`gsl` not found on Windows build

[matteodelucchi]

I suggest that there is another issue that is related to the environmental variable that specifies GSL on Windows. Because the Cygwin GSL flags are:

Run cygcheck -cd |grep gsl
  cygcheck -cd |grep gsl
  cygcheck -c libgsl-devel
  cygcheck -l libgsl-devel
  echo "-------------\n"
  echo "$GITHUB_CONTEXT"
  echo "-------------\n"
  echo "GSL DLLs in Cygwin:"
  Get-ChildItem "C:\cygwin64\bin\cyggsl*" -ErrorAction SilentlyContinue
  echo "GSL include directory:"
  Get-ChildItem "C:\cygwin64\usr\include\gsl" -ErrorAction SilentlyContinue
  echo "GSL lib directory:"
  Get-ChildItem "C:\cygwin64\lib\libgsl*" -ErrorAction SilentlyContinue
  echo "LIB_GSL:"
  echo $env:LIB_GSL
  shell: C:\Program Files\PowerShell\7\pwsh.EXE -command ". '{0}'"
  env:
    BUILD_LOC: ./build
    BRANCH: 187-issue-with-ragg-within-the-installation-workflow-for-windows
    JAGS_MAJORV: 4
    JAGS_VERSION: 4.3.1
    JAGS_URL: https://sourceforge.net/projects/mcmc-jags/files/JAGS
    GITHUB_PAT: ***
    R_KEEP_PKG_SOURCE: yes
  
Cygwin Package Information
No setup information found
No setup information found
-------------\n
-------------\n
GSL DLLs in Cygwin:
    Directory: C:\cygwin64\bin
Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a---           3/[2](https://github.com/furrer-lab/abn/actions/runs/15319433652/job/43099673319?pr=189#step:4:2)4/2017  4:47 PM        2275[3](https://github.com/furrer-lab/abn/actions/runs/15319433652/job/43099673319?pr=189#step:4:3)47 cyggsl-19.dll
GSL include directory:
GSL lib directory:
LIB_GSL:

The LIB_GSL, which is crucial for the Makevars.win, seems empty; therefore, the gsl headers can't be found when installing abn. I wonder if all the other successfully installed packages don't use gsl, if the LIB_GSL is indeed not set correctly, or if abn only doesn't find the flags.
Solutions that come to my mind:

1. Compile gsl on Windows
2. Set the flags correctly so they are found by gsl-config.
3. Check if any other successfully installed packages use gsl and check how they specify the flags.

Originally posted by @matteodelucchi in #189 (comment)

[matteodelucchi]

The WinBuilder checks are passed with notes that are unrelated to this GSL issue, so this issue is postponed in favor of pushing a new CRAN release.

winbuilder 00check.log:

* using log directory 'd:/RCompile/CRANguest/R-release/abn.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'abn/DESCRIPTION' ... OK
* this is package 'abn' version '3.1.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [14s] WARNING
Maintainer: 'Matteo Delucchi <matteo.delucchi@math.uzh.ch>'

FOSS licence with BuildVignettes: false

CRAN repository db overrides:
  Additional_repositories: https://inla.r-inla-download.org/R/stable/

Suggests or Enhances not in mainstream repositories:
  INLA
Availability using Additional_repositories specification:
  INLA   yes   https://inla.r-inla-download.org/R/stable/

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: http://www.sciencedirect.com/science/journal/01675877/110/1
    From: README.md
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/aje/article-abstract/176/11/1051/178588
    From: README.md
    Status: 403
    Message: Forbidden
  URL: https://cran.r-project.org/web/packages/rjags/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812 (moved to https://joss.theoj.org/papers/10.21105/joss.06822)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://www.sciencedirect.com/science/article/pii/S0010482522005133
    From: README.md
    Status: 403
    Message: Forbidden
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
Please use DOIs for the following publisher URLs:
  https://academic.oup.com/aje/article-abstract/176/11/1051/178588
  https://www.sciencedirect.com/science/article/pii/S0010482522005133

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'abn' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'codecov.yml'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ... [21s] NOTE
createAbnDag: no visible global function definition for
  'validate_abnDag'
Undefined global functions or variables:
  validate_abnDag
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 shell scripts ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... NOTE
  src/Makevars.in: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.in: it is not portable to include multiple SHLIB_OPENMP_*' macros in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
Extensions'. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'archive/abn_v2_2.Rmd' 'benchmarkBoxPlot-1.png' 'data_simulation.Rmd'
  'fit_model-1.png' 'mixed_effect_BN_model.Rmd'
  'model_specification.Rmd' 'multiprocessing.Rmd' 'paper.bib'
  'paper.md' 'parameter_learning.Rmd' 'precompile.R'
  'quick_start_example.Rmd' 'structure_learning.Rmd'
  'unnamed-chunk-3-1.png' 'unnamed-chunk-6-1.png'
  'vignettes_bibliography.bib'
* checking examples ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [55s] OK
  Running 'testthat.R' [55s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  'data_simulation.Rmd'
  'mixed_effect_BN_model.Rmd'
  'model_specification.Rmd'
  'multiprocessing.Rmd'
  'parameter_learning.Rmd'
  'quick_start_example.Rmd'
  'structure_learning.Rmd'
* checking running R code from vignettes ... [81s] OK
  'data_simulation.Rmd' using 'UTF-8'... OK
  'mixed_effect_BN_model.Rmd' using 'UTF-8'... [23s] OK
  'model_specification.Rmd' using 'UTF-8'... [22s] OK
  'multiprocessing.Rmd' using 'UTF-8'... OK
  'parameter_learning.Rmd' using 'UTF-8'... OK
  'quick_start_example.Rmd' using 'UTF-8'... [34s] OK
  'structure_learning.Rmd' using 'UTF-8'... OK
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [16s] OK
* DONE
Status: 3 WARNINGs, 3 NOTEs

[matteodelucchi]

Interestingly, in Makevars.in the environment variable for GSL is called GSL_LIBS but in Makevars.win it's named LIB_GSL. The latter wasn't found, but maybe the former?

[matteodelucchi]

Interestingly, in Makevars.in the environment variable for GSL is called GSL_LIBS but in Makevars.win it's named LIB_GSL. The latter wasn't found, but maybe the former?

It doesn't find any of them:

GSL DLLs in Cygwin:

    Directory: C:\cygwin64\bin

Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a---           3/24/2017  4:47 PM        2275[34](https://github.com/furrer-lab/abn/actions/runs/15322026978/job/43107725163#step:4:35)7 cyggsl-19.dll
GSL include directory:
GSL lib directory:
LIB_GSL:

GSL_LIBS:

And having GSL_LIBS in Makevars.in and LIB_GSL in Makevars.win seems to be correct as it is the same for the R package gsl (see here).

I suspect an issue with the gsl installation...