Question: Rgraphviz installation fails in R with OpenBLAS
0
gravatar for Peter Langfelder
6 months ago by
United States
Peter Langfelder1.8k wrote:

I am unable to install Rgraphviz_2.24.0 in R 3.5.1 compiled with OpenBLAS. The same package installs fine in R compiled with internal (R) BLAS, so I suspect that the use of external BLAS is to blame here. Any suggestions on how to make the installation succeed? Thanks!

The compilation error is

Error: package or namespace load failed for ‘Rgraphviz’:
 .onLoad failed in loadNamespace() for 'Rgraphviz', details:
  call: value[[3L]](cond)
  error: unable to load shared object '/usr/local/lib64/R-3.5.1-OpenBLAS/library/Rgraphviz/libs/Rgraphviz.so':
  /usr/local/lib64/R-3.5.1-OpenBLAS/library/Rgraphviz/libs/Rgraphviz.so: undefined symbol: _ZGVbN2vv___pow_finite

sessionInfo():

R version 3.5.1 Patched (2018-08-27 r75203)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 28 (Twenty Eight)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

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

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.2 compiler_3.5.1     tools_3.5.1       

 

 

 

rgraphviz • 199 views
ADD COMMENTlink written 6 months ago by Peter Langfelder1.8k

I am having same issue here on Gentoo Linux with gcc-8.2.0. Although I do have system-wide grapviz-2.40.1-r1 installed through R-3.5.1 version 2.26.0 is being picked (while logs state 2.28.0).

See https://gitlab.com/graphviz/graphviz/issues/1412

By switching to gcc-7.3.0 I can at least work around the issue.

ADD REPLYlink modified 4 months ago • written 4 months ago by mmokrejs0
First a clarification. Version 2.26 is the Rgraphviz version 2.28 is the Graphviz versioon they have nothing to do with each other, although now that 26 ~ 28 it looks weird. Second, I figured out what the issue is, but I dropped the ball in fixing it. On Wed, Nov 28, 2018 at 9:45 AM mmokrejs [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User mmokrejs <https: support.bioconductor.org="" u="" 16289=""/> wrote Comment: > Rgraphviz installation fails in R with OpenBLAS > <https: support.bioconductor.org="" p="" 113697="" #115573="">: > > I am having same issue here on Gentoo Linux with gcc-8.2.0. Although I do > have system-wide grapviz-2.40.1-r1 installed through R-3.5.1 version 2.26.0 > is being picked (while logs state 2.28.0). ``` > > BiocManager::install("ReportingTools", version = "3.8") Bioconductor > version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing > package(s) 'ReportingTools' also installing the dependencies 'Rgraphviz', > 'GOstats' trying URL ' > https://bioconductor.org/packages/3.8/bioc/src/contrib/Rgraphviz_2.26.0.tar.gz' > Content type 'application/x-gzip' length 7454958 bytes (7.1 MB) > ================================================== downloaded 7.1 MB trying > URL ' > https://bioconductor.org/packages/3.8/bioc/src/contrib/GOstats_2.48.0.tar.gz' > Content type 'application/x-gzip' length 3106621 bytes (3.0 MB) > ================================================== downloaded 3.0 MB trying > URL ' > https://bioconductor.org/packages/3.8/bioc/src/contrib/ReportingTools_2.22.0.tar.gz' > Content type 'application/x-gzip' length 2355462 bytes (2.2 MB) > ================================================== downloaded 2.2 MB * > installing *source* package 'Rgraphviz' ... configure: Using bundled > Graphviz. configure: Searching for the compilers specified by R. checking > for gcc... x86_64-pc-linux-gnu-gcc ... x86_64-pc-linux-gnu-gcc > -I"/usr/lib64/R/include" -DNDEBUG > -I/tmp/Rtmpc0yuFl/R.INSTALL3cba6536fc03/Rgraphviz/src/libunix/include/graphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -O2 -pipe -mpclmul -mpopcnt -march=native > -ftree-vectorize -c init.c -o init.o x86_64-pc-linux-gnu-gcc -shared > -L/usr/lib64/R/lib -Wl,-O1 -Wl,--as-needed -o Rgraphviz.so LL_funcs.o > Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o > buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o > libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a > libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz > -L/usr/lib64/R/lib -lR installing to > /home/mmokrejs/R/x86_64-pc-linux-gnu-library/3.5/Rgraphviz/libs ** R ** > inst ** byte-compile and prepare package for lazy loading ** help *** > installing help indices ** building package indices ** installing vignettes > ** testing if installed package can be loaded Error: package or namespace > load failed for 'Rgraphviz': .onLoad failed in loadNamespace() for > 'Rgraphviz', details: call: value[[3L]](cond) error: unable to load shared > object > '/home/mmokrejs/R/x86_64-pc-linux-gnu-library/3.5/Rgraphviz/libs/Rgraphviz.so': > /home/mmokrejs/R/x86_64-pc-linux-gnu-library/3.5/Rgraphviz/libs/Rgraphviz.so: > undefined symbol: _ZGVcN4vv___pow_finite Rgraphviz is unable to be loaded. > This typically is a symptom of an installation problem. From 2.x.x onwards, > Graphviz ought to come bundled with Rgraphviz. If you are trying to use an > external Graphviz, see additional instructions in the 'README' file of the > Rgraphviz 'source' distribution, available at > http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html``` > Likewise here 2.26.0 is picked but again the logs later state 2.28.0 (I am > puzzled): ``` > BiocManager::install("Rgraphviz") Bioconductor version 3.8 > (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) > 'Rgraphviz' trying URL ' > https://bioconductor.org/packages/3.8/bioc/src/contrib/Rgraphviz_2.26.0.tar.gz' > Content type 'application/x-gzip' length 7454958 bytes (7.1 MB) > ================================================== downloaded 7.1 MB * > installing *source* package 'Rgraphviz' ... configure: Using bundled > Graphviz. ... ``` See [https://gitlab.com/graphviz/graphviz/issues/1412]( > https://gitlab.com/graphviz/graphviz/issues/1412) > ------------------------------ > > Post tags: Rgraphviz > > You may reply via email or visit > C: Rgraphviz installation fails in R with OpenBLAS >
ADD REPLYlink written 4 months ago by Kasper Daniel Hansen6.4k

Peter,

I took a more careful look at your report. Are the two different R installations (with and without OpenBLAS) compiled with different compilers?  I know that Rgraphviz fails using GCC 8 with -O3 optimization flags, with this particular error (missing `***__pow_finite`). You don't mention in your post what C compiler you're using and whether the two R installations have been compiled with different compilers. Nevertheless, I will try to modify the configure script to address this issue in GCC 8.

Best,
Kasper

ADD REPLYlink written 4 months ago by Kasper Daniel Hansen6.4k

Apologies for this late reply, I missed your question. The compiler was the same, gcc 8 (currently at version 8.2.1 but 3 months ago the version may have been a bit lower). It is likely that one had -O2 and the other -O3 because, upon re-installation of plain R with -O3 compiler setting (which propagates to package installation), I could not install Rgraphviz in plain R either; reverting to -O2 solved the problem again.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Peter Langfelder1.8k
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