cannot able to install DirichletMultinomial

[emanuelavilla]

Hello!

I am trying to install DirichletMultinomial via BiocManager::install("DirichletMultinomial"). However, I got this error and I do not know how to solve it.

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://p3m.dev/cran/__linux__/noble/latest
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.3 (2025-02-28)
Installing package(s) 'DirichletMultinomial'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/DirichletMultinomial_1.48.0.tar.gz'
Content type 'application/x-gzip' length 1112440 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘DirichletMultinomial’ ...
** package ‘DirichletMultinomial’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
/bin/bash: line 1: gsl-config: command not found
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dirichlet_fit.c -o dirichlet_fit.o
/bin/bash: line 1: gsl-config: command not found
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dirichlet_fit_main.c -o dirichlet_fit_main.o
/bin/bash: line 1: gsl-config: command not found
dirichlet_fit_main.c:1:10: fatal error: gsl/gsl_rng.h: No such file or directory
    1 | #include <gsl/gsl_rng.h>
      |          ^~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:195: dirichlet_fit_main.o] Error 1
ERROR: compilation failed for package ‘DirichletMultinomial’
* removing ‘/hpcnfs/scratch/SM/RstudioServer/4.2_seurat5.2/home/ieo5690/Rstudio-4.2_seurat5.2-lib/DirichletMultinomial’
Warning in install.packages(...) :
  installation of package ‘DirichletMultinomial’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpjtbkTm/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
    MASS

Thanks!

[mtmorgan]

As mentioned in the DESCRIPTION file, there is a system dependency on 'gsl', the GNU Scientific Library. You'll have to install this use the package manager of your operating system, or perhaps a docker or singularity container, e.g., from Bioconductor.