CODEWITHSUNDEEP
rcompilation
H C
H C

Reputation: 17

Stuck in ERROR: compilation failed for package ‘XXXXX’

I am trying to install Arch R on my newly upgraded Debian 10 PC (my R version is 4.1.0). It stucks at installing support package "DirichletMultinomial".

dirichlet_fit_main.c: In function ‘optimise_lambda_k’: dirichlet_fit_main.c:221:9: error: ‘gsl_multimin_fdfminimizer_vector_bfgs2’ undeclared (first use in this function); did you mean ‘gsl_multimin_fdfminimizer_vector_bfgs’? T = gsl_multimin_fdfminimizer_vector_bfgs2; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gsl_multimin_fdfminimizer_vector_bfgs dirichlet_fit_main.c:221:9: note: each undeclared identifier is reported only once for each function it appears in make: *** [/usr/lib/R/etc/Makeconf:168: dirichlet_fit_main.o] Error 1 ERROR: compilation failed for package ‘DirichletMultinomial’

Does anyone have similar problem?

Upvotes: 1

Views: 435

Answers (1)

Daniel Yamamoto
Daniel Yamamoto

Reputation: 11

I was running into a very similar issue when installing ArchR on R 4.1.0. It seems like your issue might relate to the version of GSL that you have installed. The current stable version is version 2.7, and I re-installed it using the following code in terminal:

mkdir downloads
cd downloads/
wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.7.tar.gz
tar -vxf gsl-2.7.tar.gz
cd gsl-2.7
./configure
make
sudo make install

I then re-ran and ArchR installed successfully.

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

Upvotes: 1

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