Unable to install "DESeq2"(annobin.so : No such file or directory)

Question

[nakane_clan]

I have R(version 4.1.2) installed on Fedora35.

When I tried to install "DESeq2", I got the following warning.

1: .inet_warning(msg) : installation of package ‘genefilter’ had non-zero exit status

2: .inet_warning(msg) : installation of package ‘locfit’ had non-zero exit status

3: .inet_warning(msg) : installation of package ‘DESeq2’ had non-zero exit status

So, I checked the "genefilter" and "locfit" processing, and found the following.

cc1: fatal error: inaccessible plugin file/home/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/11.2.0/plugin/annobin.so expanded from short plugin name annobin: No such file or directory

compilation terminated.

make: *** [/usr/lib64/R/etc/Makeconf:168: init.o] error 1

ERROR: compilation failed for package ‘genefilter’

After much research, I found and implemented the following solution.

conda remove R

Then I tried to install "DESeq2" again, but it did not work.

Fatal Error: inaccessible plugin file /home/linuxbrew/.linuxbrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/x86_64-pc-linux-gnu/11/plugin/annobin.so expanded from short plugin name annobin: No such file or directory

compilation terminated.

make: *** [/usr/lib64/R/etc/Makeconf:191: ttest.o] error 1

ERROR: compilation failed for package ‘genefilter’

I installed R with brew before and had various problems, so I reinstalled R with dnf and uninstalled R with brew, but for some reason it seems to be using the brew path.

I don't even know how to use this site, including how to break lines. Is there a page describing how to use it?

If anyone has a solution to this problem, please let me know. Please do.

Answer 1

[Istvan Albert]

I noted how you have both conda and homebrew co-mingling.

Clean up your system, uninstall both, remove all traces then try again, but this time try to not install the same software with competing libraries.

Answer 2

[andrespara]

I am having the same issue with Fedora 36, I used a workaround brew remove --ignore-dependencies gcc , installing the needed packages and then reinstalling brew install gcc back again. It doesn't make much sense but I couldn't compile R in Fedora 36, I just installed it via sudo dnf install R .

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