SMT
why did i think that i just needed need a couple of #defines in order to use the #RStats Matrix package's #cholmod headers https://github.com/cran/Matrix/blob/master/inst/include/Matrix/cholmod.h (and Matrix.so) to compile the bcftools PGS plugin https://github.com/freeseek/score/blob/master/pgs.c ? It worked on gcc, but clang (with defaults) was much less forgiving :D
#RStats gurus : is their a #RStats package that just provides cholmod and nothing else ?
Matrix/inst/include/Matrix/cholmod.h at master · cran/Matrix

:exclamation: This is a read-only mirror of the CRAN R package repository. Matrix — Sparse and Dense Matrix Classes and Methods. Homepage: https://Matrix.R-forge.R-project.org Report bugs for thi...

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Sep 6 at 12:26pmWeb
Show threadMikael JaganSep 7
@bioinfhotep Are you not able to install SuiteSparse on your system?
Show threadSMTSep 7

@jaganmn I can, but I am making a package that bundles bcftools and the relevant gwas plugins for mostly format uniformization reasons and ETL.
But note that finding the headers reliably on my local setup is already non trivial, let alone CI machines or the final target systems the package should run on. I think I will copy the Matrix scripts and remove the patches bit and vendor SuiteSparse

WIP package here https://github.com/sounkou-bioinfo/RBCFLib

GitHub - sounkou-bioinfo/RBCFLib: `htslib` And `bcftools` Libraries And Command Line Tools Wrapper

`htslib` And `bcftools` Libraries And Command Line Tools Wrapper - sounkou-bioinfo/RBCFLib

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Show threadMikael JaganSep 7
@bioinfhotep Can you point me to the version of the sources that used 'LinkingTo: Matrix'? And also share your installation output (gcc and clang separately)? Since several other packages cope with 'LinkingTo: Matrix', my guess is that we can get it to work for you.
Show threadSMTSep 7

@jaganmn i used linking to Matrix to build a plugin that uses cholmod https://github.com/freeseek/score (this is a c shared library, not used at R binding level at all), it worked fine with gcc with warnings, but did not work on clang (exceed the number of allowed warnings)

r-universe build:
https://github.com/r-universe/sounkou-bioinfo/actions/runs/17450421937

the plugin using cholmod in the vendored directory : https://github.com/sounkou-bioinfo/RBCFLib/blob/593cfaafee6b268ace91b81aa899a0007da94be5/src/bcftools-1.22/plugins/pgs.c ,

the commit: https://github.com/sounkou-bioinfo/RBCFLib/tree/593cfaafee6b268ace91b81aa899a0007da94be5

GitHub - freeseek/score: Tools to work with GWAS-VCF summary statistics files

Tools to work with GWAS-VCF summary statistics files - freeseek/score

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Show threadSMTSep 7
@jaganmn i guess i can make a Matrix cholmod compatible version of the plugin, but this is a plugin of a c library that is "exec"'ed
I don t want that "wrapper" code to touch the R API outside of this layer https://github.com/sounkou-bioinfo/RBCFLib/blob/main/src/RC_PIPE.c since i am launching lot of forks and the underlying library and R are not thread safe
RBCFLib/src/RC_PIPE.c at main · sounkou-bioinfo/RBCFLib

`htslib` And `bcftools` Libraries And Command Line Tools Wrapper - sounkou-bioinfo/RBCFLib

GitHub