Question: Problems installing RBGL in R
1
gravatar for ngs06
9 months ago by
ngs0620
Sweden
ngs0620 wrote:

Hello,

I have updated my R software to 3.5.1. I am trying to install 'RBGL' package and had problems installing it.

Previously I was using R.3.4.4 and had no problems with 'RBGL ' installation

Can anyone help me in pointing out, what the error message corresponds to?

And here is gcc version details: gcc version 4.4.7 20120313 (Red Hat 4.4.7-23) (GCC)

BiocManager::install("RBGL", version = "3.8",lib.loc="/opt/R/lib")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'RBGL'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/RBGL_1.58.0.tar.gz'
Content type 'application/x-gzip' length 6475754 bytes (6.2 MB)
==================================================
downloaded 6.2 MB

* installing *source* package ‘RBGL’ ...
found  rbgl_trimmed_boost_1_61_0  header sources and tar archive;\n using what is there.
** libs
g++ -m64  -I"/usr/include/R" -DNDEBUG -Irbgl_trimmed_boost_1_61_0  -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bbc.cpp -o bbc.o
bbc.cpp: In function ‘SEXPREC* BGL_brandes_betweenness_centrality(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
bbc.cpp:38: error: ‘allocVector’ was not declared in this scope
bbc.cpp: In function ‘SEXPREC* BGL_betweenness_centrality_clustering(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
bbc.cpp:128: error: ‘allocVector’ was not declared in this scope
make: *** [bbc.o] Error 1
ERROR: compilation failed for package ‘RBGL’
* removing ‘/opt/R/lib/RBGL’

The downloaded source packages are in
    ‘/tmp/Rtmp4PWGJj/downloaded_packages’
Update old packages: 'mclust'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘RBGL’ had non-zero exit status

 

rbgl r package problem • 170 views
ADD COMMENTlink modified 9 months ago by Martin Morgan ♦♦ 23k • written 9 months ago by ngs0620
Answer: Problems installing RBGL in R
1
gravatar for Martin Morgan
9 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Can you try to install an updated version from github

BiocManager::install("Bioconductor/RBGL", ref="avoid-Rdefines")

This might also require that you have installed the remotes package

BiocManager::install("remotes")
ADD COMMENTlink written 9 months ago by Martin Morgan ♦♦ 23k

It worked and error is solved. Thank you very much!

ADD REPLYlink written 9 months ago by ngs0620

This is fixed in version 1.58.1 (Release 3.8) / 1.59.1 (devel), which should be available via BiocManager::install() in the next 24 - 48 hours.

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 23k
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