igraph failing to compile due to missing libgfortran.so.4 (Arch based Linux)

[OscarSouth]

A broken dependency for igraph is preventing me from installing many R libraries which depend on igraph.

I attempted to install with install.packages() and with devtools, both failed in same manner:

** testing if installed package can be loaded
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph/libs/igraph.so':
  libgfortran.so.4: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph’
Installation failed: Command failed (1)

libgfortran.so.5 is showing up here:

$ lddtree /usr/lib64/R/bin/exec/R
/usr/lib64/R/bin/exec/R (interpreter => /lib64/ld-linux-x86-64.so.2)
    libR.so => /usr/lib/R/lib/libR.so
        libblas.so.3 => /lib64/libblas.so.3
            libgfortran.so.5 => /lib64/libgfortran.so.5
                libquadmath.so.0 => /usr/lib/libquadmath.so.0
                libgcc_s.so.1 => /usr/lib/libgcc_s.so.1

R version 3.5.0 (2018-04-23)
gcc (GCC) 8.1.0

I've tried all the solutions I can find from Google. Is there any solution to this at present?

Thanks!

[OscarSouth]

Haven't had any luck solving this. Is it an issue with the igraph lib, or with R itself? (I've been able to install other packages successfully, however)

[OscarSouth]

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblas_sandybridgep-r0.2.20.so

locale:
 [1] LC_CTYPE=en_GB.utf8        LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.utf8     
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.utf8    
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> 

[alexperrone]

I thought this was included in gcc, but anyway did you try installing gfortran? sudo apt-get install gfortran

…

On Thu, May 24, 2018 at 7:08 AM, Oscar South ***@***.***> wrote: > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Manjaro Linux Matrix products: default BLAS/LAPACK: /usr/lib/libopenblas_sandybridgep-r0.2.20.so locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.5.0 > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#275 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEwlHNGxnSm0fIfPl1-jAXGRZmxDFoywks5t1pSsgaJpZM4UJMfH> .

[OscarSouth]

Thanks for the assistance.

I made sure that it’s installed on my system (as you say, it’s included with gcc, and I also double checked carefully).

I think that the issue is that gcc 8 bumped it up from libgfortran.so.4 to libgfortran.so.5 and igraph has a dependency on the former.

Since the newer dependency isn’t fulfilling the requirement and downgrading gcc isn’t exactly a good idea, I can’t see an easy solution.

I could be wrong about this, but from a few hours of unsuccessful troubleshooting, this is what it looks like to me.

Not sure if it’s something to fix on my end or a case of waiting for an igraph update that fixes the dependency.

[cramjaco]

I have essentially this same problem with ubuntu based linux 16.04. Can confirm that I have gfortran installed, as well as all of the dependencies for devtools, but when I run: devtools::install_github("igraph/rigraph") I also get the very similar error

> installing to /home/ohnoplus/R/i686-pc-linux-gnu-library/3.2/igraph/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>   unable to load shared object '/home/ohnoplus/R/i686-pc-linux-gnu-library/3.2/igraph/libs/igraph.so':
>   libgfortran.so.4: cannot open shared object file: No such file or directory
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/home/ohnoplus/R/i686-pc-linux-gnu-library/3.2/igraph’
> Installation failed: Command failed (1)

I also am unable to use igraph or install anything that depends on igraph in this case.

[ShotaOchi]

I had the same problem on Manjaro Linux.
The problem was resolved by installing gcc-fortran.
In other words, "igraph" was successfully installed after typing "pacman -S gcc-fortran".
I hope this information will help you.

[OscarSouth]

@ShotaOchi Thanks but in this case the issue is caused by a mismatched version dependency — gcc-fortran comes with libgfortran.so.5 while igraph requires the outdated libgfortran.so.4 which is not provided by the up to date gcc-fortran version.

[gaborcsardi]

while igraph requires the outdated libgfortran.so.4

no, it does not. igraph works with any version.

[gaborcsardi]

@OscarSouth I think you have a broken installation. Your R installation was built with libgfortran.so.5 and your igraph installation or package was built with libgfortran.so.4.

Did you compile igraph yourself? Then you need to re-install (=recompile) it from the source R package.

If you installed it from a binary package provided by your platform, then that package is broken, see if there is a new version of it, or install from the source R package.

[OscarSouth]

@gaborcsardi Thanks for the insight here. The discussion available through google search is a bit misleading on this issue if that is the case.

I installed R from repository using the pacman command and attempted to install igraph with the install.packages() tool inside R. Is this what you mean by the source R package, or should I attempt to install it by another method?

[gaborcsardi]

Yes, then you built from a source package, so I am not sure why it was broken. I would try to just re-install it.

You can use the --no-clean-on-error option, that keeps the installed package, even if you can't load it:

install.packages("igraph", INSTALL_opts = "--no-clean-on-error")

and then try to load it:

library(igraph)

If loading fails, check which libs the igraph shared lib links to:

ldd /home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph/libs/igraph.so

[OscarSouth]

Thanks for the assistance. This is the results of install.packages("igraph", INSTALL_opts = "--no-clean-on-error"):

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph/libs/igraph.so':
  libgfortran.so.4: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

The downloaded source packages are in
	‘/tmp/RtmpUFicvj/downloaded_packages’
Warning message:
In install.packages("igraph", INSTALL_opts = "--no-clean-on-error") :
  installation of package ‘igraph’ had non-zero exit status

This is the results of > library(igraph):

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph/libs/igraph.so':
  libgfortran.so.4: cannot open shared object file: No such file or directory

This is the results of ldd /home/oscarsouth/R/x86_64-pc-linux-gnu-library/3.5/igraph/libs/igraph.so:

	linux-vdso.so.1 (0x00007ffedbbea000)
	libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f030292f000)
	libgmp.so.10 => /usr/lib/libgmp.so.10 (0x00007f030269c000)
	libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007f0301737000)
	libgfortran.so.4 => not found
	libm.so.6 => /usr/lib/libm.so.6 (0x00007f03013a2000)
	libR.so => /usr/lib/R/lib/libR.so (0x00007f0300d1e000)
	libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f0300995000)
	libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f030077d000)
	libc.so.6 => /usr/lib/libc.so.6 (0x00007f03003c1000)
	libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f03001bd000)
	libicuuc.so.61 => /usr/lib/libicuuc.so.61 (0x00007f02ffe03000)
	libz.so.1 => /usr/lib/libz.so.1 (0x00007f02ffbec000)
	liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007f02ff9c6000)
	libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f02ff7a8000)
	libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007f02ff32e000)
	/usr/lib64/ld-linux-x86-64.so.2 (0x00007f03031da000)
	libreadline.so.7 => /usr/lib/libreadline.so.7 (0x00007f02ff0e1000)
	libpcre.so.1 => /usr/lib/libpcre.so.1 (0x00007f02fee6f000)
	libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007f02fec5f000)
	librt.so.1 => /usr/lib/librt.so.1 (0x00007f02fea57000)
	libicui18n.so.61 => /usr/lib/libicui18n.so.61 (0x00007f02fe5ac000)
	libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f02fe37e000)
	libicudata.so.61 => /usr/lib/libicudata.so.61 (0x00007f02fc7d9000)
	libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0 (0x00007f02fc598000)
	libncursesw.so.6 => /usr/lib/libncursesw.so.6 (0x00007f02fc32b000)

[gaborcsardi]

I think either you have an older gfortran on your system, or some other library links to libgfortran.so.4.