Installation fails with "inaccessible plugin" annobin.so

[Richard Schoonhoven]

Dear IRace team,

Thank you for taking the time to read my email. I'm a PhD student and I want to include IRace as a benchmark. I have tried installing the package in multiple ways. The standard install.packages("irace") in R fails with an error (see bottom of email). It references an inaccessible plugin annobin.so. I'm using Fedora 32 and gcc 8.3.0 for this. I also tried gcc 7.3.0 but this did not help. Annobin is installed since "locate annobin.so" gives:

/usr/lib/gcc/x86_64-redhat-linux/10/plugin/annobin.so
/usr/lib/gcc/x86_64-redhat-linux/10/plugin/annobin.so.0
/usr/lib/gcc/x86_64-redhat-linux/10/plugin/annobin.so.0.0.0

Going off the recommendation of the README I tried a manual installation, i.e., creating an R directory and downloading irace_3.4.1.tar.gz etc.. However, this gives the same error when I execute "R CMD INSTALL --library=~/R irace.tar.gz".

There is a similar issue on stack overflow, but it has no respsones:

https://stackoverflow.com/questions/70556776/failing-with-installig-tidyverse-of-fedora-35-annobin-problem

Can you help me? Does it look for annobin.so in the wrong location and is this something I can edit?

Kind regards,

Richard Schoonhoven (CWI)

Installation error:

gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c iracebin/irace.c -o iracebin/irace.o
cc1: fatal error: inaccessible plugin file /opt/sw/gcc-8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0/plugin/annobin.so expanded from short plugin name annobin: No such file or directory
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:172: iracebin/irace.o] Error 1
ERROR: compilation failed for package ‘irace’

[Manuel López-Ibáñez]

Hi Richard,

I'm afraid I cannot help much with this. It seems this is a Fedora issue that many people are suffering with all kinds of software packages: https://stackoverflow.com/questions/61072735/cannot-install-rails-6-due-to-annobin

Irace does not require annobin (it doesn't use it for anything), so there is nothing we can change in irace to avoid this problem. This is a problem in either some Fedora setup configuration or some broken package.

Note that CRAN automatically detects when something breaks with various Linux distros: https://cran.r-project.org/web/checks/check_results_irace.html  and they specifically test Fedora 32 (with gcc and clang): https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-gcc

so it seems something is broken in your particular installation.

Could you try with Ubuntu or another version of Fedora?

If you manage to fix it, could you let us know how in case others have a similar problem?

Cheers,

Manuel.

[Richard Schoonhoven]

Dear Manuel,

Thank you for your time and for looking at my problem. It turns out that the problem was that I was using an older gcc version which did not have annobin.so in this case. When changing to gcc 10.2 (which did have annobin.so) the problem was resolved. Again, thank you for taking the time to reply.

Kind regards,

Richard

[Nicole Adams]

Hi Richard, Can you explain how you used the new gcc version to install the package? I'm working on a cluster and am having a similar problem. I tried the following and I still get the same annobin.so error.

module load gcc/10.2.0

R

install.packages("gam")

install.packages("gam", configure.args="gcc/10.2.0")

f951: Fatal Error: inaccessible plugin file /jet/packages/spack/opt/spack/linux-centos8-zen/gcc-8.3.1/gcc-10.2.0-tfzxq7udz2a53dmujvasy4uz33t27iwv/lib/gcc/x86_64-pc-linux-gnu/10.2.0/plugin/annobin.so expanded from short plugin name annobin: No such file or directory

compilation terminated.