Unable to update to version 2.0

[gherrarte]

I have been trying to upgrade Igraph to its newest version, but I get this message:
ERROR: compilation failed for package ‘igraph’

Now all other libraries that have Igraph as a dependency are not working either. For example, tidygraph and Networkd3 are broken. I have tried to compile from source and I get the same result.

I have tried to upgrade using Fedora 39 and also Debian Bookworm with the same results. Any ideas?

[ntamas]

Please provide the full compilation log - there should be a bunch of compilation messages above ERROR: compilation failed for package ‘igraph’ that contain the root cause. The package compiles just fine on CRAN so the cause is most likely something with your local environment.

[rfsaldanha]

Hi! I'm having a problem to compile the package as well.

Session info

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Europe/Paris
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5        doParallel_1.0.17  cli_3.6.2         
 [4] rlang_1.1.3        DBI_1.2.1          KernSmooth_2.23-22
 [7] generics_0.1.3     sf_1.0-15          data.table_1.15.0 
[10] glue_1.7.0         e1071_1.7-14       geobr_1.8.2       
[13] fansi_1.0.6        grid_4.3.2         classInt_0.4-10   
[16] tibble_3.2.1       foreach_1.5.2      lifecycle_1.0.4   
[19] compiler_4.3.2     codetools_0.2-19   dplyr_1.1.4       
[22] Rcpp_1.0.12        pkgconfig_2.0.3    rstudioapi_0.15.0 
[25] R6_2.5.1           class_7.3-22       tidyselect_1.2.0  
[28] utf8_1.2.4         parallel_4.3.2     pillar_1.9.0      
[31] curl_5.2.0         magrittr_2.0.3     tools_4.3.2       
[34] proxy_0.4-27       iterators_1.0.14   units_0.8-5   

Error

Start of compiling

Installing package into ‘/home/raphael/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/igraph_2.0.1.1.tar.gz'
Content type 'application/x-gzip' length 4956775 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
libxml2 include directory: /usr/include/libxml2
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

During compilation, the following error is presented.

In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
   39 | #include <glpk.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:191: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/home/raphael/R/x86_64-pc-linux-gnu-library/4.3/igraph’
* restoring previous ‘/home/raphael/R/x86_64-pc-linux-gnu-library/4.3/igraph’
Warning in install.packages :
  installation of package ‘igraph’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp2NqKFL/downloaded_packages’

[szhorvat]

This is covered in the troubleshooting instructions: https://r.igraph.org/articles/installation-troubleshooting.html#cannot-compile-igraph-from-sources-on-linux You need to install GLPK before compiling. We'll add Fedora-specific instructions as well (I think it's yum install glpk-devel).

In the future, please use the forum for support. We would like to reserve the issue tracker for bug reports and feature requests.

[gherrarte]

Please provide the full compilation log - there should be a bunch of compilation messages above ERROR: compilation failed for package ‘igraph’ that contain the root cause. The package compiles just fine on CRAN so the cause is most likely something with your local environment.

R version 4.3.2 (2023-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora Linux 39 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP; LAPACK version 3.11.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Guatemala
tzcode source: system (glibc)

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

other attached packages:
[1] sessioninfo_1.2.2

loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.3.2 promises_1.2.1 Rcpp_1.0.12 stringr_1.5.1
[6] callr_3.7.3 later_1.3.2 fastmap_1.1.1 mime_0.12 R6_2.5.1
[11] curl_5.2.0 htmlwidgets_1.6.4 desc_1.4.3 profvis_0.3.8 shiny_1.8.0
[16] rlang_1.1.3 cachem_1.0.8 stringi_1.8.3 httpuv_1.6.14 fs_1.6.3
[21] pkgload_1.3.4 memoise_2.0.1 cli_3.6.2 magrittr_2.0.3 ps_1.7.6
[26] digest_0.6.34 processx_3.8.3 rstudioapi_0.15.0 xtable_1.8-4 remotes_2.4.2.1
[31] devtools_2.4.5 lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0 urlchecker_1.0.1
[36] pkgbuild_1.4.3 purrr_1.0.2 pkgconfig_2.0.3 tools_4.3.2 usethis_2.2.2
[41] ellipsis_0.3.2 htmltools_0.5.7

Error:

vendor/cigraph/src/io/graphml.c:46:10: fatal error: libxml/globals.h: No such file or directory
46 | #include <libxml/globals.h>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:191: vendor/cigraph/src/io/graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’

• removing ‘/home/gherrarte/R/x86_64-redhat-linux-gnu-library/4.3/igraph’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpqB26Bs/file134b1c9b311d/igraph_2.0.1.9001.tar.gz’ had non-zero exit status

[gherrarte]

I have reinstall glpk-devel gmp-devel libxml2-devel. I have also reinstall gcc gcc-c++ gcc-gfortran and the same issue persist.

[szhorvat]

FWIW I tested this with a Fedora 40 Docker image earlier, and compilation succeeded. What specific Fedora version do you have and where did you obtain R? (I used yum install R.) Did you restart R after installing the required packages?

[szhorvat]

Never mind, I see the versions in the build log above.

[szhorvat]

I just tested it on Fedora 39, and did not see problems. Are we doing something differently @gherrarte ?

I used Fedora in Docker:

docker run -it fedora:39 bash

Installed all necessary packages:

yum install gcc gcc-c++ gcc-gfortran glpk-devel gmp-devel libxml2-devel R

Then I started R and used install.packages('igraph').

Compilation succeeded and the library works.

[gherrarte]

Hi Szhorvat, I was able to run the installation, following your instructions, in Debian Bookworm and was succesful. But, for Fedora 39 the issue persist. I will look into libxml2 to see if I have something wrong set up for my own environment. I will let you know.

[szhorvat]

@gherrarte Do you use Anaconda? If yes, be sure to deactivate all conda environments before compiling igraph. Can you upload the complete build log somewhere and link to it?

[gherrarte]

@szhorvat Ok. I will try this solution. Yes. I also use Anaconda.

[szhorvat]

So, to be clear, run conda deactivate before starting R, use R from the command line, and try again. Let us know if it worked.