Failing to install epiCo in Ubuntu 22.04 LTR

[alejandrocs98]

Please place an "x" in all the boxes that apply

• I have the most recent version of linelist and R
• [ X] I have found a bug
• I have a reproducible example
• I want to request a new feature

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Please include a brief description of the problem with a code example:
I am trying to install epiCo on my PC with Ubuntu 22.04 LTR via conda but failed. I created a conda virtual environment specifically for installing the package and previous to the installation attempt I installed R (v4.2) and r-remotes (2.4.2) packages from the r anaconda channel. Then I opened an R session and run:

remotes::install_github("epiverse-trace/epiCo")

After a period loading I obtained the following error:

ERROR: dependency ‘raster’ is not available for package ‘leaflet’
* removing ‘/home/acs98/anaconda3/envs/epico/lib/R/library/leaflet’

The downloaded source packages are in
	‘/tmp/RtmpinhsiP/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Running `R CMD build`...
* checking for file ‘/tmp/RtmpinhsiP/remotes5a40353abc3f/epiverse-trace-epiCo-62dff7d/DESCRIPTION’ ... OK
* preparing ‘epiCo’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘epiCo_0.2.tar.gz’
ERROR: dependencies ‘spdep’, ‘leaflet’ are not available for package ‘epiCo’
* removing ‘/home/acs98/anaconda3/envs/epico/lib/R/library/epiCo’
Warning messages:
1: In i.p(...) : installation of package ‘terra’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘stringi’ had non-zero exit status
3: In i.p(...) : installation of package ‘units’ had non-zero exit status
4: In i.p(...) : installation of package ‘raster’ had non-zero exit status
5: In i.p(...) : installation of package ‘sf’ had non-zero exit status
6: In i.p(...) : installation of package ‘spdep’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘leaflet’ had non-zero exit status
8: In i.p(...) :
  installation of package ‘/tmp/RtmpinhsiP/file5a404ee4a0ef/epiCo_0.2.tar.gz’ had non-zero exit status

![Screenshot from 2023-10-18 14-56-59](https://github.com/epiverse-trace/epiCo/assets/87541159/2ff3e1d8-ab41-4de8-b2dc-cabf2e23d021)

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[Bisaloo]

Thanks a lot for your report!

epiCo requires some system libraries via its dependencies. From the error message you shared, it looks like some libraries were missing on your system. You can find what is needed, and how to install it, with pak::pkg_sysreqs("epiCo"):

pak::pkg_sysreqs("epiCo")
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#> 
#> ── Install scripts ───────────────────────────────────────────── Ubuntu 22.04 ──
#> apt-get -y update
#> apt-get -y install libcurl4-openssl-dev libssl-dev make libglpk-dev \
#>   libxml2-dev libjpeg-dev pandoc libpng-dev libgdal-dev gdal-bin libgeos-dev \
#>   libproj-dev libsqlite3-dev libicu-dev libfontconfig1-dev libfreetype6-dev \
#>   libudunits2-dev
#> 
#> ── Packages and their system dependencies ──────────────────────────────────────
#> curl        – libcurl4-openssl-dev, libssl-dev
#> fs          – make
#> igraph      – libglpk-dev, libxml2-dev
#> jpeg        – libjpeg-dev
#> knitr       – pandoc
#> png         – libpng-dev
#> rmarkdown   – pandoc
#> s2          – libssl-dev
#> sass        – make
#> sf          – gdal-bin, libgdal-dev, libgeos-dev, libproj-dev, libsqlite3-dev
#> stringi     – libicu-dev
#> systemfonts – libfontconfig1-dev, libfreetype6-dev
#> terra       – gdal-bin, libgdal-dev, libgeos-dev, libproj-dev, libsqlite3-dev
#> units       – libudunits2-dev
#> xml2        – libxml2-dev

^{Created on 2024-07-03 with reprex v2.1.0}