On 28/07/2016 7:19 AM, Joanne Thomas wrote:
Hi,Apologies if something similar has come up but I have been unable to find it in the archive. The company I work for has an issue with a package they've developed called ESVP. This is dependent on OpenSM, which I'm told is already somewhat delicate with respect to calls on rJava. When trying to install ESVP on a number of Scientific Linux 7.2 servers (with R 3.3.0), I get the following results: > install.packages("/data/Jupiter/GFES/Packages/ESVP_1.2.2.tar.gz", repo=NULL, type="source") Installing package into ‘/home/joannetho...@jbanorthwest.co.uk/R/x86_64-redhat-linux-gnu-library/3.3’ (as ‘lib’ is unspecified) * installing *source* package ‘ESVP’ ... ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GreatCircleDistances.cpp -o GreatCircleDistances.o g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o ESVP.so GreatCircleDistances.o RcppExports.o -L/usr/lib64/R/lib -lR installing to /home/joannetho...@jbanorthwest.co.uk/R/x86_64-redhat-linux-gnu-library/3.3/ESVP/libs ** R ** preparing package for lazy loading Warning in rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE /usr/lib64/R/bin/INSTALL: line 34: 51703 Done echo 'tools:::.install_packages()' 51704 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} Warning in install.packages : installation of package ‘/data/Jupiter/GFES/Packages/ESVP_1.2.2.tar.gz’ had non-zero exit status We also have some servers running R 3.2.3, the package installs, although the X11 warning also occurs: > install.packages("/data/GFES/Packages/ESVP_1.2.2.tar.gz", repo=NULL, type="source") Installing package into ‘/home/jbanorthwest.co.uk/joannethomas/R/x86_64-redhat-linux-gnu-library/3.2’ (as ‘lib’ is unspecified) * installing *source* package ‘ESVP’ ... ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GreatCircleDistances.cpp -o GreatCircleDistances.o g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o ESVP.so GreatCircleDistances.o RcppExports.o -L/usr/lib64/R/lib -lR installing to /home/jbanorthwest.co.uk/joannethomas/R/x86_64-redhat-linux-gnu-library/3.2/ESVP/libs ** R ** preparing package for lazy loading Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class. No protocol specified Warning in rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** help *** installing help indices converting help for package ‘ESVP’ finding HTML links ... done CheckContinuity html CheckEventDur html CheckEventFreq html CheckEventSeas html CheckEventSpCov html CheckEventWaitTime html CheckMarDistr html CheckMaxInt html CheckMaxRp html CheckNumExceed html CheckPairDep html CheckRrm html CheckRrmAtt html CheckRrmFit html CheckTailDep html CheckTcDist html CheckTcLife html CheckTcSpDistr html CheckTcTrack html CheckTimeSeries html CheckTrigDens html ESVP html PlotCatchment html PlotNearestNeighbours html PlotTransProb html RunAll html VerifyEventDef html ** building package indices ** testing if installed package can be loaded Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class. No protocol specified Warning in rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE * DONE (ESVP) Aside from R, installed Linux packages are the same versions and the library of R packages is identical. Does anyone have any suggestions on what is causing the segfault (a jump to an invalid memory address).
You can avoid the rgl.init problems by setting the environment variable RGL_USE_NULL to TRUE before running anything. That should help on your 3.2.3 servers. It's possible that the segfault on the other system is related, but I'd guess it's something else. Tracking down segfaults can be hard: you'll need to understand how to look at the core dump, and do some low level debugging.
Duncan Murdoch
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