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).
Thanks,
Jo
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