libRlapack.so: cannot open shared object file: No such file or directory

[danli349]

Hello

When I build rMATS by ./build_rmats --conda:

** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/lila/home/lid/R/x86_64-pc-linux-gnu-library/4.0/Matrix/libs/Matrix.so':
  libRlapack.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘mixtools’
* removing ‘/lila/home/lid/R/x86_64-pc-linux-gnu-library/4.0/mixtools’
* restoring previous ‘/lila/home/lid/R/x86_64-pc-linux-gnu-library/4.0/mixtools’

The downloaded source packages are in
        ‘/tmp/RtmpLY8Acf/downloaded_packages’
Loading required package: mixtools
Error: package or namespace load failed for ‘mixtools’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/lila/home/lid/R/x86_64-pc-linux-gnu-library/4.0/Matrix/libs/Matrix.so':
  libRlapack.so: cannot open shared object file: No such file or directory
Error: could not install mixtools
In addition: Warning message:
In install.packages(package$name, repos = repos) :
  installation of package ‘mixtools’ had non-zero exit status
Execution halted

The mixtools package is already installed:

> library(mixtools)
mixtools package, version 2.0.0, Released 2022-12-04
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).

Rscript -e 'sessionInfo()'

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /admin/opt/common/CentOS_7/R/R-4.2.0/lib64/R/lib/libRblas.so
LAPACK: /admin/opt/common/CentOS_7/R/R-4.2.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.2.0

How should I solve this problem?
Thanks

[EricKutschera]

./build_rmats --conda should create a conda environment in ./conda_envs/rmats where any R packages should get installed. Your output shows it trying to load a shared object from some other path: /lila/home/lid/R/x86_64-pc-linux-gnu-library/4.0/Matrix/libs/Matrix.so. For an install I did I found that file at ./conda_envs/rmats/lib/R/library/Matrix/libs/Matrix.so

Also ./build_rmats --conda should install the mixtools package from conda https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/darts_model_conda_requirements.txt#L5

But based on that output it looks like it may be installing it from CRAN because it didn't find mixtools here: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/install_r_deps.R#L41

Potentially R is looking in the wrong place for libraries due to environment variables (R_LIBS_SITE, R_LIBS_USER, R_LIBS) or config files (~/.Renviron, ~/.Rprofile): https://stackoverflow.com/questions/24387660/how-to-change-libpaths-permanently-in-r

[danli349]

@EricKutschera I removed my ~/.Rprofile file and this problem was resolved.
Thanks a lot