[R] SegFault when trying to install an inhouse package

[Joanne Thomas]

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/joannethomas at 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/joannethomas at 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).

Thanks,
Jo

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