btwns_obj) %>% names() %>% + as.integer(), edge_btwns_group = as.vector(igraph::membership(cmty_edge_btwns_obj)), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_cmty_edge_btwns(graph) at test-get_cmty.R:14:3 + 2. └─base::data.frame(...) + ── Error ('test-get_cmty.R:61:3'): the fast-greedy algorithm is functional ───── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. └─DiagrammeR::get_cmty_fast_greedy(graph) at test-get_cmty.R:61:3 + 2. └─DiagrammeR::to_igraph(graph) + 3. └─igraph::graph_from_data_frame(...) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-get_cmty.R:107:3'): the leading eigenvector algorithm is functional ── + Error in `data.frame(id = igraph::membership(cmty_l_eigenvec_obj) %>% names() %>% + as.integer(), l_eigenvec_group = as.vector(igraph::membership(cmty_l_eigenvec_obj)), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_cmty_l_eigenvec(graph) at test-get_cmty.R:107:3 + 2. └─base::data.frame(...) + ── Error ('test-get_cmty.R:151:3'): the Louvain algorithm is functional ──────── + Error in `data.frame(id = igraph::membership(cmty_louvain_obj) %>% names() %>% + as.integer(), louvain_group = as.vector(igraph::membership(cmty_louvain_obj)), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_cmty_louvain(graph) at test-get_cmty.R:151:3 + 2. └─base::data.frame(...) + ── Error ('test-get_cmty.R:197:3'): the walktrap algorithm is functional ─────── + Error in `data.frame(id = igraph::membership(cmty_walktrap_obj) %>% names() %>% + as.integer(), walktrap_group = as.vector(igraph::membership(cmty_walktrap_obj)), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_cmty_walktrap(graph) at test-get_cmty.R:197:3 + 2. └─base::data.frame(...) + ── Error ('test-get_graph_metrics.R:207:3'): Getting graph eccentricity is possible ── + Error in `data.frame(id = eccentricity %>% names() %>% as.integer(), eccentricity = eccentricity, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_eccentricity(graph) at test-get_graph_metrics.R:207:3 + 2. └─base::data.frame(...) + ── Error ('test-get_graph_metrics.R:241:3'): Getting graph periphery is possible ── + Error in `data.frame(id = eccentricity %>% names() %>% as.integer(), eccentricity = eccentricity, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_periphery(graph) at test-get_graph_metrics.R:241:3 + 2. └─DiagrammeR::get_eccentricity(graph) + 3. └─base::data.frame(...) + ── Error ('test-get_graph_metrics.R:316:3'): Checking whether the graph is connected is possible ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. ├─testthat::expect_true(is_graph_connected(graph_connected)) at test-get_graph_metrics.R:316:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─DiagrammeR::is_graph_connected(graph_connected) + 5. └─DiagrammeR::get_w_connected_cmpts(graph) + 6. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:13:3'): Getting betweenness is possible ── + Error in `data.frame(id = betweenness_scores %>% names() %>% as.integer(), + betweenness = betweenness_scores, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_betweenness(graph) at test-get_node_calculations.R:13:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:50:3'): Getting closeness is possible ── + Error in `data.frame(id = closeness_values %>% names() %>% as.integer(), + closeness = closeness_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_closeness(graph = graph, direction = "all") at test-get_node_calculations.R:50:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:84:3'): Getting coreness values is possible ── + Error in `data.frame(id = coreness_values %>% names() %>% as.integer(), + coreness = coreness_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_coreness(graph) at test-get_node_calculations.R:84:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:218:3'): Getting alpha centrality is possible ── + Error in `data.frame(id = alpha_centrality_values %>% names() %>% as.integer(), + alpha_centrality = alpha_centrality_values, stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 15 + Backtrace: + ▆ + 1. └─DiagrammeR::get_alpha_centrality(graph) at test-get_node_calculations.R:218:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:255:3'): Getting leverage centrality is possible ── + Error in `data.frame(id = degree_vals %>% names() %>% as.integer(), leverage_centrality = leverage_centrality_values %>% + round(4), stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_leverage_centrality(graph) at test-get_node_calculations.R:255:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:341:3'): Getting authority centrality is possible ── + Error in `data.frame(id = authority_centrality_values$vector %>% names() %>% + as.integer(), authority_centrality = unname(authority_centrality_values$vector), + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_authority_centrality(graph = graph_1) at test-get_node_calculations.R:341:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:477:3'): Getting eigenvector centrality is possible ── + Error in `data.frame(id = names(eigen_centrality_values$vector) %>% as.integer(), + eigen_centrality = unname(eigen_centrality_values$vector) %>% + round(4), stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_eigen_centrality(graph = graph_1) at test-get_node_calculations.R:477:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:562:3'): Getting radiality values is possible ── + Error in `data.frame(id = radiality_values %>% names() %>% as.integer(), + radiality = radiality_values %>% round(4), stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_radiality(graph) at test-get_node_calculations.R:562:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:644:3'): Getting PageRank values is possible ── + Error in `data.frame(id = names(pagerank_values) %>% as.integer(), pagerank = round(pagerank_values, + 4), stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_pagerank(graph) at test-get_node_calculations.R:644:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:703:3'): Getting weakly connected components is possible ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_w_connected_cmpts(graph) at test-get_node_calculations.R:703:3 + 2. └─base::data.frame(...) + ── Error ('test-get_node_calculations.R:736:3'): Getting strongly connected components is possible ── + Error in `data.frame(id = as.integer(names(components$membership)), sc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 5 + Backtrace: + ▆ + 1. └─DiagrammeR::get_s_connected_cmpts(graph) at test-get_node_calculations.R:736:3 + 2. └─base::data.frame(...) + ── Error ('test-get_nodes_edges.R:357:3'): getting connected nodes is possible ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. └─DiagrammeR::get_all_connected_nodes(graph = graph, node = 1) at test-get_nodes_edges.R:357:3 + 2. └─DiagrammeR::get_w_connected_cmpts(graph) + 3. └─base::data.frame(...) + ── Failure ('test-graph_actions.R:246:3'): graph actions can be triggered to modify the graph ── + Names of graph$nodes_df ('id', 'type', 'label') don't match 'id', 'type', 'label', 'pagerank', 'width', 'fillcolor' + ── Failure ('test-graph_actions.R:253:3'): graph actions can be triggered to modify the graph ── + graph$nodes_df$pagerank has type 'NULL', not 'double'. + ── Failure ('test-graph_actions.R:261:3'): graph actions can be triggered to modify the graph ── + graph$nodes_df$width has type 'NULL', not 'double'. + ── Failure ('test-graph_actions.R:269:3'): graph actions can be triggered to modify the graph ── + graph$nodes_df$fillcolor has type 'NULL', not 'character'. + ── Error ('test-graph_actions.R:272:3'): graph actions can be triggered to modify the graph ── + Error in `expect_match(graph$nodes_df$fillcolor, "#[A-F0-9]*")`: is.character(act$val) is not TRUE + Backtrace: + ▆ + 1. └─testthat::expect_match(graph$nodes_df$fillcolor, "#[A-F0-9]*") at test-graph_actions.R:272:3 + 2. └─base::stopifnot(is.character(act$val)) + ── Error ('test-is_something_some_thing.R:349:3'): Identifying the graph as a DAG is possible ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 5, the number of target vertices, not 7 + Backtrace: + ▆ + 1. ├─testthat::expect_false(is_graph_dag(non_dag)) at test-is_something_some_thing.R:349:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─DiagrammeR::is_graph_dag(non_dag) + 5. └─DiagrammeR::to_igraph(graph) + 6. └─igraph::graph_from_data_frame(...) + 7. └─igraph::add_vertices(g, length(names), attr = vattrs) + 8. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 9. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-mst.R:29:3'): the MST algorithm is functional ────────────────── + Error in `dplyr::arrange(nodes_df, id)`: Can't transform a data frame with duplicate names. + Backtrace: + ▆ + 1. ├─graph %>% transform_to_min_spanning_tree() at test-mst.R:29:3 + 2. └─DiagrammeR::transform_to_min_spanning_tree(.) + 3. └─DiagrammeR::from_igraph(igraph_mst) + 4. ├─dplyr::arrange(nodes_df, id) + 5. └─dplyr:::arrange.data.frame(nodes_df, id) + 6. └─dplyr:::arrange_rows(.data, dots = dots, locale = .locale) + 7. ├─dplyr::mutate(data, `:=`("{name}", !!dot), .keep = "none") + 8. └─dplyr:::mutate.data.frame(data, `:=`("{name}", !!dot), .keep = "none") + 9. └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) + 10. └─DataMask$new(data, by, "mutate", error_call = error_call) + 11. └─dplyr (local) initialize(...) + 12. └─rlang::abort(...) + ── Error ('test-print.R:96:3'): Printing a summary of node types works ───────── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:96:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_type_complete %>% get_printed_output(4) %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─DiagrammeR (local) get_printed_output(., 4) + 8. │ ├─... %>% unlist() at test-print.R:5:3 + 9. │ ├─testthat::capture_output(graph %>% print()) + 10. │ │ └─testthat::capture_output_lines(code, print, width = width) + 11. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 12. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 13. │ │ │ └─base::force(code) + 14. │ │ └─base::withVisible(code) + 15. │ └─graph %>% print() + 16. ├─base::unlist(.) + 17. ├─stringr::str_split(., pattern = "\n") + 18. │ └─stringr:::check_lengths(string, pattern) + 19. │ └─vctrs::vec_size_common(...) + 20. ├─base::print(.) + 21. └─DiagrammeR:::print.dgr_graph(.) + 22. └─DiagrammeR::is_graph_connected(x) + 23. └─DiagrammeR::get_w_connected_cmpts(graph) + 24. └─base::data.frame(...) + ── Error ('test-print.R:119:3'): Printing a summary of node labels works ─────── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:119:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─base::substr(., 1, 60) + 8. ├─DiagrammeR (local) get_printed_output(., 4) + 9. │ ├─... %>% unlist() at test-print.R:5:3 + 10. │ ├─testthat::capture_output(graph %>% print()) + 11. │ │ └─testthat::capture_output_lines(code, print, width = width) + 12. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 13. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 14. │ │ │ └─base::force(code) + 15. │ │ └─base::withVisible(code) + 16. │ └─graph %>% print() + 17. ├─base::unlist(.) + 18. ├─stringr::str_split(., pattern = "\n") + 19. │ └─stringr:::check_lengths(string, pattern) + 20. │ └─vctrs::vec_size_common(...) + 21. ├─base::print(.) + 22. └─DiagrammeR:::print.dgr_graph(.) + 23. └─DiagrammeR::is_graph_connected(x) + 24. └─DiagrammeR::get_w_connected_cmpts(graph) + 25. └─base::data.frame(...) + ── Error ('test-print.R:157:3'): Printing a summary of extra node attrs works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:157:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_node_attr_1 %>% get_printed_output(5) %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─DiagrammeR (local) get_printed_output(., 5) + 8. │ ├─... %>% unlist() at test-print.R:5:3 + 9. │ ├─testthat::capture_output(graph %>% print()) + 10. │ │ └─testthat::capture_output_lines(code, print, width = width) + 11. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 12. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 13. │ │ │ └─base::force(code) + 14. │ │ └─base::withVisible(code) + 15. │ └─graph %>% print() + 16. ├─base::unlist(.) + 17. ├─stringr::str_split(., pattern = "\n") + 18. │ └─stringr:::check_lengths(string, pattern) + 19. │ └─vctrs::vec_size_common(...) + 20. ├─base::print(.) + 21. └─DiagrammeR:::print.dgr_graph(.) + 22. └─DiagrammeR::is_graph_connected(x) + 23. └─DiagrammeR::get_w_connected_cmpts(graph) + 24. └─base::data.frame(...) + ── Error ('test-print.R:189:3'): Printing a summary of edge rel values works ─── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:189:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─base::substr(., 1, 45) + 8. ├─DiagrammeR (local) get_printed_output(., 6) + 9. │ ├─... %>% unlist() at test-print.R:5:3 + 10. │ ├─testthat::capture_output(graph %>% print()) + 11. │ │ └─testthat::capture_output_lines(code, print, width = width) + 12. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 13. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 14. │ │ │ └─base::force(code) + 15. │ │ └─base::withVisible(code) + 16. │ └─graph %>% print() + 17. ├─base::unlist(.) + 18. ├─stringr::str_split(., pattern = "\n") + 19. │ └─stringr:::check_lengths(string, pattern) + 20. │ └─vctrs::vec_size_common(...) + 21. ├─base::print(.) + 22. └─DiagrammeR:::print.dgr_graph(.) + 23. └─DiagrammeR::is_graph_connected(x) + 24. └─DiagrammeR::get_w_connected_cmpts(graph) + 25. └─base::data.frame(...) + ── Error ('test-print.R:227:3'): Printing a summary of extra edge attrs works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 5 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:227:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_edge_attr_1 %>% get_printed_output(7) %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─DiagrammeR (local) get_printed_output(., 7) + 8. │ ├─... %>% unlist() at test-print.R:5:3 + 9. │ ├─testthat::capture_output(graph %>% print()) + 10. │ │ └─testthat::capture_output_lines(code, print, width = width) + 11. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 12. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 13. │ │ │ └─base::force(code) + 14. │ │ └─base::withVisible(code) + 15. │ └─graph %>% print() + 16. ├─base::unlist(.) + 17. ├─stringr::str_split(., pattern = "\n") + 18. │ └─stringr:::check_lengths(string, pattern) + 19. │ └─vctrs::vec_size_common(...) + 20. ├─base::print(.) + 21. └─DiagrammeR:::print.dgr_graph(.) + 22. └─DiagrammeR::is_graph_connected(x) + 23. └─DiagrammeR::get_w_connected_cmpts(graph) + 24. └─base::data.frame(...) + ── Error ('test-print.R:256:3'): Describing if a graph is weighted works ─────── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 5 + Backtrace: + ▆ + 1. ├─testthat::expect_match(...) at test-print.R:256:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_weighted %>% get_printed_output(2) + 5. ├─DiagrammeR (local) get_printed_output(., 2) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_connected(x) + 21. └─DiagrammeR::get_w_connected_cmpts(graph) + 22. └─base::data.frame(...) + ── Error ('test-print.R:275:3'): Describing if a graph is a DAG works ────────── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 5 + Backtrace: + ▆ + 1. ├─testthat::expect_match(graph_dag %>% get_printed_output(2), "DAG") at test-print.R:275:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_dag %>% get_printed_output(2) + 5. ├─DiagrammeR (local) get_printed_output(., 2) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_connected(x) + 21. └─DiagrammeR::get_w_connected_cmpts(graph) + 22. └─base::data.frame(...) + ── Error ('test-print.R:301:3'): Describing if a graph is a property graph works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_match(graph_pg %>% get_printed_output(2), "property graph") at test-print.R:301:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_pg %>% get_printed_output(2) + 5. ├─DiagrammeR (local) get_printed_output(., 2) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_connected(x) + 21. └─DiagrammeR::get_w_connected_cmpts(graph) + 22. └─base::data.frame(...) + ── Error ('test-print.R:324:3'): Describing if a graph is a simple graph works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_match(...) at test-print.R:324:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_simple %>% get_printed_output(2) + 5. ├─DiagrammeR (local) get_printed_output(., 2) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_connected(x) + 21. └─DiagrammeR::get_w_connected_cmpts(graph) + 22. └─base::data.frame(...) + ── Error ('test-print.R:344:3'): Describing if a graph is a connected or not works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_match(...) at test-print.R:344:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_connected %>% get_printed_output(2) + 5. ├─DiagrammeR (local) get_printed_output(., 2) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_connected(x) + 21. └─DiagrammeR::get_w_connected_cmpts(graph) + 22. └─base::data.frame(...) + ── Error ('test-print.R:374:3'): The number of reported nodes is correct ─────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 0, the number of target vertices, not 4 + Backtrace: + ▆ + 1. ├─testthat::expect_match(...) at test-print.R:374:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_4_nodes %>% get_printed_output(1) + 5. ├─DiagrammeR (local) get_printed_output(., 1) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_dag(x) + 21. └─DiagrammeR::to_igraph(graph) + 22. └─igraph::graph_from_data_frame(...) + 23. └─igraph::add_vertices(g, length(names), attr = vattrs) + 24. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 25. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-print.R:393:3'): The number of reported edges is correct ─────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 0, the number of target vertices, not 4 + Backtrace: + ▆ + 1. ├─testthat::expect_no_match(...) at test-print.R:393:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─graph_no_edges %>% get_printed_output(1) + 5. ├─DiagrammeR (local) get_printed_output(., 1) + 6. │ ├─... %>% unlist() at test-print.R:5:3 + 7. │ ├─testthat::capture_output(graph %>% print()) + 8. │ │ └─testthat::capture_output_lines(code, print, width = width) + 9. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 10. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 11. │ │ │ └─base::force(code) + 12. │ │ └─base::withVisible(code) + 13. │ └─graph %>% print() + 14. ├─base::unlist(.) + 15. ├─stringr::str_split(., pattern = "\n") + 16. │ └─stringr:::check_lengths(string, pattern) + 17. │ └─vctrs::vec_size_common(...) + 18. ├─base::print(.) + 19. └─DiagrammeR:::print.dgr_graph(.) + 20. └─DiagrammeR::is_graph_dag(x) + 21. └─DiagrammeR::to_igraph(graph) + 22. └─igraph::graph_from_data_frame(...) + 23. └─igraph::add_vertices(g, length(names), attr = vattrs) + 24. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 25. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-print.R:432:3'): Printing a summary line for node/edge selections works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:432:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─base::substr(., 1, 45) + 8. ├─DiagrammeR (local) get_printed_output(., 8) + 9. │ ├─... %>% unlist() at test-print.R:5:3 + 10. │ ├─testthat::capture_output(graph %>% print()) + 11. │ │ └─testthat::capture_output_lines(code, print, width = width) + 12. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 13. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 14. │ │ │ └─base::force(code) + 15. │ │ └─base::withVisible(code) + 16. │ └─graph %>% print() + 17. ├─base::unlist(.) + 18. ├─stringr::str_split(., pattern = "\n") + 19. │ └─stringr:::check_lengths(string, pattern) + 20. │ └─vctrs::vec_size_common(...) + 21. ├─base::print(.) + 22. └─DiagrammeR:::print.dgr_graph(.) + 23. └─DiagrammeR::is_graph_connected(x) + 24. └─DiagrammeR::get_w_connected_cmpts(graph) + 25. └─base::data.frame(...) + ── Error ('test-print.R:476:3'): Printing a summary line for graph caches works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 4 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:476:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─base::substr(., 1, 45) + 8. ├─DiagrammeR (local) get_printed_output(., 9) + 9. │ ├─... %>% unlist() at test-print.R:5:3 + 10. │ ├─testthat::capture_output(graph %>% print()) + 11. │ │ └─testthat::capture_output_lines(code, print, width = width) + 12. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 13. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 14. │ │ │ └─base::force(code) + 15. │ │ └─base::withVisible(code) + 16. │ └─graph %>% print() + 17. ├─base::unlist(.) + 18. ├─stringr::str_split(., pattern = "\n") + 19. │ └─stringr:::check_lengths(string, pattern) + 20. │ └─vctrs::vec_size_common(...) + 21. ├─base::print(.) + 22. └─DiagrammeR:::print.dgr_graph(.) + 23. └─DiagrammeR::is_graph_connected(x) + 24. └─DiagrammeR::get_w_connected_cmpts(graph) + 25. └─base::data.frame(...) + ── Error ('test-print.R:551:3'): Printing a summary line for graph actions works ── + Error in `data.frame(id = as.integer(names(components$membership)), wc_component = components$membership, + stringsAsFactors = FALSE)`: arguments imply differing number of rows: 0, 10 + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-print.R:551:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% stringr::str_trim() + 5. ├─stringr::str_trim(.) + 6. │ └─stringi::stri_trim_both(string) + 7. ├─base::substr(., 1, 30) + 8. ├─DiagrammeR (local) get_printed_output(., 11) + 9. │ ├─... %>% unlist() at test-print.R:5:3 + 10. │ ├─testthat::capture_output(graph %>% print()) + 11. │ │ └─testthat::capture_output_lines(code, print, width = width) + 12. │ │ └─testthat:::eval_with_output(code, print = print, width = width) + 13. │ │ ├─withr::with_output_sink(path, withVisible(code)) + 14. │ │ │ └─base::force(code) + 15. │ │ └─base::withVisible(code) + 16. │ └─graph %>% print() + 17. ├─base::unlist(.) + 18. ├─stringr::str_split(., pattern = "\n") + 19. │ └─stringr:::check_lengths(string, pattern) + 20. │ └─vctrs::vec_size_common(...) + 21. ├─base::print(.) + 22. └─DiagrammeR:::print.dgr_graph(.) + 23. └─DiagrammeR::is_graph_connected(x) + 24. └─DiagrammeR::get_w_connected_cmpts(graph) + 25. └─base::data.frame(...) + ── Error ('test-transform_graph.R:156:3'): Creating a complement graph is possible ── + Error in `dplyr::arrange(nodes_df, id)`: Can't transform a data frame with duplicate names. + Backtrace: + ▆ + 1. ├─DiagrammeR::transform_to_complement_graph(graph) at test-transform_graph.R:156:3 + 2. │ ├─from_igraph(ig_graph) %>% get_edge_df() + 3. │ └─DiagrammeR::from_igraph(ig_graph) + 4. │ ├─dplyr::arrange(nodes_df, id) + 5. │ └─dplyr:::arrange.data.frame(nodes_df, id) + 6. │ └─dplyr:::arrange_rows(.data, dots = dots, locale = .locale) + 7. │ ├─dplyr::mutate(data, `:=`("{name}", !!dot), .keep = "none") + 8. │ └─dplyr:::mutate.data.frame(data, `:=`("{name}", !!dot), .keep = "none") + 9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) + 10. │ └─DataMask$new(data, by, "mutate", error_call = error_call) + 11. │ └─dplyr (local) initialize(...) + 12. │ └─rlang::abort(...) + 13. └─DiagrammeR::get_edge_df(.) + 14. └─DiagrammeR:::check_graph_valid(graph) + 15. └─DiagrammeR:::graph_object_valid(graph) + 16. └─... %in% names(graph) + ── Error ('test-write_graph_backup.R:486:3'): Graph backups for `transform_to_complement_graph()` works ── + Error in `dplyr::arrange(nodes_df, id)`: Can't transform a data frame with duplicate names. + Backtrace: + ▆ + 1. ├─... %>% transform_to_complement_graph() at test-write_graph_backup.R:486:3 + 2. ├─DiagrammeR::transform_to_complement_graph(.) + 3. │ ├─from_igraph(ig_graph) %>% get_edge_df() + 4. │ └─DiagrammeR::from_igraph(ig_graph) + 5. │ ├─dplyr::arrange(nodes_df, id) + 6. │ └─dplyr:::arrange.data.frame(nodes_df, id) + 7. │ └─dplyr:::arrange_rows(.data, dots = dots, locale = .locale) + 8. │ ├─dplyr::mutate(data, `:=`("{name}", !!dot), .keep = "none") + 9. │ └─dplyr:::mutate.data.frame(data, `:=`("{name}", !!dot), .keep = "none") + 10. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) + 11. │ └─DataMask$new(data, by, "mutate", error_call = error_call) + 12. │ └─dplyr (local) initialize(...) + 13. │ └─rlang::abort(...) + 14. └─DiagrammeR::get_edge_df(.) + 15. └─DiagrammeR:::check_graph_valid(graph) + 16. └─DiagrammeR:::graph_object_valid(graph) + 17. └─... %in% names(graph) + + [ FAIL 52 | WARN 0 | SKIP 23 | PASS 1423 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + +# dyndimred + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/dynverse/dyndimred +* Source code: https://github.com/cran/dyndimred +* Date/Publication: 2021-03-23 08:30:06 UTC +* Number of recursive dependencies: 161 + +Run `revdepcheck::cloud_details(, "dyndimred")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > test_check("dyndimred") + Loading required package: dyndimred + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-dimred.R:26:9'): Perform dimred with knn_fr ──────────────────── + Error in `igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x)))`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. ├─utils::capture.output(...) at test-dimred.R:23:7 + 2. │ └─base::withVisible(...elt(i)) + 3. └─dyndimred (local) dr_fun(expr) at test-dimred.R:26:9 + 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) + ── Error ('test-dimred.R:74:9'): Check sparse capable knn_fr ─────────────────── + Error in `igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x)))`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. ├─utils::capture.output(...) at test-dimred.R:70:7 + 2. │ └─base::withVisible(...elt(i)) + 3. └─dyndimred (local) dr_fun(sparse_expr) at test-dimred.R:74:9 + 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘lle’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# dynwrap + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/dynverse/dynwrap +* Source code: https://github.com/cran/dynwrap +* Date/Publication: 2023-07-19 09:20:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "dynwrap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dynwrap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: simplify_igraph_network + > ### Title: Simplify an igraph network such that consecutive linear edges + > ### are removed + > ### Aliases: simplify_igraph_network + > + > ### ** Examples + > + > net <- data.frame( + + from = 1:2, + + to = 2:3, + + length = 1, + + directed = TRUE, + + stringsAsFactors = F + + ) + > gr <- igraph::graph_from_data_frame(net) + > simplify_igraph_network(gr) + Warning: non-unique value when setting 'row.names': ‘#M#’ + Error in `map()`: + ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr) + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dynwrap) + > + > test_check("dynwrap") + [ FAIL 12 | WARN 30 | SKIP 3 | PASS 498 ] + + ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ + • On CRAN (1): 'test-method_create_ti_method_container.R:5:1' + • dyndimre2d cannot be loaded (1): 'test-wrap_add_dimred.R:110:3' + • empty test (1): 'test-adapt_orient_topology.R:50:1' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-classify_milestone_network.R:164:3'): Example trajectories match ── + + Error in `map(., classify_milestone_network)`: ℹ In index: 2. + Caused by error in `map()`: + ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on directed_linear ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on directed_diverging ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on undirected_linear ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on simple_branching ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on simple_undirected_branching ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on branching ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on branching_converging ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Failure ('test-simplify_igraph_network.R:176:5'): Testing simplify_igraph_network on cyclical ── + `pass_check` is not TRUE + + `actual`: FALSE + `expected`: TRUE + ── Error ('test-simplify_igraph_network.R:157:5'): Testing simplify_igraph_network on undirected_branching_converging ── + + Error in `map(.x, .f, ...)`: ℹ In index: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Backtrace: + ▆ + 1. ├─dynwrap::simplify_igraph_network(gr, allow_duplicated_edges = TRUE) at test-simplify_igraph_network.R:157:5 + 2. │ └─purrr::map_df(subgrs, igraph::as_data_frame, what = "vertices") + 3. │ └─purrr::map(.x, .f, ...) + 4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 5. │ ├─purrr:::with_indexed_errors(...) + 6. │ │ └─base::withCallingHandlers(...) + 7. │ ├─purrr:::call_with_cleanup(...) + 8. │ └─igraph (local) .f(.x[[i]], ...) + 9. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 10. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 11. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 12. │ └─base::`.rowNamesDF<-`(x, value = value) + 13. │ └─base::stop("duplicate 'row.names' are not allowed") + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + ── Error ('test-simplify_igraph_network.R:184:3'): simplify_igraph_network's allow_duplicated_edges parameter ── + Error in `igraph::graph_from_data_frame(net, directed = TRUE, vertices = 1:4)`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─igraph::graph_from_data_frame(net, directed = TRUE, vertices = 1:4) at test-simplify_igraph_network.R:184:3 + ── Error ('test-wrap_add_dimred.R:279:3'): Test get_dimred ───────────────────── + Error in `(function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, + tol = 1e-05, v = NULL, right_only = FALSE, verbose = FALSE, + scale = NULL, center = NULL, shift = NULL, mult = NULL, fastpath = TRUE, + svtol = tol, smallest = FALSE, ...) + { + ropts <- options(warn = 1) + mflag <- new.env() + mflag$flag <- FALSE + on.exit(options(ropts)) + interchange <- FALSE + eps <- .Machine$double.eps + mcall <- as.list(match.call()) + random <- eval(mcall[["rng"]]) + if (is.null(random)) + random <- rnorm + maxritz <- eval(mcall[["maxritz"]]) + if (is.null(maxritz)) + maxritz <- 3 + eps2 <- eval(mcall[["invariant_subspace_tolerance"]]) + if (is.null(eps2)) + eps2 <- eps^(4/5) + du <- eval(mcall[["du"]]) + dv <- eval(mcall[["dv"]]) + ds <- eval(mcall[["ds"]]) + deflate <- is.null(du) + is.null(ds) + is.null(dv) + if (is.logical(scale) && !scale) + scale <- NULL + if (is.logical(shift) && !shift) + shift <- NULL + if (is.logical(center) && !center) + center <- NULL + if (smallest) + fastpath <- FALSE + if (any(dim(A) > 2^32 - 1)) + fastpath <- FALSE + if (deflate == 3) { + deflate <- FALSE + } + else if (deflate == 0) { + deflate <- TRUE + warning("The deflation options have been deprecated. Please modify your code to not use them.") + if (length(ds) > 1) + stop("deflation limited to one dimension") + if (!is.null(dim(du))) + du <- du[, 1] + if (!is.null(dim(dv))) + dv <- dv[, 1] + } + else stop("all three du ds dv parameters must be specified for deflation") + if (!is.null(center)) { + if (is.logical(center) && center) + center <- colMeans(A) + if (deflate) + stop("the center parameter can't be specified together with deflation parameters") + if (length(center) != ncol(A)) + stop("center must be a vector of length ncol(A)") + if (fastpath && !right_only) + du <- NULL + else du <- 1 + ds <- 1 + dv <- center + deflate <- TRUE + } + if ("integer" == typeof(A)) + A <- A + 0 + iscomplex <- is.complex(A) + m <- nrow(A) + n <- ncol(A) + if (is.null(nu)) + nu <- nv + if (!is.null(mult) && deflate) + stop("the mult parameter can't be specified together with deflation parameters") + missingmult <- FALSE + if (is.null(mult)) { + missingmult <- TRUE + mult <- `%*%` + } + k <- max(nu, nv) + if (k <= 0) + stop("max(nu, nv) must be positive") + if (k > min(m - 1, n - 1)) + stop("max(nu, nv) must be strictly less than min(nrow(A), ncol(A))") + if (k >= 0.5 * min(m, n)) { + warning("You're computing too large a percentage of total singular values, use a standard svd instead.") + } + if (work <= 1) + stop("work must be greater than 1") + if (tol < 0) + stop("tol must be non-negative") + if (maxit <= 0) + stop("maxit must be positive") + if (work <= k && !right_only) + work <- k + 1 + if (work >= min(n, m)) { + work <- min(n, m) + if (work <= k) { + k <- work - 1 + warning("Requested subspace dimension too large! Reduced to ", + k) + } + } + k_org <- k + w_dim <- work + if (right_only) { + w_dim <- 1 + fastpath <- FALSE + } + if (n > m && smallest) { + interchange <- TRUE + temp <- m + m <- n + n <- temp + } + if (verbose) { + message("Working dimension size ", work) + } + if (min(m, n) < 6) { + A <- as.matrix(A) + if (verbose) + message("Tiny problem detected, using standard `svd` function.") + if (!is.null(scale)) { + A <- sweep(A, 2, scale, "/") + dv <- dv/scale + } + if (!is.null(shift)) + A <- A + diag(shift, nrow(A), ncol(A)) + if (deflate) { + if (is.null(du)) + du <- rep(1, nrow(A)) + A <- A - (ds * du) %*% t(dv) + } + s <- svd(A) + if (smallest) { + return(list(d = tail(s$d, k), u = s$u[, tail(seq(ncol(s$u)), + k), drop = FALSE], v = s$v[, tail(seq(ncol(s$v), + k)), drop = FALSE], iter = 0, mprod = 0)) + } + return(list(d = s$d[1:k], u = s$u[, 1:nu, drop = FALSE], + v = s$v[, 1:nv, drop = FALSE], iter = 0, mprod = 0)) + } + if (deflate) + fastpath <- fastpath && is.null(du) + fastpath <- fastpath && (("Matrix" %in% attributes(class(A)) && + ("dgCMatrix" %in% class(A))) || "matrix" %in% class(A)) + if (fastpath && missingmult && !iscomplex && !right_only) { + RESTART <- 0L + RV <- RW <- RS <- NULL + if (is.null(v)) { + v <- random(n) + if (verbose) + message("Initializing starting vector v with samples from standard normal distribution.\nUse `set.seed` first for reproducibility.") + } + else if (is.list(v)) { + if (is.null(v$v) || is.null(v$d) || is.null(v$u)) + stop("restart requires left and right singular vectors") + if (max(nu, nv) <= min(ncol(v$u), ncol(v$v))) + return(v) + RESTART <- as.integer(length(v$d)) + RND <- random(n) + RND <- orthog(RND, v$v) + RV <- cbind(v$v, RND/norm2(RND)) + RW <- v$u + RS <- v$d + v <- NULL + } + SP <- ifelse(is.matrix(A), 0L, 1L) + if (verbose) + message("irlba: using fast C implementation") + SCALE <- NULL + SHIFT <- NULL + CENTER <- NULL + if (!is.null(scale)) { + if (length(scale) != ncol(A)) + stop("scale length must match number of matrix columns") + SCALE <- as.double(scale) + } + if (!is.null(shift)) { + if (length(shift) != 1) + stop("shift length must be 1") + SHIFT <- as.double(shift) + } + if (deflate) { + if (length(center) != ncol(A)) + stop("the centering vector length must match the number of matrix columns") + CENTER <- as.double(center) + } + ans <- .Call(C_IRLB, A, as.integer(k), as.double(v), + as.integer(work), as.integer(maxit), as.double(tol), + as.double(eps2), as.integer(SP), as.integer(RESTART), + RV, RW, RS, SCALE, SHIFT, CENTER, as.double(svtol)) + if (ans[[6]] == 0 || ans[[6]] == -2) { + names(ans) <- c("d", "u", "v", "iter", "mprod", "err") + ans$u <- matrix(head(ans$u, m * nu), nrow = m, ncol = nu) + ans$v <- matrix(head(ans$v, n * nv), nrow = n, ncol = nv) + if (tol * ans$d[1] < eps) + warning("convergence criterion below machine epsilon") + if (ans[[6]] == -2) + warning("did not converge--results might be invalid!; try increasing work or maxit") + return(ans[-6]) + } + errors <- c("invalid dimensions", "didn't converge", + "out of memory", "starting vector near the null space", + "linear dependency encountered") + erridx <- abs(ans[[6]]) + if (erridx > 1) + warning("fast code path error ", errors[erridx], + "; re-trying with fastpath=FALSE.", immediate. = TRUE) + } + W <- matrix(0, m, w_dim) + F <- matrix(0, n, 1) + restart <- FALSE + if (is.list(v)) { + if (is.null(v$v) || is.null(v$d) || is.null(v$u)) + stop("restart requires left and right singular vectors") + if (max(nu, nv) <= min(ncol(v$u), ncol(v$v))) + return(v) + right_only <- FALSE + W[, 1:ncol(v$u)] <- v$u + d <- v$d + V <- matrix(0, n, work) + V[, 1:ncol(v$v)] <- v$v + restart <- TRUE + } + else if (is.null(v)) { + V <- matrix(0, n, work) + V[, 1] <- random(n) + } + else { + V <- matrix(0, n, work) + V[1:length(v)] <- v + } + B <- NULL + Bsz <- NULL + eps23 <- eps^(2/3) + iter <- 1 + mprod <- 0 + R_F <- NULL + sqrteps <- sqrt(eps) + Smax <- 1 + Smin <- NULL + lastsv <- c() + if (restart) { + B <- cbind(diag(d), 0) + k <- length(d) + F <- random(n) + F <- orthog(F, V[, 1:k]) + V[, k + 1] <- F/norm2(F) + } + if (deflate && is.null(du)) + du <- 1 + while (iter <= maxit) { + j <- 1 + if (iter == 1 && !restart) { + V[, 1] <- V[, 1]/norm2(V[, 1]) + } + else j <- k + 1 + j_w <- ifelse(w_dim > 1, j, 1) + VJ <- V[, j] + if (!is.null(scale)) { + VJ <- VJ/scale + } + if (interchange) + avj <- mult(VJ, A) + else avj <- mult(A, VJ) + W[, j_w] <- as.vector(avj) + mprod <- mprod + 1 + if (!is.null(shift)) { + W[, j_w] <- W[, j_w] + shift * VJ + } + if (deflate) { + W[, j_w] <- W[, j_w] - ds * drop(cross(dv, VJ)) * + du + } + if (iter != 1 && w_dim > 1 && reorth) { + W[, j] <- orthog(W[, j, drop = FALSE], W[, 1:(j - + 1), drop = FALSE]) + } + S <- norm2(W[, j_w, drop = FALSE]) + if (is.na(S) || S < eps2 && j == 1) + stop("starting vector near the null space") + if (is.na(S) || S < eps2) { + if (verbose) + message_once("invariant subspace found", flag = mflag) + W[, j_w] <- random(nrow(W)) + if (w_dim > 1) + W[, j] <- orthog(W[, j], W[, 1:(j - 1)]) + W[, j_w] <- W[, j_w]/norm2(W[, j_w]) + S <- 0 + } + else W[, j_w] <- W[, j_w]/S + while (j <= work) { + j_w <- ifelse(w_dim > 1, j, 1) + if (iscomplex) { + if (interchange) + F <- Conj(t(drop(mult(A, Conj(drop(W[, j_w])))))) + else F <- Conj(t(drop(mult(Conj(drop(W[, j_w])), + A)))) + } + else { + if (interchange) + F <- t(drop(mult(A, drop(W[, j_w])))) + else F <- t(drop(mult(drop(W[, j_w]), A))) + } + if (!is.null(shift)) + F <- F + shift * W[, j_w] + if (!is.null(scale)) + F <- F/scale + if (deflate) { + sub <- sum(W[, j_w]) * dv + if (!is.null(scale)) + sub <- sub/scale + F <- F - sub + } + mprod <- mprod + 1 + F <- drop(F - S * V[, j]) + F <- orthog(F, V[, 1:j, drop = FALSE]) + if (j + 1 <= work) { + R <- norm2(F) + if (R < eps2) { + if (verbose) + message_once("invariant subspace found", + flag = mflag) + F <- matrix(random(dim(V)[1]), dim(V)[1], 1) + F <- orthog(F, V[, 1:j, drop = FALSE]) + V[, j + 1] <- F/norm2(F) + R <- 0 + } + else V[, j + 1] <- F/R + if (is.null(B)) + B <- cbind(S, R) + else B <- rbind(cbind(B, 0), c(rep(0, ncol(B) - + 1), S, R)) + jp1_w <- ifelse(w_dim > 1, j + 1, 1) + w_old <- W[, j_w] + VJP1 <- V[, j + 1] + if (!is.null(scale)) { + VJP1 <- VJP1/scale + } + if (interchange) + W[, jp1_w] <- drop(mult(drop(VJP1), A)) + else W[, jp1_w] <- drop(mult(A, drop(VJP1))) + mprod <- mprod + 1 + if (!is.null(shift)) { + W[, jp1_w] <- W[, jp1_w] + shift * VJP1 + } + if (deflate) { + W[, jp1_w] <- W[, jp1_w] - ds * drop(cross(dv, + VJP1)) * du + } + W[, jp1_w] <- W[, jp1_w] - R * w_old + if (reorth && w_dim > 1) + W[, j + 1] <- orthog(W[, j + 1], W[, 1:j]) + S <- norm2(W[, jp1_w]) + if (S < eps2) { + if (verbose) + message_once("invariant subspace found", + flag = mflag) + W[, jp1_w] <- random(nrow(W)) + if (w_dim > 1) + W[, j + 1] <- orthog(W[, j + 1], W[, 1:j]) + W[, jp1_w] <- W[, jp1_w]/norm2(W[, jp1_w]) + S <- 0 + } + else W[, jp1_w] <- W[, jp1_w]/S + } + else { + B <- rbind(B, c(rep(0, j - 1), S)) + } + j <- j + 1 + } + Bsz <- nrow(B) + R_F <- norm2(F) + F <- F/R_F + Bsvd <- svd(B) + if (iter == 1) { + Smax <- Bsvd$d[1] + Smin <- Bsvd$d[Bsz] + } + else { + Smax <- max(Smax, Bsvd$d[1]) + Smin <- min(Smin, Bsvd$d[Bsz]) + } + Smax <- max(eps23, Smax) + if (!reorth && Smin/Smax < sqrteps) { + warning("The matrix is ill-conditioned. Basis will be reorthogonalized.") + reorth <- TRUE + } + if (smallest) { + jj <- seq(ncol(Bsvd$u), 1, by = -1) + Bsvd$u <- Bsvd$u[, jj] + Bsvd$d <- Bsvd$d[jj] + Bsvd$v <- Bsvd$v[, jj] + } + R <- R_F * Bsvd$u[Bsz, , drop = FALSE] + ct <- convtests(Bsz, tol, k_org, Bsvd, abs(R), k, Smax, + lastsv, svtol, maxritz, work, S) + if (verbose) { + message("iter= ", iter, ", mprod= ", mprod, ", sv[", + k_org, "]=", sprintf("%.2e", Bsvd$d[k_org]), + ", %change=", sprintf("%.2e", (Bsvd$d[k_org] - + lastsv[k_org])/Bsvd$d[k_org]), ", k=", ct$k) + } + lastsv <- Bsvd$d + k <- ct$k + if (ct$converged) + break + if (iter >= maxit) + break + if (smallest && (Smin/Smax > sqrteps)) { + Bsvd2.d <- Bsvd$d + Bsvd2.d <- diag(Bsvd2.d, nrow = length(Bsvd2.d)) + Bsvd2 <- svd(cbind(Bsvd2.d, t(R))) + jj <- seq(ncol(Bsvd2$u), 1, by = -1) + Bsvd2$u <- Bsvd2$u[, jj] + Bsvd2$d <- Bsvd2$d[jj] + Bsvd2$v <- Bsvd2$v[, jj] + Bsvd$d <- Bsvd2$d + Bsvd$u <- Bsvd$u %*% Bsvd2$u + Bsvd$v <- cbind(rbind(Bsvd$v, rep(0, Bsz)), c(rep(0, + Bsz), 1)) %*% Bsvd2$v + V_B_last <- Bsvd$v[Bsz + 1, 1:k] + s <- R_F * solve(B, cbind(c(rep(0, Bsz - 1), 1))) + Bsvd$v <- Bsvd$v[1:Bsz, , drop = FALSE] + s %*% Bsvd$v[Bsz + + 1, ] + qrv <- qr(cbind(rbind(Bsvd$v[, 1:k], 0), rbind(-s, + 1))) + Bsvd$v <- qr.Q(qrv) + R <- qr.R(qrv) + V[, 1:(k + 1)] <- cbind(V, F) %*% Bsvd$v + UT <- t(R[1:(k + 1), 1:k] + R[, k + 1] %*% rbind(V_B_last)) + B <- diag(Bsvd$d[1:k], nrow = k) %*% (UT * upper.tri(UT, + diag = TRUE))[1:k, 1:(k + 1)] + } + else { + V[, 1:(k + dim(F)[2])] <- cbind(V[, 1:(dim(Bsvd$v)[1]), + drop = FALSE] %*% Bsvd$v[, 1:k], F) + B <- cbind(diag(Bsvd$d[1:k], nrow = k), R[1:k]) + } + if (w_dim > 1) { + W[, 1:k] <- W[, 1:(dim(Bsvd$u)[1]), drop = FALSE] %*% + Bsvd$u[, 1:k] + } + iter <- iter + 1 + } + if (!ct$converged) + warning("did not converge--results might be invalid!; try increasing maxit or work") + d <- Bsvd$d[1:k_org] + if (!right_only) { + u <- W[, 1:(dim(Bsvd$u)[1]), drop = FALSE] %*% Bsvd$u[, + 1:k_org, drop = FALSE] + } + v <- V[, 1:(dim(Bsvd$v)[1]), drop = FALSE] %*% Bsvd$v[, 1:k_org, + drop = FALSE] + if (smallest) { + reverse <- seq(length(d), 1) + d <- d[reverse] + if (!right_only) + u <- u[, reverse] + v <- v[, reverse] + } + if (tol * d[1] < eps) + warning("convergence criterion below machine epsilon") + if (right_only) + return(list(d = d, v = v[, 1:nv, drop = FALSE], iter = iter, + mprod = mprod)) + return(list(d = d, u = u[, 1:nu, drop = FALSE], v = v[, 1:nv, + drop = FALSE], iter = iter, mprod = mprod)) + })(A = new("dgCMatrix", i = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, + 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, + 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, + 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, + 2L, 3L, 4L, 5L), p = c(0L, 6L, 12L, 18L, 24L, 30L, 36L, 42L, + 48L, 54L, 60L), Dim = c(6L, 10L), Dimnames = list(c("truth", + "universally", "acknowledged", "that", "a", "single"), c("G1", + "G2", "G3", "G4", "G5", "G6", "G7", "G8", "G9", "G10")), x = c(6.4262647547021, + 6.61470984411521, 6.4262647547021, 6.62935662007961, 6.49185309632967, + 6.4594316186373, 6.53915881110803, 6.71424551766612, 6.52356195605701, + 6.52356195605701, 6.68650052718322, 6.52356195605701, 6.71424551766612, + 6.62935662007961, 6.74146698640115, 6.4262647547021, 6.49185309632967, + 6.79441586635011, 6.75488750216347, 6.82017896241519, 6.44294349584873, + 6.56985560833095, 6.53915881110803, 6.7279204545632, 6.84549005094437, + 6.53915881110803, 7.01122725542325, 6.5077946401987, 6.7279204545632, + 6.7279204545632, 6.74146698640115, 6.76818432477693, 6.61470984411521, + 6.8073549220576, 6.84549005094437, 6.59991284218713, 6.52356195605701, + 6.61470984411521, 6.59991284218713, 6.59991284218713, 6.8703647195834, + 6.74146698640115, 6.74146698640115, 6.44294349584873, 6.70043971814109, + 6.8073549220576, 6.79441586635011, 6.6724253419715, 6.8703647195834, + 6.75488750216347, 6.4093909361377, 6.93073733756289, 6.61470984411521, + 6.56985560833095, 6.39231742277876, 6.59991284218713, 6.28540221886225, + 6.62935662007961, 6.83289001416474, 6.7279204545632), factors = list()), + nv = 2, center = c(G1 = 6.507980114761, G2 = 6.5850984540214, + G3 = 6.63293380692146, G4 = 6.64249080573826, G5 = 6.72658527780013, + G6 = 6.72951982841373, G7 = 6.65832153175517, G8 = 6.6931743884617, + G9 = 6.69165765798227, G10 = 6.57796659543928))`: function 'sexp_as_cholmod_sparse' not provided by package 'Matrix' + Backtrace: + ▆ + 1. └─dynwrap::get_dimred(wr_withdimred, dimred = dyndimred::dimred_pca) at test-wrap_add_dimred.R:279:3 + 2. └─dyndimred::dimred(expression) + 3. └─irlba::prcomp_irlba(x, n = ndim) + 4. ├─base::do.call(irlba, args = args) + 5. └─irlba (local) ``(A = ``, nv = 2, center = ``) + + [ FAIL 12 | WARN 30 | SKIP 3 | PASS 498 ] + Error: Test failures + Execution halted + ``` + +# egor + +
+ +* Version: 1.24.2 +* GitHub: https://github.com/tilltnet/egor +* Source code: https://github.com/cran/egor +* Date/Publication: 2024-02-02 05:30:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "egor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘egor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ego_constraint + > ### Title: Calculate Burt constraint for the egos of ego-centered networks + > ### Aliases: ego_constraint + > + > ### ** Examples + > + > data(egor32) + > ego_constraint(egor32) + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Error in `purrr::map_dbl()`: + ℹ In index: 1. + ℹ With name: 1. + Caused by error in `simple_vs_index()`: + ! Unknown vertex selected + Backtrace: + ▆ + 1. ├─egor::ego_constraint(egor32) + 2. │ └─purrr::map_dbl(...) + 3. │ └─purrr:::map_("double", .x, .f, ..., .progress = .progress) + 4. │ ├─purrr:::with_indexed_errors(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ ├─purrr:::call_with_cleanup(...) + 7. │ └─egor (local) .f(.x[[i]], ...) + 8. │ ├─igraph::constraint(...) + 9. │ │ └─igraph:::as_igraph_vs(graph, nodes) + 10. │ ├─igraph::V(.)[igraph::V(.)$name == "ego"] + 11. │ └─igraph:::`[.igraph.vs`(igraph::V(.), igraph::V(.)$name == "ego") + 12. │ └─base::lapply(...) + 13. │ └─igraph (local) FUN(X[[i]], ...) + 14. │ └─igraph:::simple_vs_index(x, ii, na_ok) + 15. │ └─base::stop("Unknown vertex selected") + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(egor) + Loading required package: dplyr + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + + matches + + The following objects are masked from 'package:stats': + + filter, lag + + The following objects are masked from 'package:base': + + intersect, setdiff, setequal, union + + Loading required package: tibble + > library(dplyr) + > + > test_check("egor") + 5 Egos/ Ego Networks + 90 Alters + Min. Netsize 10 + Average Netsize 18 + Max. Netsize 26 + Average Density 0.520252057805534 + + Ego sampling design: + Independent Sampling design (with replacement) + Called via srvyr + Sampling variables: + - ids: `1` + - weights: sampling_weight + Data variables: .egoID (dbl), sex (chr), age (fct), age.years (int), country + (chr), income (dbl), sampling_weight (dbl), avg_nts (dbl) + Alter survey design: + Maximum nominations: Inf + 5 Egos/ Ego Networks + 90 Alters + Min. Netsize 10 + Average Netsize 18 + Max. Netsize 26 + Average Density 0.520252057805534 + + Ego sampling design: + Independent Sampling design (with replacement) + Called via srvyr + Sampling variables: + - ids: `1` + - weights: sampling_weight + Data variables: .egoID (dbl), sex (chr), age (fct), age.years (int), country + (chr), income (dbl), sampling_weight (dbl), avg_nts (dbl) + Alter survey design: + Maximum nominations: Inf + 3 Egos/ Ego Networks + 44 Alters + Min. Netsize 7 + Average Netsize 14.6666666666667 + Max. Netsize 19 + Average Density 0.505643192949695 + Alter survey design: + Maximum nominations: Inf + 32 Egos/ Ego Networks + 384 Alters + Min. Netsize 12 + Average Netsize 12 + Max. Netsize 12 + Average Density 0.5 + + Ego sampling design: + Independent Sampling design (with replacement) + Called via srvyr + Data variables: .egoID (dbl), sex (fct), age (fct), age.years (int), country + (chr), income (dbl), avg_nts (dbl) + Alter survey design: + Maximum nominations: Inf + 5 Egos/ Ego Networks + 16 Alters + Min. Netsize 4 + Average Netsize 4 + Max. Netsize 4 + Average Density 1.33333333333333 + Alter survey design: + Maximum nominations: Inf + 4 Egos/ Ego Networks + 16 Alters + Min. Netsize 4 + Average Netsize 4 + Max. Netsize 4 + Average Density 1.33333333333333 + Alter survey design: + Maximum nominations: Inf + Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Filtering out empty alter entries using provided network size values: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: [ FAIL 21 | WARN 330 | SKIP 15 | PASS 188 ] + + ══ Skipped tests (15) ══════════════════════════════════════════════════════════ + • On CRAN (15): 'test-ei.R:3:11', 'test-ei.R:72:13', 'test-ei.R:85:13', + 'test-ei.R:95:13', 'test-ei.R:125:13', 'test-ei.R:141:3', 'test-ei.R:150:3', + 'test-ei.R:164:3', 'test-onefile_to_egor.R:5:3', + 'test-onefile_to_egor.R:35:3', 'test-onefile_to_egor.R:67:3', + 'test-twofiles_to_egor.R:2:3', 'test-twofiles_to_egor.R:34:3', + 'test-twofiles_to_egor.R:65:3', 'test-twofiles_to_egor.R:94:13' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-as_egor.R:23:3'): as.egor.list() works for igraph objects. ─── + `as.egor(x = ig_l2, ego_name = "ego")` threw an error. + Message: ℹ In index: 1. + ℹ With name: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Class: purrr_error_indexed/rlang_error/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-as_egor.R:23:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─egor::as.egor(x = ig_l2, ego_name = "ego") + 7. ├─egor:::as.egor.list(x = ig_l2, ego_name = "ego") + 8. │ └─egor:::as_egor_igraph(x, ego_name) + 9. │ └─purrr::map_dfr(x, igraph::as_data_frame, what = "vertices", .id = "ego_id") + 10. │ └─purrr::map(.x, .f, ...) + 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 12. │ ├─purrr:::with_indexed_errors(...) + 13. │ │ └─base::withCallingHandlers(...) + 14. │ ├─purrr:::call_with_cleanup(...) + 15. │ └─igraph (local) .f(.x[[i]], ...) + 16. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 17. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 18. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 19. │ └─base::`.rowNamesDF<-`(x, value = value) + 20. │ └─base::stop("duplicate 'row.names' are not allowed") + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + ── Failure ('test-as_egor.R:24:3'): as.egor.list() works for igraph objects. ─── + `as.egor(x = ig_l2, ego_name = rep("ego", 32))` threw an error. + Message: ℹ In index: 1. + ℹ With name: 1. + Caused by error in `.rowNamesDF<-`: + ! duplicate 'row.names' are not allowed + Class: purrr_error_indexed/rlang_error/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-as_egor.R:24:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─egor::as.egor(x = ig_l2, ego_name = rep("ego", 32)) + 7. ├─egor:::as.egor.list(x = ig_l2, ego_name = rep("ego", 32)) + 8. │ └─egor:::as_egor_igraph(x, ego_name) + 9. │ └─purrr::map_dfr(x, igraph::as_data_frame, what = "vertices", .id = "ego_id") + 10. │ └─purrr::map(.x, .f, ...) + 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) + 12. │ ├─purrr:::with_indexed_errors(...) + 13. │ │ └─base::withCallingHandlers(...) + 14. │ ├─purrr:::call_with_cleanup(...) + 15. │ └─igraph (local) .f(.x[[i]], ...) + 16. │ └─base::`rownames<-`(`*tmp*`, value = rn) + 17. │ ├─base::`row.names<-`(`*tmp*`, value = value) + 18. │ └─base::`row.names<-.data.frame`(`*tmp*`, value = value) + 19. │ └─base::`.rowNamesDF<-`(x, value = value) + 20. │ └─base::stop("duplicate 'row.names' are not allowed") + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + ── Failure ('test-clustered_graphs.R:36:5'): Methods work (properly) with NAs in grouping variable. ── + `clustered_graphs(mpf, "country")` threw an error. + Message: Length of new attribute value must be 1 or 21, the number of target vertices, not 18 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(clustered_graphs(mpf, "country"), NA) at test-clustered_graphs.R:36:5 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─egor::clustered_graphs(mpf, "country") + 7. └─egor:::clustered_graphs.egor(mpf, "country") + 8. ├─egor::clustered_graphs(...) + 9. └─egor:::clustered_graphs.list(...) + 10. └─base::mapply(...) + 11. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 12. └─igraph::graph.data.frame(d = x, vertices = y, directed = FALSE) + 13. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 14. └─igraph::add_vertices(g, length(names), attr = vattrs) + 15. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 16. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-clustered_graphs.R:39:5'): Methods work (properly) with NAs in grouping variable. ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 21, the number of target vertices, not 18 + Backtrace: + ▆ + 1. ├─igraph::V(clustered_graphs(mpf, "country")[[1]]) at test-clustered_graphs.R:39:5 + 2. │ └─igraph:::ensure_igraph(graph) + 3. ├─egor::clustered_graphs(mpf, "country") + 4. └─egor:::clustered_graphs.egor(mpf, "country") + 5. ├─egor::clustered_graphs(...) + 6. └─egor:::clustered_graphs.list(...) + 7. └─base::mapply(...) + 8. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 9. └─igraph::graph.data.frame(d = x, vertices = y, directed = FALSE) + 10. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 11. └─igraph::add_vertices(g, length(names), attr = vattrs) + 12. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 13. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-conversions.R:44:13'): as_igraph.nested_egor works ─────────── + `{ ... }` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-conversions.R:44:13 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─egor::as_igraph(en, include.ego = T, ego.attrs = c("sex", "age")) at test-conversions.R:49:15 + 7. └─egor:::as_igraph.nested_egor(...) + 8. └─base::mapply(...) + 9. └─egor (local) ``(dots[[1L]][[3L]], dots[[2L]][[3L]]) + 10. └─igraph::graph.data.frame(...) + 11. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 12. └─igraph::add_vertices(g, length(names), attr = vattrs) + 13. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 14. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-ego_constraint.R:4:3'): ego_constraint works without weight ── + `ego_constraint(object = e1)` threw an error. + Message: Length of new attribute value must be 1 or 8, the number of target vertices, not 9 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(ego_constraint(object = e1), NA) at test-ego_constraint.R:4:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::ego_constraint(object = e1) + 7. ├─egor::as_igraph(object, include.ego = TRUE, ego.alter.weights = ego.alter.weights) + 8. └─egor:::as_igraph.egor(object, include.ego = TRUE, ego.alter.weights = ego.alter.weights) + 9. ├─egor::as_igraph(...) + 10. └─egor:::as_igraph.nested_egor(...) + 11. └─base::mapply(...) + 12. └─egor (local) ``(dots[[1L]][[12L]], dots[[2L]][[12L]]) + 13. └─igraph::graph.data.frame(...) + 14. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 15. └─igraph::add_vertices(g, length(names), attr = vattrs) + 16. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 17. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-ego_constraint.R:14:3'): ego_constraint works with weight ──── + `ego_constraint(object = e1, weight = "weight")` threw an error. + Message: ℹ In index: 1. + ℹ With name: 1. + Caused by error in `simple_vs_index()`: + ! Unknown vertex selected + Class: purrr_error_indexed/rlang_error/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-ego_constraint.R:14:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─egor::ego_constraint(object = e1, weight = "weight") + 7. │ └─purrr::map_dbl(...) + 8. │ └─purrr:::map_("double", .x, .f, ..., .progress = .progress) + 9. │ ├─purrr:::with_indexed_errors(...) + 10. │ │ └─base::withCallingHandlers(...) + 11. │ ├─purrr:::call_with_cleanup(...) + 12. │ └─egor (local) .f(.x[[i]], ...) + 13. │ ├─igraph::constraint(...) + 14. │ │ └─igraph:::as_igraph_vs(graph, nodes) + 15. │ ├─igraph::V(.)[igraph::V(.)$name == "ego"] + 16. │ └─igraph:::`[.igraph.vs`(igraph::V(.), igraph::V(.)$name == "ego") + 17. │ └─base::lapply(...) + 18. │ └─igraph (local) FUN(X[[i]], ...) + 19. │ └─igraph:::simple_vs_index(x, ii, na_ok) + 20. │ └─base::stop("Unknown vertex selected") + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + ── Error ('test-ego_constraint.R:24:3'): ego_constraint() returns tbl_svy object, when ego_design present ── + + Error in `purrr::map_dbl(graphs, ~igraph::constraint(., weights = if (is.null(weights)) rep(1, + length(igraph::E(.))) else igraph::get.edge.attribute(., + weights), nodes = igraph::V(.)[igraph::V(.)$name == "ego"]))`: ℹ In index: 1. + ℹ With name: 1. + Caused by error in `simple_vs_index()`: + ! Unknown vertex selected + Backtrace: + ▆ + 1. ├─egor::ego_constraint(object = x) at test-ego_constraint.R:24:3 + 2. │ └─purrr::map_dbl(...) + 3. │ └─purrr:::map_("double", .x, .f, ..., .progress = .progress) + 4. │ ├─purrr:::with_indexed_errors(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ ├─purrr:::call_with_cleanup(...) + 7. │ └─egor (local) .f(.x[[i]], ...) + 8. │ ├─igraph::constraint(...) + 9. │ │ └─igraph:::as_igraph_vs(graph, nodes) + 10. │ ├─igraph::V(.)[igraph::V(.)$name == "ego"] + 11. │ └─igraph:::`[.igraph.vs`(igraph::V(.), igraph::V(.)$name == "ego") + 12. │ └─base::lapply(...) + 13. │ └─igraph (local) FUN(X[[i]], ...) + 14. │ └─igraph:::simple_vs_index(x, ii, na_ok) + 15. │ └─base::stop("Unknown vertex selected") + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + ── Failure ('test-plot_egor.R:9:3'): plot plots egor objects ─────────────────── + `{ ... }` threw an error. + Message: Length of new attribute value must be 1 or 3, the number of target vertices, not 4 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:9:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─base::plot(...) at test-plot_egor.R:12:5 + 7. └─egor:::plot.egor(...) + 8. └─egor::plot_egor(x, ...) + 9. └─egor::plot_ego_graphs(...) + 10. └─egor:::plot_one_ego_graph(...) + 11. ├─egor::as_igraph(...) + 12. └─egor:::as_igraph.egor(...) + 13. ├─egor::as_igraph(...) + 14. └─egor:::as_igraph.nested_egor(...) + 15. └─base::mapply(...) + 16. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 17. └─igraph::graph.data.frame(...) + 18. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 19. └─igraph::add_vertices(g, length(names), attr = vattrs) + 20. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 21. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-plot_egor.R:110:3'): plot_ego_graphs works with minmal arguments ── + `{ ... }` threw an error. + Message: Length of new attribute value must be 1 or 4, the number of target vertices, not 5 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:110:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_ego_graphs(e) at test-plot_egor.R:112:5 + 7. └─egor:::plot_one_ego_graph(...) + 8. ├─egor::as_igraph(...) + 9. └─egor:::as_igraph.egor(...) + 10. ├─egor::as_igraph(...) + 11. └─egor:::as_igraph.nested_egor(...) + 12. └─base::mapply(...) + 13. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 14. └─igraph::graph.data.frame(...) + 15. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 16. └─igraph::add_vertices(g, length(names), attr = vattrs) + 17. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 18. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-plot_egor.R:117:3'): plot_ego_graphs works with vertex_color_var ── + `{ ... }` threw an error. + Message: zero-length 'labels' specified + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:117:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_ego_graphs(e, vertex_color_var = "sex") at test-plot_egor.R:119:5 + 7. └─egor:::plot_one_ego_graph(...) + 8. └─igraph::plot.igraph(...) + 9. ├─graphics::text(...) + 10. └─graphics::text.default(...) + ── Failure ('test-plot_egor.R:131:3'): plot_egograms doesn't fail on empty alters or aaties ── + `plot_egograms(x = e, venn_var = "sex", pie_var = "country", show_venn_labels = TRUE)` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:131:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_egograms(...) + 7. └─egor:::plot_egogram(...) + 8. ├─egor::as_igraph(ego_object, include.ego = include_ego) + 9. └─egor:::as_igraph.egor(ego_object, include.ego = include_ego) + 10. ├─egor::as_igraph(...) + 11. └─egor:::as_igraph.nested_egor(...) + 12. └─base::mapply(...) + 13. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 14. └─igraph::graph.data.frame(...) + 15. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 16. └─igraph::add_vertices(g, length(names), attr = vattrs) + 17. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 18. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-plot_egor.R:152:3'): plot_egograms plots with and without venn labels ── + `{ ... }` threw an error. + Message: arguments imply differing number of rows: 2, 3 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:152:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_egograms(...) at test-plot_egor.R:154:5 + 7. └─egor:::plot_egogram(...) + 8. ├─egor::as_igraph(ego_object, include.ego = include_ego) + 9. └─egor:::as_igraph.egor(ego_object, include.ego = include_ego) + 10. ├─egor::as_igraph(...) + 11. └─egor:::as_igraph.nested_egor(...) + 12. └─base::mapply(...) + 13. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 14. └─igraph::graph.data.frame(...) + 15. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 16. └─base::cbind(data.frame(name = names), vertices) + 17. └─base::cbind(deparse.level, ...) + 18. └─base::data.frame(..., check.names = FALSE) + ── Failure ('test-plot_egor.R:171:13'): plotting works when active data level is not ego ── + `{ ... }` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:171:13 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_egograms(...) at test-plot_egor.R:175:15 + 7. └─egor:::plot_egogram(...) + 8. ├─egor::as_igraph(ego_object, include.ego = include_ego) + 9. └─egor:::as_igraph.egor(ego_object, include.ego = include_ego) + 10. ├─egor::as_igraph(...) + 11. └─egor:::as_igraph.nested_egor(...) + 12. └─base::mapply(...) + 13. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 14. └─igraph::graph.data.frame(...) + 15. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 16. └─igraph::add_vertices(g, length(names), attr = vattrs) + 17. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 18. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-plot_egor.R:206:3'): plot_ego_graphs is fast ───────────────── + `{ ... }` threw an error. + Message: zero-length 'labels' specified + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:206:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_ego_graphs(make_egor(12, 16)) at test-plot_egor.R:207:5 + 7. └─egor:::plot_one_ego_graph(...) + 8. └─igraph::plot.igraph(...) + 9. ├─graphics::text(...) + 10. └─graphics::text.default(...) + ── Failure ('test-plot_egor.R:214:3'): plot_ego_gram adjusts node size according to venn count ── + `{ ... }` threw an error. + Message: arguments imply differing number of rows: 4, 5 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:214:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_egograms(x = e, ego_no = 2, venn_var = "sex", pie_var = "country") at test-plot_egor.R:217:5 + 7. └─egor:::plot_egogram(...) + 8. ├─egor::as_igraph(ego_object, include.ego = include_ego) + 9. └─egor:::as_igraph.egor(ego_object, include.ego = include_ego) + 10. ├─egor::as_igraph(...) + 11. └─egor:::as_igraph.nested_egor(...) + 12. └─base::mapply(...) + 13. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 14. └─igraph::graph.data.frame(...) + 15. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 16. └─base::cbind(data.frame(name = names), vertices) + 17. └─base::cbind(deparse.level, ...) + 18. └─base::data.frame(..., check.names = FALSE) + ── Failure ('test-plot_egor.R:248:3'): plot_ego_gram works with edge arguments ── + `{ ... }` threw an error. + Message: zero-length 'labels' specified + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-plot_egor.R:248:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─egor::plot_ego_graphs(...) at test-plot_egor.R:261:5 + 7. └─egor:::plot_one_ego_graph(...) + 8. └─igraph::plot.igraph(...) + 9. ├─graphics::text(...) + 10. └─graphics::text.default(...) + ── Error ('test-plot_egor.R:460:3'): egograms with reverse ordered alters plot correctly ── + Error in `data.frame(..., check.names = FALSE)`: arguments imply differing number of rows: 0, 3 + Backtrace: + ▆ + 1. └─egor::plot_egograms(...) at test-plot_egor.R:460:3 + 2. └─egor:::plot_egogram(...) + 3. ├─egor::as_igraph(ego_object, include.ego = include_ego) + 4. └─egor:::as_igraph.egor(ego_object, include.ego = include_ego) + 5. ├─egor::as_igraph(...) + 6. └─egor:::as_igraph.nested_egor(...) + 7. └─base::mapply(...) + 8. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 9. └─igraph::graph.data.frame(...) + 10. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 11. └─base::cbind(data.frame(name = names), vertices) + 12. └─base::cbind(deparse.level, ...) + 13. └─base::data.frame(..., check.names = FALSE) + ── Failure ('test-rotate.R:13:3'): rotate_xy() works with a 2x2 matrix ───────── + ``%>%`(...)` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-rotate.R:13:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─... %>% rotate_xy(1) + 7. ├─egor:::rotate_xy(., 1) + 8. ├─igraph::layout_in_circle(.) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─egor::as_igraph(.) + 11. └─egor:::as_igraph.egor(.) + 12. ├─egor::as_igraph(...) + 13. └─egor:::as_igraph.nested_egor(...) + 14. └─base::mapply(...) + 15. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 16. └─igraph::graph.data.frame(...) + 17. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 18. └─igraph::add_vertices(g, length(names), attr = vattrs) + 19. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 20. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-rotate.R:35:3'): rotate_to_equilibrium() works with a 2x2 matrix ── + ``%>%`(...)` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-rotate.R:35:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─... %>% rotate_to_equilibrium() + 7. ├─egor:::rotate_to_equilibrium(.) + 8. ├─igraph::layout_in_circle(.) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─egor::as_igraph(.) + 11. └─egor:::as_igraph.egor(.) + 12. ├─egor::as_igraph(...) + 13. └─egor:::as_igraph.nested_egor(...) + 14. └─base::mapply(...) + 15. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 16. └─igraph::graph.data.frame(...) + 17. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 18. └─igraph::add_vertices(g, length(names), attr = vattrs) + 19. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 20. └─igraph:::i_set_vertex_attr(...) + ── Failure ('test-rotate.R:44:3'): rotate_to_equilibrium() works with a 2x2 matrix ── + ``%>%`(...)` threw an error. + Message: Length of new attribute value must be 1 or 0, the number of target vertices, not 2 + Class: simpleError/error/condition + Backtrace: + ▆ + 1. ├─testthat::expect_error(...) at test-rotate.R:44:3 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─... %>% rotate_to_equilibrium() + 7. ├─egor:::rotate_to_equilibrium(.) + 8. ├─igraph::layout_as_star(.) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─egor::as_igraph(.) + 11. └─egor:::as_igraph.egor(.) + 12. ├─egor::as_igraph(...) + 13. └─egor:::as_igraph.nested_egor(...) + 14. └─base::mapply(...) + 15. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 16. └─igraph::graph.data.frame(...) + 17. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + 18. └─igraph::add_vertices(g, length(names), attr = vattrs) + 19. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 20. └─igraph:::i_set_vertex_attr(...) + + [ FAIL 21 | WARN 330 | SKIP 15 | PASS 188 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘egor_allbus.Rmd’ + ... + + > e_kontakte <- e_kontakte %>% activate(aatie) %>% filter(weight != + + 3) %>% activate(ego) + + > plot(e_freunde, ego_no = 4, x_dim = 2, y_dim = 1) + Warning: Unknown or uninitialised column: `name`. + + When sourcing ‘egor_allbus.R’: + Error: arguments imply differing number of rows: 2, 3 + Execution halted + when running code in ‘using_egor.Rmd’ + ... + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + Warning: Unknown or uninitialised column: `name`. + + When sourcing ‘using_egor.R’: + Error: arguments imply differing number of rows: 5, 7 + Execution halted + + ‘egor_allbus.Rmd’ using ‘UTF-8’... failed + ‘qualtrics.Rmd’ using ‘UTF-8’... OK + ‘using_egor.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘egor_allbus.Rmd’ using rmarkdown + + Quitting from lines at lines 179-181 [unnamed-chunk-11] (egor_allbus.Rmd) + Error: processing vignette 'egor_allbus.Rmd' failed with diagnostics: + arguments imply differing number of rows: 2, 3 + --- failed re-building ‘egor_allbus.Rmd’ + + --- re-building ‘qualtrics.Rmd’ using rmarkdown + --- finished re-building ‘qualtrics.Rmd’ + + --- re-building ‘using_egor.Rmd’ using rmarkdown + + Quitting from lines at lines 222-241 [unnamed-chunk-16] (using_egor.Rmd) + Error: processing vignette 'using_egor.Rmd' failed with diagnostics: + arguments imply differing number of rows: 5, 7 + --- failed re-building ‘using_egor.Rmd’ + + SUMMARY: processing the following files failed: + ‘egor_allbus.Rmd’ ‘using_egor.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# epicontacts + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/reconhub/epicontacts +* Source code: https://github.com/cran/epicontacts +* Date/Publication: 2023-03-28 13:10:12 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "epicontacts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epicontacts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.igraph.epicontacts + > ### Title: Create igraph object from contact data + > ### Aliases: as.igraph.epicontacts + > + > ### ** Examples + > + > + > if (require(outbreaks) && require(igraph)) { + + ## build data + + + + x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts, + + id = "case_id", to = "case_id", from ="infector", + + directed = TRUE) + + + + + + ## subset data - keep 50 cases from linelist with contacts + + + + ids <- get_id(x, "common")[1:50] + + ids + + x <- x[ids, ids] + + + + + + ## make igraph object with associated attributes from epicontacts object + + + + net <- as.igraph(x) + + net + + plot(net, vertex.label = "", vertex.size = 10, + + vertex.color = cases_pal(50)) + + } + Loading required package: outbreaks + Loading required package: igraph + + Attaching package: ‘igraph’ + + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 35, 50 + Calls: as.igraph ... as.igraph.epicontacts -> -> cbind -> cbind -> data.frame + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘epicontacts.Rmd’ + ... + # ℹ 23 more rows + + + > nodes <- c("SK_14", "SK_145") + + > subset(merskor15, cluster_id = nodes) + + When sourcing ‘epicontacts.R’: + Error: arguments imply differing number of rows: 97, 162 + Execution halted + + ‘epicontacts.Rmd’ using ‘UTF-8’... failed + ‘epicontacts_class.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘epicontacts.Rmd’ using rmarkdown + + Quitting from lines at lines 128-130 [unnamed-chunk-9] (epicontacts.Rmd) + Error: processing vignette 'epicontacts.Rmd' failed with diagnostics: + arguments imply differing number of rows: 97, 162 + --- failed re-building ‘epicontacts.Rmd’ + + --- re-building ‘epicontacts_class.Rmd’ using rmarkdown + --- finished re-building ‘epicontacts_class.Rmd’ + + SUMMARY: processing the following file failed: + ‘epicontacts.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘colorspace’ + All declared Imports should be used. + ``` + +# erah + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/xdomingoal/erah-devel +* Source code: https://github.com/cran/erah +* Date/Publication: 2023-12-20 10:10:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "erah")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(erah) + + + _____ _ + | __ \ | | eRah R package: + ___| |__) | __ _| |__ ---------------- + / _ \ _ // _` | _ \ Untargeted GC-MS metabolomics profiling + | __/ | \ \ (_| | | | | + \___|_| \_\__,_|_| |_| Version 2.0.1 + + - Type 'citation('erah')' for citing this R package in publications. + - Type 'vignette('eRahManual', package='erah')' for a tutorial on eRah's usage. + - For bugs, problems and issues, please do not hesitate in contacting xavier.domingoa@eurecat.org or opening an issue on the Github repository (https://github.com/xdomingoal/erah-devel/issues). + > + > test_check("erah") + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 10 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-erah.R:39:3'): erah works ────────────────────────────────────── + Error in `min.list[[j]] <- list(dist = group.distance, elements = w.minn)`: attempt to select less than one element in integerOneIndex + Backtrace: + ▆ + 1. ├─erah::alignComp(deconvolvedEx, alParameters = ex.al.par) at test-erah.R:39:3 + 2. └─erah::alignComp(deconvolvedEx, alParameters = ex.al.par) + 3. └─erah:::align.factors(...) + 4. └─base::lapply(...) + 5. └─erah (local) FUN(X[[i]], ...) + 6. └─erah:::comp.clusters(inter.distance.matrix, class.vector[clust]) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# fastRG + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/RoheLab/fastRG +* Source code: https://github.com/cran/fastRG +* Date/Publication: 2023-08-21 21:40:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "fastRG")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(fastRG) + Loading required package: Matrix + + Attaching package: 'fastRG' + + The following object is masked from 'package:testthat': + + expectation + + > + > test_check("fastRG") + + Attaching package: 'igraph' + + The following object is masked from 'package:fastRG': + + sbm + + The following object is masked from 'package:testthat': + + compare + + The following objects are masked from 'package:stats': + + decompose, spectrum + + The following object is masked from 'package:base': + + union + + + Attaching package: 'magrittr' + + The following objects are masked from 'package:testthat': + + equals, is_less_than, not + + + Attaching package: 'tidygraph' + + The following object is masked from 'package:igraph': + + groups + + The following object is masked from 'package:testthat': + + matches + + The following object is masked from 'package:stats': + + filter + + + Attaching package: 'dplyr' + + The following objects are masked from 'package:igraph': + + as_data_frame, groups, union + + The following object is masked from 'package:testthat': + + matches + + The following objects are masked from 'package:stats': + + filter, lag + + The following objects are masked from 'package:base': + + intersect, setdiff, setequal, union + + [ FAIL 1 | WARN 26 | SKIP 0 | PASS 96 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-retain-isolated-nodes.R:36:3'): sampling from undirected factor models doesn't drop isolated nodes ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 9999, the number of target vertices, not 10000 + Backtrace: + ▆ + 1. ├─fastRG::sample_igraph(latent) at test-retain-isolated-nodes.R:36:3 + 2. └─fastRG:::sample_igraph.undirected_factor_model(latent) + 3. └─igraph::graph_from_data_frame(edgelist, directed = FALSE, vertices = nodes) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + + [ FAIL 1 | WARN 26 | SKIP 0 | PASS 96 ] + Error: Test failures + Execution halted + ``` + +# fbnet + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/MarsicoFL/fbnet +* Source code: https://github.com/cran/fbnet +* Date/Publication: 2023-07-01 18:20:02 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "fbnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fbnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: buildCPTs + > ### Title: buildCPTs: a function for building conditional probability + > ### tables based on pedigree bayesian network. + > ### Aliases: buildCPTs + > + > ### ** Examples + > + > pbn <- initBN(toyped) + > bnet <- buildBN(pbn,QP=3) + > bn1 <- buildCPTs(bnet) + Error in lSelectorCPTs[[aux]] : no such index at level 1 + Calls: buildCPTs + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘assertthat’ ‘utils’ + All declared Imports should be used. + ``` + +# GGally + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/ggobi/ggally +* Source code: https://github.com/cran/GGally +* Date/Publication: 2024-02-14 00:53:32 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "GGally")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (requireNamespace("testthat", quietly = TRUE)) { + + library(testthat) + + library(GGally) + + + + test_check("GGally") + + } + Loading required package: ggplot2 + Registered S3 method overwritten by 'GGally': + method from + +.gg ggplot2 + [ FAIL 3 | WARN 1 | SKIP 26 | PASS 474 ] + + ══ Skipped tests (26) ══════════════════════════════════════════════════════════ + • On CRAN (26): 'test-gg-plots.R:2:1', 'test-ggally_colbar.R:9:3', + 'test-ggally_colbar.R:71:3', 'test-ggally_cross.R:7:3', + 'test-ggally_trends.R:5:3', 'test-ggbivariate.R:6:3', 'test-ggcoef.R:7:3', + 'test-ggcorr.R:7:3', 'test-ggcorr.R:67:3', 'test-ggcorr.R:88:3', + 'test-ggcorr.R:95:3', 'test-ggfacet.R:20:3', 'test-gglegend.R:19:5', + 'test-gglegend.R:31:3', 'test-gglegend.R:84:3', 'test-ggmatrix.R:28:3', + 'test-ggmatrix.R:90:3', 'test-ggmatrix.R:119:3', 'test-ggmatrix.R:145:3', + 'test-ggnostic.R:61:3', 'test-ggscatmat.R:10:3', 'test-ggscatmat.R:19:3', + 'test-ggsurv.R:112:3', 'test-ggtable.R:6:3', 'test-vig_ggally.R:2:3', + 'test-zzz_ggpairs.R:2:1' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-ggnet.R:235:5'): examples ────────────────────────────────────── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─GGally::ggnet(asIgraph(n)) at test-ggnet.R:235:5 + 2. ├─intergraph::asIgraph(n) + 3. └─intergraph:::asIgraph.network(n) + 4. ├─intergraph::asIgraph(...) + 5. └─intergraph:::asIgraph.data.frame(...) + 6. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-ggnet2.R:266:5'): examples ───────────────────────────────────── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─GGally::ggnet2(asIgraph(n), color = "group") at test-ggnet2.R:266:5 + 2. ├─intergraph::asIgraph(n) + 3. └─intergraph:::asIgraph.network(n) + 4. ├─intergraph::asIgraph(...) + 5. └─intergraph:::asIgraph.data.frame(...) + 6. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-ggnetworkmap.R:224:5'): igraph conversion ────────────────────── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(flights) at test-ggnetworkmap.R:224:5 + 2. └─intergraph:::asIgraph.network(flights) + 3. ├─intergraph::asIgraph(...) + 4. └─intergraph:::asIgraph.data.frame(...) + 5. └─igraph::delete_vertex_attr(rval, "name") + + [ FAIL 3 | WARN 1 | SKIP 26 | PASS 474 ] + Error: Test failures + Execution halted + ``` + +# ggraph + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/thomasp85/ggraph +* Source code: https://github.com/cran/ggraph +* Date/Publication: 2024-03-07 12:40:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_edges + > ### Title: Create small multiples based on edge attributes + > ### Aliases: facet_edges + > + > ### ** Examples + > + > gr <- tidygraph::as_tbl_graph(highschool) + Error in igraph::delete_vertex_attr(gr, "name") : + No such vertex attribute: name + Calls: ... as_tbl_graph.data.frame -> as_graph_edge_df -> + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Edges.Rmd’ using rmarkdown + + Quitting from lines at lines 40-75 [unnamed-chunk-2] (Edges.Rmd) + Error: processing vignette 'Edges.Rmd' failed with diagnostics: + No such vertex attribute: name + --- failed re-building ‘Edges.Rmd’ + + --- re-building ‘Layouts.Rmd’ using rmarkdown + + Quitting from lines at lines 35-45 [unnamed-chunk-2] (Layouts.Rmd) + Error: processing vignette 'Layouts.Rmd' failed with diagnostics: + No such vertex attribute: name + --- failed re-building ‘Layouts.Rmd’ + + --- re-building ‘Nodes.Rmd’ using rmarkdown + + Quitting from lines at lines 27-35 [unnamed-chunk-2] (Nodes.Rmd) + Error: processing vignette 'Nodes.Rmd' failed with diagnostics: + No such vertex attribute: name + --- failed re-building ‘Nodes.Rmd’ + + --- re-building ‘tidygraph.Rmd’ using rmarkdown + + Quitting from lines at lines 67-77 [unnamed-chunk-2] (tidygraph.Rmd) + Error: processing vignette 'tidygraph.Rmd' failed with diagnostics: + No such vertex attribute: name + --- failed re-building ‘tidygraph.Rmd’ + + SUMMARY: processing the following files failed: + ‘Edges.Rmd’ ‘Layouts.Rmd’ ‘Nodes.Rmd’ ‘tidygraph.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Edges.Rmd’ + ... + + path, ...) { .... [TRUNCATED] + + > hairball <- mutate(activate(mutate(as_tbl_graph(highschool), + + year_pop = map_local(mode = "in", .f = function(neighborhood, + + ...) { + .... [TRUNCATED] + + When sourcing ‘Edges.R’: + Error: No such vertex attribute: name + Execution halted + when running code in ‘Layouts.Rmd’ + ... + filter + + + > set_graph_style(plot_margin = margin(1, 1, 1, 1)) + + > graph <- as_tbl_graph(highschool) + + When sourcing ‘Layouts.R’: + Error: No such vertex attribute: name + Execution halted + when running code in ‘Nodes.Rmd’ + ... + filter + + + > set_graph_style(plot_margin = margin(1, 1, 1, 1)) + + > gr <- as_tbl_graph(highschool) + + When sourcing ‘Nodes.R’: + Error: No such vertex attribute: name + Execution halted + when running code in ‘tidygraph.Rmd’ + ... + + filter + + + > graph <- as_tbl_graph(data.frame(from = sample(5, + + 20, TRUE), to = sample(5, 20, TRUE), weight = runif(20))) + + When sourcing ‘tidygraph.R’: + Error: No such vertex attribute: name + Execution halted + + ‘Edges.Rmd’ using ‘UTF-8’... failed + ‘Layouts.Rmd’ using ‘UTF-8’... failed + ‘Nodes.Rmd’ using ‘UTF-8’... failed + ‘tidygraph.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 9.9Mb + sub-directories of 1Mb or more: + doc 3.9Mb + libs 4.4Mb + ``` + +# grainscape + +
+ +* Version: 0.4.4 +* GitHub: https://github.com/achubaty/grainscape +* Source code: https://github.com/cran/grainscape +* Date/Publication: 2023-04-20 08:40:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "grainscape")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘grainscape-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GOC + > ### Title: Produce a grains of connectivity model at multiple scales + > ### (patch-based or lattice GOC) + > ### Aliases: GOC GOC,mpg-method + > + > ### ** Examples + > + > ## Load raster landscape + > tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape")) + > + > ## Create a resistance surface from a raster using an is-becomes reclassification + > tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12))) + > ## Produce a patch-based MPG where patches are resistance features=1 + > tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Calls: MPG ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > test_check("grainscape") + Loading required package: grainscape + [ FAIL 18 | WARN 0 | SKIP 1 | PASS 0 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + • empty test (1): 'test-examples.R:1:1' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-MPG.R:17:3'): MPG handles NA values correctly (#28) ──────────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 6, the number of target vertices, not 2 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = c, patch = p) at test-MPG.R:17:3 + 2. └─grainscape::MPG(cost = c, patch = p) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-MPG.R:70:3'): MPG contains links to all patches (#32) ────────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = (tinyCost == 1)) at test-MPG.R:70:3 + 2. └─grainscape::MPG(cost = tinyCost, patch = (tinyCost == 1)) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-corridor-distance-point.R:22:3'): corridor handles NA values ─── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 627, the number of target vertices, not 589 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost, cost == 1) at test-corridor-distance-point.R:22:3 + 2. └─grainscape::MPG(cost, cost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-corridor-distance-point.R:42:3'): distance handles NA values ─── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 637, the number of target vertices, not 597 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost, cost == 1) at test-corridor-distance-point.R:42:3 + 2. └─grainscape::MPG(cost, cost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-corridor-distance-point.R:63:3'): point handles NA values ────── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 635, the number of target vertices, not 585 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost, cost == 1) at test-corridor-distance-point.R:63:3 + 2. └─grainscape::MPG(cost, cost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/GOC.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/MPG.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/corridor.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/distance.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/export.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/ggGS.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/grain.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/graphdf.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/patchFilter.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 252, the number of target vertices, not 162 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = filteredPatch) + 2. └─grainscape::MPG(cost = tinyCost, patch = filteredPatch) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/plot.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/point.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/theme_grainscape.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-examples.R:2:3'): /tmp/workdir/grainscape/new/grainscape.Rcheck/00_pkg_src/grainscape/man/threshold.Rd ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 107, the number of target vertices, not 43 + Backtrace: + ▆ + 1. ├─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 2. └─grainscape::MPG(cost = tinyCost, patch = tinyCost == 1) + 3. └─igraph::graph_from_data_frame(toGraphE, directed = FALSE, vertices = toGraphV) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + + [ FAIL 18 | WARN 0 | SKIP 1 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘grainscape_vignette.Rmd’ + ... + > ggplot() + geom_raster(data = patchyCost_df, aes(x = x, + + y = y, fill = value)) + scale_fill_brewer(type = "div", palette = "Paired", + + gu .... [TRUNCATED] + + > patchyMPG <- MPG(patchyCost, patch = (patchyCost == + + 1)) + + When sourcing ‘grainscape_vignette.R’: + Error: Length of new attribute value must be 1 or 42, the number of target vertices, not 13 + Execution halted + + ‘MPG_algorithm.Rmd’ using ‘UTF-8’... OK + ‘grainscape_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + doc 1.5Mb + libs 2.5Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MPG_algorithm.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2023) is older than remote repository (2024). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/bookmark.sty'' had status 1 + ! LaTeX Error: File `bookmark.sty' not found. + + ! Emergency stop. + + + Error: processing vignette 'MPG_algorithm.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/grainscape/new/grainscape.Rcheck/vign_test/grainscape/vignettes/MPG_algorithm.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MPG_algorithm.log for more info. + --- failed re-building ‘MPG_algorithm.Rmd’ + + --- re-building ‘grainscape_vignette.Rmd’ using rmarkdown + + Quitting from lines at lines 204-205 [model_01_step_02] (grainscape_vignette.Rmd) + Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics: + Length of new attribute value must be 1 or 42, the number of target vertices, not 13 + --- failed re-building ‘grainscape_vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘MPG_algorithm.Rmd’ ‘grainscape_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# graphlayouts + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/schochastics/graphlayouts +* Source code: https://github.com/cran/graphlayouts +* Date/Publication: 2024-03-09 20:00:02 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "graphlayouts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphlayouts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_manipulate + > ### Title: Manipulate graph + > ### Aliases: graph_manipulate reorder_edges + > + > ### ** Examples + > + > library(igraph) + + Attaching package: ‘igraph’ + + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + > library(ggraph) + Loading required package: ggplot2 + > + > g <- sample_gnp(10, 0.5) + > E(g)$attr <- 1:ecount(g) + > gn <- reorder_edges(g,"attr") + Error in igraph::graph_from_data_frame(d = edges_df, directed = igraph::is.directed(g), : + `vertices` must be a data frame or a character vector if given + Calls: reorder_edges -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(graphlayouts) + > + > test_check("graphlayouts") + [ FAIL 1 | WARN 5 | SKIP 0 | PASS 139 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-graph_manipulate.R:4:4'): reorder_edges works ────────────────── + Error in `igraph::graph_from_data_frame(d = edges_df, directed = igraph::is.directed(g), + vertices = vertices)`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─graphlayouts::reorder_edges(g, "weight") at test-graph_manipulate.R:4:4 + 2. └─igraph::graph_from_data_frame(...) + + [ FAIL 1 | WARN 5 | SKIP 0 | PASS 139 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘graphlayouts.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + When sourcing ‘graphlayouts.R’: + Error: invalid font type + Execution halted + + ‘graphlayouts.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 13.9Mb + sub-directories of 1Mb or more: + doc 1.9Mb + help 2.0Mb + libs 9.7Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 22 marked UTF-8 strings + ``` + +# intergraph + +
+ +* Version: 2.0-4 +* GitHub: https://github.com/mbojan/intergraph +* Source code: https://github.com/cran/intergraph +* Date/Publication: 2024-02-01 17:30:02 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "intergraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘intergraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: asIgraph + > ### Title: Coerce an object to class "igraph" + > ### Aliases: asIgraph asIgraph.network asIgraph.data.frame + > + > ### ** Examples + > + > ### using 'asIgraph' on objects of class 'network' + > + > g <- asIgraph(exNetwork) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Calls: asIgraph ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(intergraph) + > + > test_check("intergraph") + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 40 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + • On CRAN (1): 'test-netcompare.R:5:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-asIgraph.R:7:3'): Disassembling to d.f and assembling back to igraph gives the same result ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(l$edges, vertices = l$vertexes) at test-asIgraph.R:7:3 + 2. └─intergraph:::asIgraph.data.frame(l$edges, vertices = l$vertexes) + 3. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-asIgraph.R:26:3'): Vertex names are properly set via 'vnames' argument for directed network ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(l$edges, vertices = l$vertexes, vnames = "label") at test-asIgraph.R:26:3 + 2. └─intergraph:::asIgraph.data.frame(...) + 3. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-asIgraph.R:36:3'): Vertex names are properly set via 'vnames' argument for undirected network ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(l$edges, vertices = l$vertexes, directed = FALSE) at test-asIgraph.R:36:3 + 2. └─intergraph:::asIgraph.data.frame(...) + 3. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 4. └─igraph::add_vertices(g, length(names), attr = vattrs) + 5. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 6. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-asIgraph.R:49:3'): Igraph is created from edgelist as tibble ─── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─testthat::expect_silent(net <- asIgraph(edb)) at test-asIgraph.R:49:3 + 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. ├─intergraph::asIgraph(edb) + 10. └─intergraph:::asIgraph.data.frame(edb) + 11. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-asIgraph.R:65:3'): Network is created from tibbles ───────────── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─testthat::expect_silent(net <- asIgraph(edb, vertices = vdb)) at test-asIgraph.R:65:3 + 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. ├─intergraph::asIgraph(edb, vertices = vdb) + 10. └─intergraph:::asIgraph.data.frame(edb, vertices = vdb) + 11. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-asIgraph.R:82:3'): Conversion for exNetwork is OK tested with netcompare ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::netcompare(asIgraph(exNetwork), exNetwork, test = TRUE) at test-asIgraph.R:82:3 + 2. ├─intergraph::asIgraph(exNetwork) + 3. └─intergraph:::asIgraph.network(exNetwork) + 4. ├─intergraph::asIgraph(...) + 5. └─intergraph:::asIgraph.data.frame(...) + 6. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 7. └─igraph::add_vertices(g, length(names), attr = vattrs) + 8. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 9. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-asIgraph.R:88:3'): Conversion for exNetwork2 is OK tested with netcompare ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::netcompare(asIgraph(exNetwork2), exNetwork2, test = TRUE) at test-asIgraph.R:88:3 + 2. ├─intergraph::asIgraph(exNetwork2) + 3. └─intergraph:::asIgraph.network(exNetwork2) + 4. ├─intergraph::asIgraph(...) + 5. └─intergraph:::asIgraph.data.frame(...) + 6. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 7. └─igraph::add_vertices(g, length(names), attr = vattrs) + 8. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 9. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-attrmap.R:15:3'): 'na' vertex attribute can be dropped when going network->igraph ── + Error in `i_set_vertex_attr(graph = graph, name = name, index = index, + value = value)`: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(net, amap = aa) at test-attrmap.R:15:3 + 2. └─intergraph:::asIgraph.network(net, amap = aa) + 3. ├─intergraph::asIgraph(...) + 4. └─intergraph:::asIgraph.data.frame(...) + 5. └─igraph::graph_from_data_frame(object, directed = directed, vertices = vertices) + 6. └─igraph::add_vertices(g, length(names), attr = vattrs) + 7. └─igraph::set_vertex_attr(graph, nam[[i]], idx, attr) + 8. └─igraph:::i_set_vertex_attr(...) + ── Error ('test-github_issues.R:8:3'): NAs are preserved in edge attributes ──── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(net) at test-github_issues.R:8:3 + 2. └─intergraph:::asIgraph.network(net) + 3. ├─intergraph::asIgraph(...) + 4. └─intergraph:::asIgraph.data.frame(...) + 5. └─igraph::delete_vertex_attr(rval, "name") + ── Error ('test-github_issues.R:17:3'): NAs are preserved in vertex attributes ── + Error in `igraph::delete_vertex_attr(rval, "name")`: No such vertex attribute: name + Backtrace: + ▆ + 1. ├─intergraph::asIgraph(net) at test-github_issues.R:17:3 + 2. └─intergraph:::asIgraph.network(net) + 3. ├─intergraph::asIgraph(...) + 4. └─intergraph:::asIgraph.data.frame(...) + 5. └─igraph::delete_vertex_attr(rval, "name") + + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 40 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘howto.Rmd’ + ... + label + + > class(exNetwork) + [1] "network" + + > g <- asIgraph(exNetwork) + + When sourcing ‘howto.R’: + Error: Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + Execution halted + + ‘howto.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘howto.Rmd’ using rmarkdown + + Quitting from lines at lines 89-95 [network2igraph] (howto.Rmd) + Error: processing vignette 'howto.Rmd' failed with diagnostics: + Length of new attribute value must be 1 or 14, the number of target vertices, not 15 + --- failed re-building ‘howto.Rmd’ + + SUMMARY: processing the following file failed: + ‘howto.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# interplex + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/tdaverse/interplex +* Source code: https://github.com/cran/interplex +* Date/Publication: 2024-02-20 10:20:07 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "interplex")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘interplex-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as_cmplx + > ### Title: Coerce objects to lists of simplices + > ### Aliases: as_cmplx as_cmplx.default as_cmplx.Rcpp_SimplexTree + > ### as_cmplx.gudhi.simplex_tree.SimplexTree as_cmplx.igraph + > ### as_cmplx.network + > + > ### ** Examples + > + > if (requireNamespace("TDA", quietly = TRUE)) { + + # pick the simplicial complex from a TDA filtration object + + t <- 2 * pi * c(0, 1, 3, 6) / 7 + + rf <- TDA::ripsFiltration( + + cbind(x = cos(t), y = sin(t)), + + maxdimension = 2L, maxscale = 1.7 + + ) + + print(rf$cmplx) + + cp_rf <- as_cmplx(rf) + + print(cp_rf) + + } + [[1]] + [1] 1 + + [[2]] + [1] 2 + + [[3]] + [1] 3 + + [[4]] + [1] 4 + + [[5]] + [1] 2 1 + + [[6]] + [1] 4 1 + + [[7]] + [1] 3 2 + + [[8]] + [1] 4 2 + + [[9]] + [1] 4 2 1 + + Warning in ensure_cmplx(x) : + Taking `cmplx` element as the simplicial complex. + [[1]] + [1] 1 + + [[2]] + [1] 2 + + [[3]] + [1] 3 + + [[4]] + [1] 4 + + [[5]] + [1] 2 1 + + [[6]] + [1] 4 1 + + [[7]] + [1] 3 2 + + [[8]] + [1] 4 2 + + [[9]] + [1] 4 2 1 + + > + > if (requireNamespace("simplextree", quietly = TRUE)) { + + # convert a simplextree object + + st <- simplextree::simplex_tree() + + st$insert(list(3:5, 5:6, 8)) + + cp_st <- as_cmplx(st) + + print(cp_st) + + } + [[1]] + [1] 3 + + [[2]] + [1] 4 + + [[3]] + [1] 5 + + [[4]] + [1] 6 + + [[5]] + [1] 8 + + [[6]] + [1] 3 4 + + [[7]] + [1] 3 5 + + [[8]] + [1] 4 5 + + [[9]] + [1] 5 6 + + > + > ## Not run: + > ##D + > ##D if (requireNamespace("reticulate", quietly = TRUE)) { + > ##D # convert a Python GUDHI simplex tree + > ##D gd <- reticulate::import("gudhi") + > ##D gd_st <- gd$SimplexTree() + > ##D for (s in list(3:5, 5:6, 8)) gd_st$insert(as.list(s)) + > ##D cp_gd <- as_cmplx(gd_st) + > ##D print(cp_gd) + > ##D } + > ## End(Not run) + > + > if (requireNamespace("igraph", quietly = TRUE)) { + + # convert an igraph object + + ig <- igraph::graph(c(1,2, 2,3, 1,3, 3,4)) + + set.seed(0L) + + ig <- igraph::set_vertex_attr(ig, "id", value = sample(igraph::vcount(ig))) + + print(ig) + + cp_ig <- as_cmplx(ig, index = "id") + + print(cp_ig) + + } + IGRAPH 180afb4 D--- 4 4 -- + + attr: id (v/n) + + edges from 180afb4: + [1] 1->2 2->3 1->3 3->4 + [[1]] + [1] 2 + + [[2]] + [1] 1 + + [[3]] + [1] 4 + + [[4]] + [1] 3 + + [[5]] + [1] 2 1 + + [[6]] + [1] 1 4 + + [[7]] + [1] 2 4 + + [[8]] + [1] 4 3 + + > + > if (requireNamespace("network", quietly = TRUE)) { + + # convert a network object + + el <- data.frame(tails = c(1, 2, 1, 3), heads = c(2, 3, 3, 4)) + + nw <- network::network.edgelist(el, network::network.initialize(4)) + + print(nw) + + cp_nw <- as_cmplx(nw) + + print(cp_nw) + + } + Network attributes: + vertices = 4 + directed = TRUE + hyper = FALSE + loops = FALSE + multiple = FALSE + bipartite = FALSE + total edges= 4 + missing edges= 0 + non-missing edges= 4 + + Vertex attribute names: + vertex.names + + No edge attributes + Error in igraph::delete_vertex_attr(rval, "name") : + No such vertex attribute: name + Calls: as_cmplx ... asIgraph.network -> asIgraph -> asIgraph.data.frame -> + Execution halted + ``` + +# LTFHPlus + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/EmilMiP/LTFHPlus +* Source code: https://github.com/cran/LTFHPlus +* Date/Publication: 2024-02-12 16:40:06 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "LTFHPlus")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘LTFHPlus-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_based_covariance_construction + > ### Title: Constructing covariance matrix from local family graph + > ### Aliases: graph_based_covariance_construction + > + > ### ** Examples + > + > fam <- data.frame( + + id = c("pid", "mom", "dad", "pgf"), + + dadcol = c("dad", 0, "pgf", 0), + + momcol = c("mom", 0, 0, 0)) + > + > thresholds <- data.frame( + + id = c("pid", "mom", "dad", "pgf"), + + lower = c(-Inf, -Inf, 0.8, 0.7), + + upper = c(0.8, 0.8, 0.8, 0.7)) + > + > graph <- prepare_graph(fam, icol = "id", fcol = "dadcol", mcol = "momcol", thresholds = thresholds) + > + > graph_based_covariance_construction(pid = "id", + + cur_proband_id = "pid", + + cur_family_graph = graph, + + h2 = 0.5) + Error in `rename()`: + ! Names must be unique. + ✖ These names are duplicated: + * "id" at locations 1 and 2. + Backtrace: + ▆ + 1. ├─LTFHPlus::graph_based_covariance_construction(...) + 2. │ └─... %>% relocate(!!as.symbol(pid)) + 3. ├─dplyr::relocate(., !!as.symbol(pid)) + 4. ├─dplyr::rename(., `:=`(!!as.symbol(pid), name)) + 5. └─dplyr:::rename.data.frame(., `:=`(!!as.symbol(pid), name)) + 6. └─tidyselect::eval_rename(expr(c(...)), .data) + 7. └─tidyselect:::rename_impl(...) + 8. ├─tidyselect:::with_subscript_errors(...) + 9. │ └─base::withCallingHandlers(...) + 10. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call) + 11. └─vctrs (local) ``() + 12. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 13. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 14. └─vctrs:::stop_names(...) + 15. └─vctrs:::stop_vctrs(...) + 16. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +# manynet + +
+ +* Version: 0.4.4 +* GitHub: https://github.com/stocnet/manynet +* Source code: https://github.com/cran/manynet +* Date/Publication: 2024-03-15 19:20:10 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "manynet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘manynet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: features + > ### Title: Marking networks features + > ### Aliases: features is_connected is_perfect_matching is_eulerian + > ### is_acyclic is_aperiodic + > + > ### ** Examples + > + > is_connected(ison_southern_women) + [1] TRUE + > is_perfect_matching(ison_southern_women) + Error in igraph::graph_from_data_frame(.data) : + Vertex name NA in edge list is not listed in vertex data frame + Calls: is_perfect_matching -> to_matching -> to_matching.igraph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(manynet) + Registered S3 method overwritten by 'manynet': + method from + print.tbl_graph tidygraph + > + > test_check("manynet") + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 18 | PASS 334 ] + + ══ Skipped tests (18) ══════════════════════════════════════════════════════════ + • On CRAN (18): 'test-manip_as.R:86:3', 'test-manip_split.R:50:3', + 'test-map_autographr.R:2:3', 'test-map_autographr.R:17:3', + 'test-map_autographr.R:31:3', 'test-map_autographr.R:49:3', + 'test-map_autographr.R:68:3', 'test-map_autographr.R:96:3', + 'test-map_autographr.R:108:3', 'test-map_autographr.R:117:3', + 'test-map_autographr.R:123:3', 'test-map_autographr.R:130:3', + 'test-map_autographr.R:143:3', 'test-map_autographr.R:160:3', + 'test-mark_nodes.R:13:3', 'test-mark_nodes.R:22:3', 'test-mark_ties.R:24:3', + 'test-mark_ties.R:33:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-mark_is.R:12:3'): is_ tests return correct values ────────────── + Error in `igraph::graph_from_data_frame(.data)`: Vertex name NA in edge list is not listed in vertex data frame + Backtrace: + ▆ + 1. ├─testthat::expect_false(is_perfect_matching(ison_southern_women)) at test-mark_is.R:12:3 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─manynet::is_perfect_matching(ison_southern_women) + 5. ├─manynet::to_matching(.data, mark = mark) + 6. └─manynet:::to_matching.igraph(.data, mark = mark) + 7. ├─base::suppressWarnings(as_igraph(el, twomode = TRUE)) + 8. │ └─base::withCallingHandlers(...) + 9. ├─manynet::as_igraph(el, twomode = TRUE) + 10. └─manynet:::as_igraph.data.frame(el, twomode = TRUE) + 11. └─igraph::graph_from_data_frame(.data) + ── Error ('test-manip_transform.R:43:3'): to matching works ──────────────────── + Error in `igraph::graph_from_data_frame(.data)`: Vertex name NA in edge list is not listed in vertex data frame + Backtrace: + ▆ + 1. ├─manynet::as_edgelist(to_matching(ison_southern_women)) at test-manip_transform.R:43:3 + 2. ├─manynet::to_matching(ison_southern_women) + 3. └─manynet:::to_matching.tbl_graph(ison_southern_women) + 4. ├─manynet::as_tidygraph(to_matching.igraph(.data), mark) + 5. └─manynet:::to_matching.igraph(.data) + 6. ├─base::suppressWarnings(as_igraph(el, twomode = TRUE)) + 7. │ └─base::withCallingHandlers(...) + 8. ├─manynet::as_igraph(el, twomode = TRUE) + 9. └─manynet:::as_igraph.data.frame(el, twomode = TRUE) + 10. └─igraph::graph_from_data_frame(.data) + + [ FAIL 2 | WARN 0 | SKIP 18 | PASS 334 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘Rgraphviz’ + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7 marked UTF-8 strings + ``` + +# massiveGST + +
+ +* Version: 1.2.3 +* GitHub: NA +* Source code: https://github.com/cran/massiveGST +* Date/Publication: 2023-03-29 16:40:02 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "massiveGST")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘massiveGST-Ex.R’ failed + The error most likely occurred in: + + > ### Name: massiveORT + > ### Title: A wrapper to fisher.test to get over representation analysis of + > ### gene sets. + > ### Aliases: massiveORT + > + > ### ** Examples + > + > library(massiveGST) + > + > # get the gene profile + > fname <- system.file("extdata", package="massiveGST") + > fname <- file.path(fname, "pre_ranked_list.txt") + > geneProfile <- get_geneProfile(fname) + > geneList <- names(head(geneProfile, 1000)) + > + > # get the gene-sets + > geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol") + msigdbr: R package version 7.5.1 + > geneSets <- geneSets[1:250] + > + > # run the function + > ans <- massiveORT(geneList, geneSets) + greater + > cut_by_significance(ans) + collection universe_size geneList_size + GOCC_CELL_PROJECTION_MEMBRANE C5 CC 8295 401 + GOCC_BASOLATERAL_PLASMA_MEMBRANE C5 CC 8295 401 + GOCC_BASAL_PART_OF_CELL C5 CC 8295 401 + GOCC_CELL_BODY C5 CC 8295 401 + GOCC_APICAL_PART_OF_CELL C5 CC 8295 401 + GOCC_APICAL_PLASMA_MEMBRANE C5 CC 8295 401 + GOCC_CELL_LEADING_EDGE C5 CC 8295 401 + GOCC_ASTROCYTE_PROJECTION C5 CC 8295 401 + geneSet_size geneList_in_GeneSet odds_ratio + GOCC_CELL_PROJECTION_MEMBRANE 340 34 2.297037 + GOCC_BASOLATERAL_PLASMA_MEMBRANE 228 25 2.518609 + GOCC_BASAL_PART_OF_CELL 271 28 2.363035 + GOCC_CELL_BODY 544 45 1.873152 + GOCC_APICAL_PART_OF_CELL 426 36 1.897590 + GOCC_APICAL_PLASMA_MEMBRANE 360 31 1.926338 + GOCC_CELL_LEADING_EDGE 416 35 1.885567 + GOCC_ASTROCYTE_PROJECTION 19 6 9.202590 + log2_odds_ratio p.value BH.value + GOCC_CELL_PROJECTION_MEMBRANE 1.1997739 4.033451e-05 0.00929476 + GOCC_BASOLATERAL_PLASMA_MEMBRANE 1.3326274 1.010680e-04 0.00929476 + GOCC_BASAL_PART_OF_CELL 1.2406412 1.115371e-04 0.00929476 + GOCC_CELL_BODY 0.9054679 2.431327e-04 0.01215663 + GOCC_APICAL_PART_OF_CELL 0.9241682 7.008917e-04 0.02920382 + GOCC_APICAL_PLASMA_MEMBRANE 0.9458607 1.210876e-03 0.03783986 + GOCC_CELL_LEADING_EDGE 0.9149986 8.991179e-04 0.03211136 + GOCC_ASTROCYTE_PROJECTION 3.2020399 1.948196e-04 0.01215663 + B.value relevance + GOCC_CELL_PROJECTION_MEMBRANE 0.01008363 268 + GOCC_BASOLATERAL_PLASMA_MEMBRANE 0.02526701 267 + GOCC_BASAL_PART_OF_CELL 0.02788428 265 + GOCC_CELL_BODY 0.06078317 255 + GOCC_APICAL_PART_OF_CELL 0.17522293 252 + GOCC_APICAL_PLASMA_MEMBRANE 0.30271890 250 + GOCC_CELL_LEADING_EDGE 0.22477949 249 + GOCC_ASTROCYTE_PROJECTION 0.04870491 247 + link + GOCC_CELL_PROJECTION_MEMBRANE https://igordot.github.io/msigdbr/ + GOCC_BASOLATERAL_PLASMA_MEMBRANE https://igordot.github.io/msigdbr/ + GOCC_BASAL_PART_OF_CELL https://igordot.github.io/msigdbr/ + GOCC_CELL_BODY https://igordot.github.io/msigdbr/ + GOCC_APICAL_PART_OF_CELL https://igordot.github.io/msigdbr/ + GOCC_APICAL_PLASMA_MEMBRANE https://igordot.github.io/msigdbr/ + GOCC_CELL_LEADING_EDGE https://igordot.github.io/msigdbr/ + GOCC_ASTROCYTE_PROJECTION https://igordot.github.io/msigdbr/ + > + > plot(cut_by_significance(ans), geneSets,as.network = TRUE) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 7, the number of target vertices, not 8 + Calls: plot ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette.Rmd’ + ... + > plot(ans) + + > plot(cut_by_significance(ans), top = 30) + + > plot(cut_by_significance(ans), gene_sets = geneSets, + + as.network = TRUE) + + When sourcing ‘vignette.R’: + Error: Length of new attribute value must be 1 or 18, the number of target vertices, not 19 + Execution halted + + ‘vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette.Rmd’ using rmarkdown + ``` + +# MEGENA + +
+ +* Version: 1.3.7 +* GitHub: https://github.com/songw01/MEGENA +* Source code: https://github.com/cran/MEGENA +* Date/Publication: 2018-09-10 19:00:03 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "MEGENA")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MEGENA_pipeline_10062016.Rmd’ + ... + Calculating distance metric and similarity... + iteration:1 + - #. tested:1 + - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25, + - #. of split:4 + - assess improvements over compactness + + When sourcing ‘MEGENA_pipeline_10062016.R’: + Error: invalid first argument + Execution halted + + ‘MEGENA_pipeline_10062016.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MEGENA_pipeline_10062016.Rmd’ using rmarkdown + + Quitting from lines at lines 77-93 [MCA] (MEGENA_pipeline_10062016.Rmd) + Error: processing vignette 'MEGENA_pipeline_10062016.Rmd' failed with diagnostics: + invalid first argument + --- failed re-building ‘MEGENA_pipeline_10062016.Rmd’ + + SUMMARY: processing the following file failed: + ‘MEGENA_pipeline_10062016.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + data 1.8Mb + libs 3.1Mb + ``` + +# morph + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/morph +* Date/Publication: 2023-02-14 15:40:02 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "morph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘morph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: morph3d + > ### Title: Performs a morphological segmentation of a binary 3D array + > ### Aliases: morph3d + > ### Keywords: manip array + > + > ### ** Examples + > + > # SET FINALPLOT=TRUE IF THE INTERACTIVE 3D PLOT IS DESIRED + > # THAT CONTAINS THE FINAL SEGMENTATION CATEGORIES + > # IF A PLOT FOR EACH CATEGORY IS REQUIRED, SET PLOT=TRUE + > LEdemoOut <- morph3d(LEdemo, PLOT=FALSE, FINALPLOT=FALSE) + + + Input data passess all initial checks for integrity. + + + Error in add_edges(g, edges, attr = eattrs) : + At vendor/cigraph/src/graph/type_indexededgelist.c:261 : Out-of-range vertex IDs when adding edges. Invalid vertex ID + Calls: morph3d -> graph_from_data_frame -> add_edges + Execution halted + ``` + +# motifr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/marioangst/motifr +* Source code: https://github.com/cran/motifr +* Date/Publication: 2020-12-10 15:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "motifr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘motifr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dummy_net + > ### Title: Three-level network dummy example + > ### Aliases: dummy_net + > ### Keywords: datasets + > + > ### ** Examples + > + > plot_mnet(dummy_net) + Error in igraph::delete_vertex_attr(rval, "name") : + No such vertex attribute: name + Calls: plot_mnet ... asIgraph.network -> asIgraph -> asIgraph.data.frame -> + Execution halted + ``` + +# mstknnclust + +
+ +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/mstknnclust +* Date/Publication: 2023-01-27 14:10:02 UTC +* Number of recursive dependencies: 32 + +Run `revdepcheck::cloud_details(, "mstknnclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mstknnclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mst.knn + > ### Title: Performs the MST-kNN clustering algorithm + > ### Aliases: mst.knn + > + > ### ** Examples + > + > + > set.seed(1987) + > + > ##load package + > library("mstknnclust") + > + > ##Generates a data matrix of dimension 100X15 + > + > n=100; m=15 + > + > x <- matrix(runif(n*m, min = -5, max = 10), nrow=n, ncol=m) + > + > ##Computes a distance matrix of x. + > + > library("stats") + > d <- base::as.matrix(stats::dist(x, method="euclidean")) + > + > ##Performs MST-kNN clustering using euclidean distance. + > + > results <- mst.knn(d) + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + + Only singletons are yielded + Error in (function (edges, n = max(edges), directed = TRUE) : + At rinterface_extra.c:78 : Expecting a scalar integer but received a vector of length 0. Invalid value + Calls: mst.knn ... only.single.graphs -> -> do.call -> + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘guide.Rmd’ + ... + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + Warning in .igraph.graph.union.or.intersection("intersection", ..., byname = byname, : + Some, but not all graphs are named, not using vertex names + + When sourcing ‘guide.R’: + Error: `d` should contain at least two columns + Execution halted + + ‘guide.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘guide.Rmd’ using rmarkdown + + Quitting from lines at lines 77-79 [unnamed-chunk-4] (guide.Rmd) + Error: processing vignette 'guide.Rmd' failed with diagnostics: + `d` should contain at least two columns + --- failed re-building ‘guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# multinet + +
+ +* Version: 4.1.2 +* GitHub: NA +* Source code: https://github.com/cran/multinet +* Date/Publication: 2023-02-14 10:20:03 UTC +* Number of recursive dependencies: 12 + +Run `revdepcheck::cloud_details(, "multinet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multinet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: multinet.conversion + > ### Title: Conversion to a simple or multi graph + > ### Aliases: multinet.conversion as.igraph.multinet + > ### as.igraph.Rcpp_RMLNetwork + > + > ### ** Examples + > + > net <- ml_aucs() + > # using the default merge.actors=TRUE we create a multigraph, + > # where each actor corresponds to a vertex in the result + > multigraph <- as.igraph(net) + Error in graph_from_data_frame(vertices = a_df, e_df, directed = dir) : + `vertices` must be a data frame or a character vector if given + Calls: as.igraph -> as.igraph.Rcpp_RMLNetwork -> graph_from_data_frame + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++14: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 170.9Mb + sub-directories of 1Mb or more: + libs 170.7Mb + ``` + +# nda + +
+ +* Version: 0.1.13 +* GitHub: https://github.com/kzst/nda +* Source code: https://github.com/cran/nda +* Date/Publication: 2023-09-27 07:20:06 UTC +* Number of recursive dependencies: 44 + +Run `revdepcheck::cloud_details(, "nda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ndr + > ### Title: Genearlized Network-based Dimensionality Reduction and Analysis + > ### (GNDA) + > ### Aliases: ndr + > ### Keywords: multivariate nonparametric + > + > ### ** Examples + > + > + > # Dimension reduction + > + > data(swiss) + > df<-swiss + > p<-ndr(df) + > summary(p) + + Summary of the NDA: + + Number of latent variables: 1 + Number of observations: 47 + Communalities: + Fertility Agriculture Examination Education Catholic Infant.Mortality + [1,] 0.310332 0.3326062 0.3424287 0.1007481 0.682701 0.04166014 + + Factor loadings: + NDA1 + Fertility 0.5570745 + Agriculture 0.5767202 + Examination -0.5851741 + Education -0.3174085 + Catholic 0.8262572 + Infant.Mortality 0.2041082 + + + Correlation matrix of factor scores: + NDA1 + NDA1 1 + > plot(p) + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 5, 6 + Calls: plot ... -> -> cbind -> cbind -> data.frame + Execution halted + ``` + +# Neighboot + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/Neighboot +* Date/Publication: 2022-05-31 23:20:08 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "Neighboot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Neighboot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: to.rds + > ### Title: Tranform an 'sample.RDS' object to an 'rds.data.frame' object. + > ### Aliases: to.rds + > + > ### ** Examples + > + > #Load the synthetic population network dataset. + > data("pop.network") + > + > #Draw an RDS sample from the simulated network using the sampleRDS function + > #from the package RDStreeboot. + > require(RDStreeboot) + Loading required package: RDStreeboot + > RDS.samp <- sample.RDS(pop.network$traits, pop.network$adj.mat, 200, 10, + + 3, c(1/6,1/3,1/3,1/6), FALSE) + > + > #Tranform RDS.samp to an rds.data.frame object + > require(RDS) + Loading required package: RDS + > to.rds(RDS.data=RDS.samp) + Error in data.frame(id = as.numeric(unlist(seed.l)), seed.id = seed.id) : + arguments imply differing number of rows: 10, 0 + Calls: to.rds -> data.frame + Execution halted + ``` + +# PCGII + +
+ +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/PCGII +* Date/Publication: 2024-02-02 18:30:05 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "PCGII")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Introduction.Rmd’ + ... + + > dim(links) + [1] 99 2 + + > my_net <- graph_from_data_frame(d = links, vertices = nodenames, + + directed = F) + + When sourcing ‘Introduction.R’: + Error: `vertices` must be a data frame or a character vector if given + Execution halted + + ‘Introduction.Rmd’ using ‘UTF-8’... failed + ``` + +# pmd + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/yufree/pmd +* Source code: https://github.com/cran/pmd +* Date/Publication: 2021-01-21 23:20:08 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "pmd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pmd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getcda + > ### Title: Perform correlation directed analysis for peaks list. + > ### Aliases: getcda + > + > ### ** Examples + > + > data(spmeinvivo) + > cluster <- getcorcluster(spmeinvivo) + 75 retention time cluster found. + Error in aggregate.data.frame(as.data.frame(x), ...) : + no rows to aggregate + Calls: getcorcluster ... -> aggregate.default -> aggregate.data.frame + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘globalstd.Rmd’ + ... + > stdcluster2 <- getcluster(std, corcutoff = 0.9) + + > stdcluster3 <- getcluster(std2, corcutoff = 0.9) + + > corcluster <- getcorcluster(spmeinvivo) + 75 retention time cluster found. + + When sourcing ‘globalstd.R’: + Error: no rows to aggregate + Execution halted + when running code in ‘reactomics.Rmd’ + ... + > net <- graph_from_data_frame(chain$sdac, directed = F) + + > pal <- grDevices::rainbow(5) + + > plot(net, vertex.label = round(as.numeric(V(net)$name), + + 2), vertex.size = 5, edge.width = 3, edge.color = pal[as.numeric(as.factor(E(net)$dif .... [TRUNCATED] + + When sourcing ‘reactomics.R’: + Error: zero-length 'labels' specified + Execution halted + + ‘globalstd.Rmd’ using ‘UTF-8’... failed + ‘reactomics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘globalstd.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + data 3.3Mb + doc 1.3Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 62 marked UTF-8 strings + ``` + +# polymapR + +
+ +* Version: 1.1.5 +* GitHub: NA +* Source code: https://github.com/cran/polymapR +* Date/Publication: 2024-01-08 21:30:03 UTC +* Number of recursive dependencies: 197 + +Run `revdepcheck::cloud_details(, "polymapR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘polymapR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: screen_for_duplicate_markers + > ### Title: Screen for and remove duplicated markers + > ### Aliases: screen_for_duplicate_markers + > + > ### ** Examples + > + > data("screened_data3") + > dupmscreened <- screen_for_duplicate_markers(screened_data3) + Error in apply(sub, 1, function(x) sum(is.na(x))) : + dim(X) must have a positive length + Calls: screen_for_duplicate_markers -> apply + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Vignette_polymapR.Rmd’ + ... + There are now 205 individuals leftover in the dataset. + + > screened_data3 <- screen_for_duplicate_individuals(dosage_matrix = screened_data2, + + cutoff = 0.95, plot_cor = TRUE) + + Combining P1 & NA into P1 + + When sourcing ‘Vignette_polymapR.R’: + Error: dim(X) must have a positive length + Execution halted + + ‘Vignette_genotype_probabilities.Rmd’ using ‘UTF-8’... OK + ‘Vignette_polymapR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Vignette_genotype_probabilities.Rmd’ using rmarkdown + --- finished re-building ‘Vignette_genotype_probabilities.Rmd’ + + --- re-building ‘Vignette_polymapR.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 20.1Mb + sub-directories of 1Mb or more: + R 14.4Mb + data 4.6Mb + ``` + +# ptools + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/apwheele/ptools +* Source code: https://github.com/cran/ptools +* Date/Publication: 2023-02-07 19:02:30 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "ptools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ptools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: near_strings1 + > ### Title: Strings of Near Repeats + > ### Aliases: near_strings1 + > + > ### ** Examples + > + > # Simplified example showing two clusters + > s <- c(0,0,0,4,4) + > ccheck <- c(1,1,1,2,2) + > dat <- data.frame(x=1:5,y=0, + + ti=s, + + id=1:5) + > res1 <- near_strings1(dat,'id','x','y','ti',2,1) + Error in igraph::graph_from_data_frame(pa, directed = FALSE, vertices = MyData[, : + `vertices` must be a data frame or a character vector if given + Calls: near_strings1 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ptools) + > + > test_check("ptools") + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 40 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-nearstring.R:7:3'): test near_string1 (loop version) ─────────── + Error in `igraph::graph_from_data_frame(pa, directed = FALSE, vertices = MyData[, + id])`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 1, 1) at test-nearstring.R:7:3 + 2. └─igraph::graph_from_data_frame(...) + ── Error ('test-nearstring.R:21:3'): test near_string2 (kdtree version) ──────── + Error in `igraph::graph_from_data_frame(dist_p, directed = FALSE, vertices = MyData[, + id])`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─ptools::near_strings2(dat, "id", "x", "y", "ti", 1, 1) at test-nearstring.R:21:3 + 2. └─igraph::graph_from_data_frame(...) + ── Error ('test-nearstring.R:34:3'): two near_string versions should have the same output ── + Error in `igraph::graph_from_data_frame(pa, directed = FALSE, vertices = MyData[, + id])`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 1, 1) at test-nearstring.R:34:3 + 2. └─igraph::graph_from_data_frame(...) + ── Error ('test-nearstring.R:46:3'): Checking two components ─────────────────── + Error in `igraph::graph_from_data_frame(pa, directed = FALSE, vertices = MyData[, + id])`: `vertices` must be a data frame or a character vector if given + Backtrace: + ▆ + 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 2, 1) at test-nearstring.R:46:3 + 2. └─igraph::graph_from_data_frame(...) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 40 ] + Error: Test failures + Execution halted + ``` + +# RavenR + +
+ +* Version: 2.2.0 +* GitHub: https://github.com/rchlumsk/RavenR +* Source code: https://github.com/cran/RavenR +* Date/Publication: 2022-10-28 21:02:50 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "RavenR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RavenR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rvn_calc_runoff_coeff + > ### Title: Generate runoff coefficients upstream of gauges + > ### Aliases: rvn_calc_runoff_coeff + > + > ### ** Examples + > + > myrvh <- system.file("extdata","Nith.rvh", package="RavenR") + > mycust <- system.file("extdata", "run1_PRECIP_Daily_Average_BySubbasin.csv", package="RavenR") + > myhyd <- system.file("extdata", "run1_Hydrographs.csv", package="RavenR") + > + > rcs <- rvn_calc_runoff_coeff(myrvh, mycust, myhyd, correct=TRUE) + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 43, the number of target vertices, not 4 + Calls: rvn_calc_runoff_coeff ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Introduction_to_RavenR.Rmd’ + ... + > rvn_rvi_write_template(template_name = "HMETS", filename = tf, + + author = "Your Name") + [1] TRUE + + > rvh <- rvn_rvh_read(system.file("extdata", "Nith.rvh", + + package = "RavenR")) + + When sourcing ‘Introduction_to_RavenR.R’: + Error: Length of new attribute value must be 1 or 43, the number of target vertices, not 4 + Execution halted + + ‘Introduction_to_RavenR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Introduction_to_RavenR.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + doc 1.0Mb + extdata 1.0Mb + libs 2.0Mb + ``` + +# rdracor + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/dracor-org/rdracor +* Source code: https://github.com/cran/rdracor +* Date/Publication: 2024-04-03 23:40:06 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "rdracor")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(rdracor) + > + > test_check("rdracor") + DraCor API URL: https://dracor.org/api/v1 + name: DraCor API v1 + version: 1.0.2 + status: stable + existdb: 6.2.0 + base: https://dracor.org/api/v1[ FAIL 5 | WARN 1 | SKIP 0 | PASS 36 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-net.R:23:3'): cooccur_igraph is returned by get_net_cooccur_igraph() ── + Error in `igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes)`: Vertex name podkolesin in edge list is not listed in vertex data frame + Backtrace: + ▆ + 1. ├─testthat::expect_s3_class(...) at test-net.R:23:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─rdracor::get_net_cooccur_igraph("gogol-zhenitba", "rus") + 5. └─igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes) + ── Error ('test-net.R:30:3'): label_cooccur_igraph() return come NA for big network ── + Error in `igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes)`: Duplicate vertex names + Backtrace: + ▆ + 1. └─rdracor::get_net_cooccur_igraph("henry-iv-part-i", "shake") at test-net.R:30:3 + 2. └─igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes) + ── Error ('test-net.R:37:5'): label_cooccur_igraph() do not return NA after max_graph_size adjustment ── + Error in `igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes)`: Duplicate vertex names + Backtrace: + ▆ + 1. └─rdracor::get_net_cooccur_igraph("henry-iv-part-i", "shake") at test-net.R:37:5 + 2. └─igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes) + ── Error ('test-net.R:43:3'): summary.cooccur_igraph() prints appropriate number of rows ── + Error in `igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes)`: Duplicate vertex names + Backtrace: + ▆ + 1. └─rdracor::get_net_cooccur_igraph("henry-iv-part-i", "shake") at test-net.R:43:3 + 2. └─igraph::graph_from_data_frame(edges, directed = FALSE, vertices = nodes) + ── Error ('test-net.R:48:3'): relations_igraph is returned by get_net_relations_igraph() ── + Error in `graph_from_data_frame(d = d, directed = directed, vertices = vertices)`: Vertex name kochkarev in edge list is not listed in vertex data frame + Backtrace: + ▆ + 1. ├─testthat::expect_s3_class(...) at test-net.R:48:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─rdracor::get_net_relations_igraph("gogol-zhenitba", "rus") + 5. └─igraph::graph.data.frame(...) + 6. └─igraph::graph_from_data_frame(d = d, directed = directed, vertices = vertices) + + [ FAIL 5 | WARN 1 | SKIP 0 | PASS 36 ] + Error: Test failures + Execution halted + ``` + +# ReDaMoR + +
+ +* Version: 0.7.4 +* GitHub: https://github.com/patzaw/ReDaMoR +* Source code: https://github.com/cran/ReDaMoR +* Date/Publication: 2024-02-07 06:20:02 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "ReDaMoR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ReDaMoR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: df_to_model + > ### Title: Create a RelDataModel object from column names of data frames + > ### Aliases: df_to_model + > + > ### ** Examples + > + > ## Read data files ---- + > to_read <- list.files( + + system.file("examples/HPO-subset", package="ReDaMoR"), + + full.names=TRUE + + ) + > hpo_tables <- list() + > for(f in to_read){ + + hpo_tables[[sub("[.]txt$", "", basename(f))]] <- readr::read_tsv(f) + + } + Rows: 89 Columns: 2 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): id, alt + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 972 Columns: 2 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): id, descendant + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 2594 Columns: 3 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): db, hp + dbl (1): id + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 2337 Columns: 4 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): db, synonym + dbl (1): id + lgl (1): preferred + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 1903 Columns: 3 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): db, label + dbl (1): id + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 500 Columns: 4 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (3): id, name, description + dbl (1): level + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 95 Columns: 2 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (2): id, parent + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 2 Columns: 2 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (1): url + date (1): current + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + Rows: 730 Columns: 3 + ── Column specification ──────────────────────────────────────────────────────── + Delimiter: "\t" + chr (3): id, synonym, type + + ℹ Use `spec()` to retrieve the full column specification for this data. + ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. + > ## Build the model from a list of data frames ---- + > new_model <- df_to_model( + + list=names(hpo_tables), envir=as.environment(hpo_tables) + + ) + > ## Plot the model ---- + > new_model %>% + + auto_layout(lengthMultiplier=250) %>% + + plot() + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 0, 9 + Calls: %>% ... -> -> cbind -> cbind -> data.frame + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ReDaMoR.Rmd’ + ... + + > new_model <- df_to_model(list = names(hpo_tables), + + envir = as.environment(hpo_tables)) + + > new_model %>% auto_layout(lengthMultiplier = 250) %>% + + plot() + + When sourcing ‘ReDaMoR.R’: + Error: arguments imply differing number of rows: 0, 9 + Execution halted + + ‘ReDaMoR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ReDaMoR.Rmd’ using rmarkdown + + Quitting from lines at lines 383-390 [unnamed-chunk-12] (ReDaMoR.Rmd) + Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics: + arguments imply differing number of rows: 0, 9 + --- failed re-building ‘ReDaMoR.Rmd’ + + SUMMARY: processing the following file failed: + ‘ReDaMoR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rgexf + +
+ +* Version: 0.16.2 +* GitHub: https://github.com/gvegayon/rgexf +* Source code: https://github.com/cran/rgexf +* Date/Publication: 2021-08-12 21:30:02 UTC +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "rgexf")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("rgexf") + + } + + test-bugs.r................... 0 tests + test-bugs.r................... 0 tests + test-bugs.r................... 1 tests OK + test-bugs.r................... 1 tests OK + test-bugs.r................... 1 tests OK + test-bugs.r................... 2 tests OK 0.2s + 1ms + + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 0 tests + test-igraph.r................. 1 tests 1 fails + test-igraph.r................. 2 tests 1 fails + test-igraph.r................. 2 tests 1 fails + test-igraph.r................. 2 tests 1 fails + test-igraph.r................. 2 tests 1 fails + test-igraph.r................. 3 tests 1 fails 71ms + + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 0 tests + test-rgexf.r.................. 1 tests OK + test-rgexf.r.................. 1 tests OK + test-rgexf.r.................. 1 tests OK + test-rgexf.r.................. 2 tests OK + test-rgexf.r.................. 3 tests OK + test-rgexf.r.................. 4 tests OK + test-rgexf.r.................. 5 tests OK + test-rgexf.r.................. 6 tests OK + test-rgexf.r.................. 7 tests OK + test-rgexf.r.................. 8 tests OK + test-rgexf.r.................. 9 tests OK + test-rgexf.r.................. 10 tests OK 74ms + ----- FAILED[data]: test-igraph.r<21--21> + call| expect_equal(ne, 0) + diff| Mean absolute difference: 8 + Error: 1 out of 15 tests failed + In addition: Warning message: + `barabasi.game()` was deprecated in igraph 2.0.0. + ℹ Please use `sample_pa()` instead. + Execution halted + ``` + +# RNewsflow + +
+ +* Version: 1.2.8 +* GitHub: NA +* Source code: https://github.com/cran/RNewsflow +* Date/Publication: 2024-04-03 11:03:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "RNewsflow")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RNewsflow-Ex.R’ failed + The error most likely occurred in: + + > ### Name: create_document_network + > ### Title: Create a document similarity network + > ### Aliases: create_document_network + > + > ### ** Examples + > + > d = data.frame(x = c(1,1,1,2,2,3), + + y = c(2,3,5,4,5,6), + + v = c(0.3,0.4,0.7,0.5,0.2,0.9)) + > + > meta = data.frame(document_id = 1:8, + + date = seq.POSIXt(from = as.POSIXct('2010-01-01 12:00:00'), + + by='hour', length.out = 8), + + medium = c(rep('Newspapers', 4), rep('Blog', 4))) + > + > g = create_document_network(d, meta) + > + > igraph::get.data.frame(g, 'both') + Warning: `get.data.frame()` was deprecated in igraph 2.0.0. + ℹ Please use `as_data_frame()` instead. + Warning: non-unique values when setting 'row.names': + Error in `.rowNamesDF<-`(x, value = value) : + duplicate 'row.names' are not allowed + Calls: ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- + Execution halted + ``` + +## In both + +* checking for missing documentation entries ... WARNING + ``` + Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "ndiMatrix" of class "replValueSp"; definition not updated + Warning in .recacheSubclasses(def@className, def, env) : + undefined subclass "pcorMatrix" of class "replValueSp"; definition not updated + All user-level objects in a package should have documentation entries. + See chapter ‘Writing R documentation files’ in the ‘Writing R + Extensions’ manual. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 9.2Mb + sub-directories of 1Mb or more: + libs 8.3Mb + ``` + +# rsetse + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/JonnoB/rSETSe +* Source code: https://github.com/cran/rsetse +* Date/Publication: 2021-06-11 10:00:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "rsetse")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rsetse-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calc_spring_constant + > ### Title: Calculate the spring constant + > ### Aliases: calc_spring_constant + > + > ### ** Examples + > + > + > library(igraph) + + Attaching package: ‘igraph’ + + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + > set.seed(234) + > g_prep <- generate_peels_network("A") %>% + + set.edge.attribute(., name = "edge_characteristic", value = rep(1:16, each = 10)) %>% + + #set some pretend Young's modulus value + + set.edge.attribute(., name = "E", value = rep(c(1e5, 5e5, 2e5, 3e5), each = 40)) %>% + + #calculate the spring area from another edge characteristic + + calc_spring_area(., value = "edge_characteristic", minimum_value = 10, range = 20) %>% + + prepare_edges() %>% + + prepare_categorical_force(., node_names = "name", + + force_var = "class") + Warning: There was 1 warning in `dplyr::mutate()`. + ℹ In argument: `dplyr::across(...)`. + Caused by warning: + ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0. + ℹ Please supply `.cols` instead. + Error in `dplyr::select()`: + ! Can't select columns that don't exist. + ✖ Column `name` doesn't exist. + Backtrace: + ▆ + 1. ├─... %>% ... + 2. ├─rsetse::prepare_categorical_force(., node_names = "name", force_var = "class") + 3. │ ├─igraph::graph_from_data_frame(...) + 4. │ └─vertices_df %>% dplyr::select(node_names, dplyr::everything()) + 5. ├─dplyr::select(., node_names, dplyr::everything()) + 6. ├─dplyr:::select.data.frame(., node_names, dplyr::everything()) + 7. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call) + 8. │ └─tidyselect:::eval_select_impl(...) + 9. │ ├─tidyselect:::with_subscript_errors(...) + 10. │ │ └─base::withCallingHandlers(...) + 11. │ └─tidyselect:::vars_select_eval(...) + 12. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) + 13. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) + 14. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) + 15. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) + 16. │ └─tidyselect:::as_indices_sel_impl(...) + 17. │ └─tidyselect:::as_indices_impl(...) + 18. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg) + 19. │ └─vctrs::vec_as_location(...) + 20. └─vctrs (local) ``() + 21. └─vctrs:::stop_subscript_oob(...) + 22. └─vctrs:::stop_subscript(...) + 23. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘separate-peels-quintet.Rmd’ + ... + Warning: `set.vertex.attribute()` was deprecated in igraph 2.0.0. + ℹ Please use `set_vertex_attr()` instead. + Warning: `get.vertex.attribute()` was deprecated in igraph 2.0.0. + ℹ Please use `vertex_attr()` instead. + + When sourcing ‘separate-peels-quintet.R’: + Error: ℹ In index: 1. + Caused by error in `i_set_vertex_attr()`: + ! Length of new attribute value must be 1 or 40, the number of target vertices, not 0 + Execution halted + + ‘Categorical-and-continuous-features.Rmd’ using ‘UTF-8’... OK + ‘separate-peels-quintet.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown + ``` + +# rTwig + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/aidanmorales/rTwig +* Source code: https://github.com/cran/rTwig +* Date/Publication: 2024-04-08 15:00:02 UTC +* Number of recursive dependencies: 188 + +Run `revdepcheck::cloud_details(, "rTwig")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rTwig-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qsm_summary + > ### Title: QSM Summary + > ### Aliases: qsm_summary + > + > ### ** Examples + > + > + > ## TreeQSM Processing Chain + > file <- system.file("extdata/QSM.mat", package = "rTwig") + > qsm <- import_qsm(file) + Importing TreeQSM .mat + > cylinder <- qsm$cylinder + > cylinder <- update_cylinders(cylinder) + Updating Cylinder Ordering + Calculating Growth Length + Error in add_edges(g, edges, attr = eattrs) : + At vendor/cigraph/src/graph/type_indexededgelist.c:261 : Out-of-range vertex IDs when adding edges. Invalid vertex ID + Calls: update_cylinders -> -> add_edges + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘SimpleForest.Rmd’ + ... + > cylinder %>% ggplot(aes(x = growthLength, y = radius, + + color = branchID)) + geom_point() + facet_wrap(~branchOrder) + + + labs(title = "Rad ..." ... [TRUNCATED] + + > cylinder <- correct_radii(cylinder, twigRad = 4.23) + Generating Branch Paths + + When sourcing ‘SimpleForest.R’: + Error: only 0's may be mixed with negative subscripts + Execution halted + when running code in ‘TreeQSM.Rmd’ + ... + + > cylinder <- qsm$cylinder + + > cylinder <- update_cylinders(cylinder) + Updating Cylinder Ordering + Calculating Growth Length + + When sourcing ‘TreeQSM.R’: + Error: At vendor/cigraph/src/graph/type_indexededgelist.c:261 : Out-of-range vertex IDs when adding edges. Invalid vertex ID + Execution halted + + ‘Box-Dimension.Rmd’ using ‘UTF-8’... OK + ‘SimpleForest.Rmd’ using ‘UTF-8’... failed + ‘TreeQSM.Rmd’ using ‘UTF-8’... failed + ‘Twigs.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Box-Dimension.Rmd’ using rmarkdown + ``` + +# skynet + +
+ +* Version: 1.4.3 +* GitHub: https://github.com/ropensci/skynet +* Source code: https://github.com/cran/skynet +* Date/Publication: 2022-06-17 13:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "skynet")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(skynet) + > + > test_check("skynet") + [ FAIL 4 | WARN 25 | SKIP 4 | PASS 46 ] + + ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ + • On CRAN (4): 'test_download_db1b.R:6:3', 'test_download_ontime.R:6:3', + 'test_download_t100.R:6:3', 'test_download_t100.R:13:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_netDir.R:16:3'): make_net_dir with disp ──────────────────────── + + Error in `rename(nodes, airport = name)`: Names must be unique. + ✖ These names are duplicated: + * "airport" at locations 1 and 2. + Backtrace: + ▆ + 1. └─skynet::make_net_dir(OD_Sample, disp = TRUE) at test_netDir.R:16:3 + 2. ├─dplyr::rename(nodes, airport = name) + 3. └─dplyr:::rename.data.frame(nodes, airport = name) + 4. └─tidyselect::eval_rename(expr(c(...)), .data) + 5. └─tidyselect:::rename_impl(...) + 6. ├─tidyselect:::with_subscript_errors(...) + 7. │ └─base::withCallingHandlers(...) + 8. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call) + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + ── Error ('test_netDir.R:27:3'): make_net_dir with cap ───────────────────────── + + Error in `rename(nodes, airport = name)`: Names must be unique. + ✖ These names are duplicated: + * "airport" at locations 1 and 2. + Backtrace: + ▆ + 1. └─skynet::make_net_dir(OD_Sample, cap = TRUE) at test_netDir.R:27:3 + 2. ├─dplyr::rename(nodes, airport = name) + 3. └─dplyr:::rename.data.frame(nodes, airport = name) + 4. └─tidyselect::eval_rename(expr(c(...)), .data) + 5. └─tidyselect:::rename_impl(...) + 6. ├─tidyselect:::with_subscript_errors(...) + 7. │ └─base::withCallingHandlers(...) + 8. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call) + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + ── Error ('test_netUnd.R:16:3'): make_net_und with disp ──────────────────────── + + Error in `rename(nodes, airport = name)`: Names must be unique. + ✖ These names are duplicated: + * "airport" at locations 1 and 2. + Backtrace: + ▆ + 1. └─skynet::make_net_und(OD_Sample, disp = TRUE, alpha = 0.003) at test_netUnd.R:16:3 + 2. ├─dplyr::rename(nodes, airport = name) + 3. └─dplyr:::rename.data.frame(nodes, airport = name) + 4. └─tidyselect::eval_rename(expr(c(...)), .data) + 5. └─tidyselect:::rename_impl(...) + 6. ├─tidyselect:::with_subscript_errors(...) + 7. │ └─base::withCallingHandlers(...) + 8. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call) + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + ── Error ('test_netUnd.R:27:3'): make_net_und with cap ───────────────────────── + + Error in `rename(nodes, airport = name)`: Names must be unique. + ✖ These names are duplicated: + * "airport" at locations 1 and 2. + Backtrace: + ▆ + 1. └─skynet::make_net_und(OD_Sample, cap = TRUE, pct = 10) at test_netUnd.R:27:3 + 2. ├─dplyr::rename(nodes, airport = name) + 3. └─dplyr:::rename.data.frame(nodes, airport = name) + 4. └─tidyselect::eval_rename(expr(c(...)), .data) + 5. └─tidyselect:::rename_impl(...) + 6. ├─tidyselect:::with_subscript_errors(...) + 7. │ └─base::withCallingHandlers(...) + 8. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call) + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + + [ FAIL 4 | WARN 25 | SKIP 4 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘maps’ + All declared Imports should be used. + ``` + +# SOMbrero + +
+ +* Version: 1.4-2 +* GitHub: https://github.com/tuxette/SOMbrero +* Source code: https://github.com/cran/SOMbrero +* Date/Publication: 2024-01-25 22:10:10 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "SOMbrero")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SOMbrero-Ex.R’ failed + The error most likely occurred in: + + > ### Name: projectIGraph + > ### Title: Compute the projection of a graph on a grid + > ### Aliases: projectIGraph projectIGraph.somRes + > + > ### ** Examples + > + > data(lesmis) + > set.seed(7383) + > mis.som <- trainSOM(x.data=dissim.lesmis, type="relational", nb.save=10) + > proj.lesmis <- projectIGraph(mis.som, lesmis) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 25, the number of target vertices, not 12 + Calls: projectIGraph ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +# TDApplied + +
+ +* Version: 3.0.3 +* GitHub: https://github.com/shaelebrown/TDApplied +* Source code: https://github.com/cran/TDApplied +* Date/Publication: 2024-03-12 23:00:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "TDApplied")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TDApplied-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_vr_graph + > ### Title: Plot a VR graph using the igraph package. + > ### Aliases: plot_vr_graph + > + > ### ** Examples + > + > + > if(require("TDAstats") & require("igraph")) + + { + + # simulate data from the unit circle and calculate + + # its diagram + + df <- TDAstats::circle2d[sample(1:100,25),] + + diag <- TDAstats::calculate_homology(df, + + dim = 1, + + threshold = 2) + + + + # get minimum death radius of any data cluster + + min_death_H0 <- + + min(diag[which(diag[,1] == 0),3L]) + + + + # get birth and death radius of the loop + + loop_birth <- as.numeric(diag[nrow(diag),2L]) + + loop_death <- as.numeric(diag[nrow(diag),3L]) + + + + # compute VR graphs at radii half of + + # min_death_H0 and the mean of loop_birth and + + # loop_death, returning clusters + + graphs <- vr_graphs(X = df,eps = + + c(0.5*min_death_H0,(loop_birth + loop_death)/2)) + + + + # plot graph of smaller (first) radius + + plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0, + + plot_isolated_vertices = TRUE) + + + + # plot graph of larger (second) radius + + plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2) + + + + # repeat but with rownames for df, each vertex + + # will be plotted with its rownames + + rownames(df) <- paste0("V",1:25) + + graphs <- vr_graphs(X = df,eps = + + c(0.5*min_death_H0,(loop_birth + loop_death)/2)) + + plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0, + + plot_isolated_vertices = TRUE) + + + + # plot without vertex labels + + plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2, + + vertex_labels = FALSE) + + + + # plot only the graph component containing vertex "1" + + plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0, + + component_of = "V1",plot_isolated_vertices = TRUE) + + + + # save the layout of the graph for adding features to + + # the same graph layout, like color + + layout <- plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2, + + return_layout = TRUE,vertex_labels = TRUE) + + cols <- rep("blue",25) + + cols[1:5] <- "red" + + plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,cols = cols, + + layout = layout) + + + + } + Loading required package: TDAstats + + Attaching package: ‘TDAstats’ + + The following object is masked from ‘package:TDApplied’: + + permutation_test + + Loading required package: igraph + + Attaching package: ‘igraph’ + + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 0, the number of target vertices, not 25 + Calls: plot_vr_graph ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘HCP_analysis.Rmd’ + ... + + > cols_time_since_last_block <- readRDS("cols_time_since_last_block.rds") + + > plot_vr_graph(g, eps = as.numeric(names(g$graphs)), + + cols = cols_respiratory, component_of = 20, vertex_labels = F, + + layout = l, title = .... [TRUNCATED] + + When sourcing ‘HCP_analysis.R’: + Error: Length of new attribute value must be 1 or 176, the number of target vertices, not 174 + Execution halted + + ‘HCP_analysis.Rmd’ using ‘UTF-8’... failed + ‘ML_and_Inference.Rmd’ using ‘UTF-8’... OK + ‘Speed.Rmd’ using ‘UTF-8’... OK + ‘comparing_calcs.Rmd’ using ‘UTF-8’... OK + ‘personalized_analyses.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘HCP_analysis.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.9Mb + sub-directories of 1Mb or more: + doc 7.5Mb + libs 4.9Mb + ``` + +# textrank + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/bnosac/textrank +* Source code: https://github.com/cran/textrank +* Date/Publication: 2020-10-12 11:50:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "textrank")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘textrank-Ex.R’ failed + The error most likely occurred in: + + > ### Name: textrank_sentences + > ### Title: Textrank - extract relevant sentences + > ### Aliases: textrank_sentences + > + > ### ** Examples + > + > ## Don't show: + > if(require(udpipe)) { + + ## End(Don't show) + + library(udpipe) + + data(joboffer) + + head(joboffer) + + joboffer$textrank_id <- unique_identifier(joboffer, c("doc_id", "paragraph_id", "sentence_id")) + + sentences <- unique(joboffer[, c("textrank_id", "sentence")]) + + cat(sentences$sentence) + + terminology <- subset(joboffer, upos %in% c("NOUN", "ADJ"), select = c("textrank_id", "lemma")) + + head(terminology) + + + + ## Textrank for finding the most relevant sentences + + tr <- textrank_sentences(data = sentences, terminology = terminology) + + summary(tr, n = 2) + + summary(tr, n = 5, keep.sentence.order = TRUE) + + + + ## Not run: + + ##D ## Using minhash to reduce sentence combinations - relevant if you have a lot of sentences + + ##D library(textreuse) + + ##D minhash <- minhash_generator(n = 1000, seed = 123456789) + + ##D candidates <- textrank_candidates_lsh(x = terminology$lemma, sentence_id = terminology$textrank_id, + + ##D minhashFUN = minhash, bands = 500) + + ##D tr <- textrank_sentences(data = sentences, terminology = terminology, + + ##D textrank_candidates = candidates) + + ##D summary(tr, n = 2) + + ## End(Not run) + + ## You can also reduce the number of sentence combinations by sampling + + tr <- textrank_sentences(data = sentences, terminology = terminology, max = 100) + + tr + + summary(tr, n = 2) + + ## Don't show: + + } # End of main if statement running only if the required packages are installed + Loading required package: udpipe + Statistical expert / data scientist / analytical developer BNOSAC (Belgium Network of Open Source Analytical Consultants), is a Belgium consultancy company specialized in data analysis and statistical consultancy using open source tools. In order to increase and enhance the services provided to our clients, we are on the lookout for an all-round statistical expert, data scientist and analytical developer. Function: Your main task will be the execution of a diverse range of consultancy services in the field of statistics and data science. You will be involved in a small team where you handle the consultancy services from the start of the project until the end. This covers: Joint meeting with clients on the topic of the analysis. Acquaintance with the data. Analysis of the techniques that are required to execute the study. Mostly standard statistical and biostatistical modelling, predictive analytics & machine learning techniques. Perform statistical design, modeling and analysis, together with more seniors. Building the report on the data analysis. Automating and R/Python package development. Integration of the models into the existing architecture. Giving advise to the client on the research questions, design or integration. Next to that, you will help in building data products and help sell them. These cover text mining, integration of predictive analytics in existing tools and the creation of specific data analysis tools and web services. You also might be involved in providing data science related courses for clients. Profile: You have a master degree in the domain of Statistics, Biostatistics, Mathematics, Commercial or Industrial Engineering, Economics or similar. You have a strong interest in statistics and data analysis. You have good communication skills, are fluent in English and know either Dutch or French. You soak up new knowledge and either just make things work or have the attitude of 'I can do this'. Besides this, you have attention to detail and adapt to changes quickly. You have programming experience in R or you really want to switch to using R. You have a sound knowledge of another data analysis language (Python, SQL, javascript) and you don't care in which relational database, Excel, bigdata or noSQL store your data is located. Interested in robotics is a plus. Offer: A half or full-time employment depending on your personal situation. The ability to get involved in a whole range of sectors and topics and the flexibility to shape your own future. The usage of a diverse range of statistical & data science techniques. Support in getting up to speed quickly in the usage of R. An environment in which you can develop your talent and make your own proposals the standard way to go. Liberty in managing your open source projects during working hours. Contact: To apply or in order to get more information about the job content, please contact us at: http://bnosac.be/index.php/contact/get-in-touchError in data.frame(textrank_id = names(pr$vector), textrank = as.numeric(pr$vector), : + arguments imply differing number of rows: 0, 37 + Calls: textrank_sentences ... merge.data.frame -> nrow -> as.data.frame -> data.frame + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘textrank.Rmd’ + ... + 4 1 data + 5 1 scientist + 7 1 analytical + 8 1 developer + + > tr <- textrank_sentences(data = sentences, terminology = terminology) + + When sourcing ‘textrank.R’: + Error: arguments imply differing number of rows: 0, 37 + Execution halted + + ‘textrank.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘textrank.Rmd’ using rmarkdown + + Quitting from lines at lines 116-121 [unnamed-chunk-7] (textrank.Rmd) + Error: processing vignette 'textrank.Rmd' failed with diagnostics: + arguments imply differing number of rows: 0, 37 + --- failed re-building ‘textrank.Rmd’ + + SUMMARY: processing the following file failed: + ‘textrank.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# tidygraph + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/thomasp85/tidygraph +* Source code: https://github.com/cran/tidygraph +* Date/Publication: 2024-01-30 13:40:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "tidygraph")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + > + > library(testthat) + > library(tidygraph) + + Attaching package: 'tidygraph' + + The following object is masked from 'package:testthat': + + matches + + The following object is masked from 'package:stats': + + filter + + > + > test_check("tidygraph") + Ungrouping `.data`... + Splitting by nodes + Unfocusing graph... + `focus()` selected all nodes. Returning unfocused graph + `focus()` didn't select any nodes. Returning unfocused graph + Unfocusing graph... + Unfocusing prior to grouping + Unfocusing prior to morphing + Unfocusing graph... + Joining with `by = join_by(from, to)` + Joining with `by = join_by(from, to)` + Joining with `by = join_by(from, to)` + Joining with `by = join_by(from, to)` + Joining with `by = join_by(from, to)` + Joining with `by = join_by(from, to)` + Ungrouping `.data`... + Subsetting by nodes + Splitting by nodes + Unfocusing prior to morphing + [ FAIL 13 | WARN 2 | SKIP 1 | PASS 426 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + • On CRAN (1): 'test-random-walk.R:19:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-graph_measures.R:17:3'): graph measures returns scalars ──────── + Error in `radius_dijkstra_impl(graph, weights = weights, mode = mode)`: At vendor/cigraph/src/paths/distances.c:328 : Weight vector length (1) does not match number of edges (8). Invalid value + Backtrace: + ▆ + 1. ├─testthat::expect_length(graph_radius(), 1) at test-graph_measures.R:17:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─tidygraph::graph_radius() + 5. └─igraph::radius(graph, mode) + 6. └─igraph:::radius_dijkstra_impl(graph, weights = weights, mode = mode) + ── Failure ('test-graph_measures.R:32:1'): graph context is empty after test ─── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-group.R:92:1'): graph context is empty after test ──────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-group_by.R:15:1'): graph context is empty after test ───────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-local.R:37:1'): graph context is empty after test ──────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-morph.R:135:1'): graph context is empty after test ─────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-mutate.R:15:1'): graph context is empty after test ─────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-node_measures.R:78:1'): graph context is empty after test ──── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-node_types.R:58:1'): graph context is empty after test ─────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-pair_measures.R:58:1'): graph context is empty after test ──── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-search.R:58:1'): graph context is empty after test ─────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-slice.R:27:1'): graph context is empty after test ──────────── + environment(.graph_context$free)$private$context has length 1, not length 0. + ── Failure ('test-tidyr-utils.R:18:1'): graph context is empty after test ────── + environment(.graph_context$free)$private$context has length 1, not length 0. + + [ FAIL 13 | WARN 2 | SKIP 1 | PASS 426 ] + Error: Test failures + Execution halted + ``` + +# timeordered + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/timeordered +* Date/Publication: 2023-08-20 22:20:02 UTC +* Number of recursive dependencies: 12 + +Run `revdepcheck::cloud_details(, "timeordered")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘timeordered-Ex.R’ failed + The error most likely occurred in: + + > ### Name: applynetworkfunction + > ### Title: Applies a function (typically a descriptive statistic) to + > ### multiple time-aggregated networks + > ### Aliases: applynetworkfunction + > + > ### ** Examples + > + > data(ants) + > allindivs <- c(union(ants$VertexFrom, ants$VertexTo), "NULL1", "NULL2") + > g <- generatetonetwork(ants, allindivs) + > td100 <- generatetimedeltas(0,1500,100) + > ns100 <- generatenetworkslices(g, td100) + Error in data.frame(..., check.names = FALSE) : + arguments imply differing number of rows: 20, 91 + Calls: generatenetworkslices ... graph_from_data_frame -> cbind -> cbind -> data.frame + Execution halted + ``` + +# wikkitidy + +
+ +* Version: 0.1.12 +* GitHub: https://github.com/wikihistories/wikkitidy +* Source code: https://github.com/cran/wikkitidy +* Date/Publication: 2024-02-09 08:00:03 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "wikkitidy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘wikkitidy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: query_category_members + > ### Title: Explore Wikipedia's category system + > ### Aliases: query_category_members build_category_tree + > + > ### ** Examples + > + > # Get the first 10 pages in 'Category:Physics' on English Wikipedia + > physics_members <- wiki_action_request() %>% + + query_category_members("Physics") %>% next_batch() + > physics_members + + ℹ There are more results on the server. Retrieve them with `next_batch()` or `retrieve_all()` + ✔ Data complete for all records + # A tibble: 10 × 3 + pageid ns title + + 1 6019 0 Computational chemistry + 2 22939 0 Physics + 3 1653925 100 Portal:Physics + 4 14647723 0 Disclination + 5 74985603 0 Edge states + 6 75395346 0 Dynamic toroidal dipole + 7 75558170 0 Charge based boundary element fast multipole method + 8 75702882 1 Talk:Dynamic toroidal dipole + 9 76067366 0 Fiveling + 10 76122969 0 Action principles + > + > + > # Build the tree of all albums for the Melbourne band Custard + > tree <- build_category_tree("Category:Custard_(band)_albums") + ⠙ Walking subcategories: 1 done (458/s) | 3ms + ⠹ Walking subcategories: 2 done (20/s) | 98ms + > tree + $nodes + # A tibble: 11 × 4 + pageid ns title type + + 1 41181643 14 Category:Custard_(band)_albums root + 2 47888836 0 Come Back, All Is Forgiven page + 3 59271122 0 The Common Touch (album) page + 4 30333352 0 Loverama page + 5 63691299 0 Respect All Lifeforms page + 6 43770191 0 Wahooti Fandango page + 7 30333401 0 We Have the Technology page + 8 43769837 0 Wisenheimer page + 9 41148700 14 Category:Custard (band) compilation albums subcat + 10 43770688 0 Brisbane 1990–1993 page + 11 43770872 0 Goodbye Cruel World (Custard album) page + + $edges + # A tibble: 10 × 3 + source target timestamp + + 1 41181643 47888836 2015-09-21T10:58:43Z + 2 41181643 59271122 2019-01-06T17:20:32Z + 3 41181643 30333352 2013-11-24T21:09:05Z + 4 41181643 63691299 2020-04-18T06:08:40Z + 5 41181643 43770191 2014-09-08T08:02:46Z + 6 41181643 30333401 2013-11-24T21:09:09Z + 7 41181643 43769837 2014-09-08T06:31:49Z + 8 41181643 41148700 2013-11-21T14:38:43Z + 9 41148700 43770688 2015-05-20T06:12:07Z + 10 41148700 43770872 2015-04-26T23:42:41Z + + > + > # For network analysis and visualisation, you can pass the category tree + > # to igraph + > tree_graph <- igraph::graph_from_data_frame(tree$edges, vertices = tree$nodes) + Warning: Unknown or uninitialised column: `name`. + Error in i_set_vertex_attr(graph = graph, name = name, index = index, : + Length of new attribute value must be 1 or 63691299, the number of target vertices, not 11 + Calls: ... add_vertices -> set_vertex_attr -> i_set_vertex_attr + Execution halted + ``` +