[R-sig-Debian] R crashes when making graphs
Manderscheid Katharina
Katharina.Manderscheid at unilu.ch
Wed Dec 8 22:30:06 CET 2010
hi paul,
thanks for helping.
i just removed JGR (remove.packages("JGR")) and Deducer and then reinstalled it.
here is the installation report - there are some warnings in which do not make sense to me.
i was then thinking about deleting all librarys and re-installing them as root. however, since i am not an ubuntu-crack, i was not sure whether i can just delete the folders as root.
best,
katharina
versuche URL 'http://www.rforge.net/src/contrib/rJava_0.8-8.tar.gz'
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versuche URL 'http://stat.ethz.ch/CRAN/src/contrib/JavaGD_0.5-3.tar.gz'
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downloaded 99 Kb
versuche URL 'http://stat.ethz.ch/CRAN/src/contrib/iplots_1.1-3.tar.gz'
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* installing *source* package ‘rJava’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/tmp/RtmpgMykck/R.INSTALL16e07da8/rJava/jri)
configure: running /bin/bash ./configure '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c Rglue.c -o Rglue.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c arrayc.c -o arrayc.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c callJNI.c -o callJNI.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c callback.c -o callback.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c fields.c -o fields.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c jri_glue.c -o jri_glue.o
jri_glue.c: In function ‘PushToREXP’:
jri_glue.c:24: warning: cast from pointer to integer of different size
jri_glue.c: In function ‘RReleaseREXP’:
jri_glue.c:52: warning: cast to pointer from integer of different size
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c loader.c -o loader.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c otables.c -o otables.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c rJava.c -o rJava.o
gcc -I/usr/share/R/include -I. -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -std=gnu99 -O3 -pipe -g -c tools.c -o tools.o
gcc -shared -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm -L/usr/lib/R/lib -lR
(cd ../jri && make)
make[1]: Betrete Verzeichnis '/tmp/RtmpgMykck/R.INSTALL16e07da8/rJava/jri'
make -C src JRI.jar
make[2]: Betrete Verzeichnis '/tmp/RtmpgMykck/R.INSTALL16e07da8/rJava/jri/src'
/usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
gcc -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -I/usr/share/R/include -I/usr/share/R/include
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniParse’:
Rengine.c:121: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniEval’:
Rengine.c:135: warning: cast to pointer from integer of different size
Rengine.c:136: warning: cast to pointer from integer of different size
Rengine.c:159: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniAssign’:
Rengine.c:179: warning: cast to pointer from integer of different size
Rengine.c:180: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniProtect’:
Rengine.c:189: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniRelease’:
Rengine.c:201: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPreserve’:
Rengine.c:207: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPrintValue’:
Rengine.c:213: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniParentEnv’:
Rengine.c:219: warning: cast to pointer from integer of different size
Rengine.c:219: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniFindVar’:
Rengine.c:228: warning: cast to pointer from integer of different size
Rengine.c:228: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniListEnv’:
Rengine.c:234: warning: cast to pointer from integer of different size
Rengine.c:234: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniSpecialObject’:
Rengine.c:241: warning: cast from pointer to integer of different size
Rengine.c:242: warning: cast from pointer to integer of different size
Rengine.c:243: warning: cast from pointer to integer of different size
Rengine.c:244: warning: cast from pointer to integer of different size
Rengine.c:245: warning: cast from pointer to integer of different size
Rengine.c:246: warning: cast from pointer to integer of different size
Rengine.c:247: warning: cast from pointer to integer of different size
Rengine.c:248: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniXrefToJava’:
Rengine.c:256: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniJavaToXref’:
Rengine.c:266: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetString’:
Rengine.c:272: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetStringArray’:
Rengine.c:279: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetIntArray’:
Rengine.c:285: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetRawArray’:
Rengine.c:291: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetBoolArrayI’:
Rengine.c:297: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetDoubleArray’:
Rengine.c:303: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetVector’:
Rengine.c:309: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniExpType’:
Rengine.c:315: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutString’:
Rengine.c:335: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutStringArray’:
Rengine.c:341: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutIntArray’:
Rengine.c:347: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutRawArray’:
Rengine.c:353: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutBoolArrayI’:
Rengine.c:359: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutBoolArray’:
Rengine.c:365: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutDoubleArray’:
Rengine.c:371: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutVector’:
Rengine.c:377: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetAttr’:
Rengine.c:384: warning: cast to pointer from integer of different size
Rengine.c:386: warning: cast to pointer from integer of different size
Rengine.c:387: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetAttrNames’:
Rengine.c:394: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniSetAttr’:
Rengine.c:426: warning: cast to pointer from integer of different size
Rengine.c:428: warning: cast to pointer from integer of different size
Rengine.c:428: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniInstallSymbol’:
Rengine.c:441: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetSymbolName’:
Rengine.c:447: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniInherits’:
Rengine.c:457: warning: cast to pointer from integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniCons’:
Rengine.c:468: warning: cast to pointer from integer of different size
Rengine.c:468: warning: cast to pointer from integer of different size
Rengine.c:470: warning: cast to pointer from integer of different size
Rengine.c:470: warning: cast to pointer from integer of different size
Rengine.c:472: warning: cast to pointer from integer of different size
Rengine.c:473: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniCAR’:
Rengine.c:480: warning: cast to pointer from integer of different size
Rengine.c:481: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniCDR’:
Rengine.c:490: warning: cast to pointer from integer of different size
Rengine.c:491: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniTAG’:
Rengine.c:500: warning: cast to pointer from integer of different size
Rengine.c:501: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniPutList’:
Rengine.c:516: warning: cast from pointer to integer of different size
Rengine.c:521: warning: cast to pointer from integer of different size
Rengine.c:526: warning: cast from pointer to integer of different size
Rengine.c: In function ‘Java_org_rosuda_JRI_Rengine_rniGetList’:
Rengine.c:533: warning: cast to pointer from integer of different size
Rengine.c:560: warning: cast from pointer to integer of different size
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -I/usr/share/R/include -I/usr/share/R/include
jri.c: In function ‘jri_putSEXPLArray’:
jri.c:193: warning: cast from pointer to integer of different size
jri.c: In function ‘jri_getObjectArray’:
jri.c:308: warning: cast from pointer to integer of different size
jri.c: In function ‘jri_getSEXPLArray’:
jri.c:472: warning: cast to pointer from integer of different size
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/share/R/include -I/usr/share/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -std=gnu99 -O3 -pipe -g -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -fpic -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux
rjava.c: In function ‘RJava_request_lock’:
rjava.c:22: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
rjava.c: In function ‘RJava_clear_lock’:
rjava.c:30: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
rjava.c: In function ‘RJava_request_callback’:
rjava.c:39: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
rjava.c: In function ‘RJava_init_ctrl’:
rjava.c:51: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
rjava.c:52: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm -L/usr/lib/R/lib -lR
/usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
/usr/bin/jar fc JRI.jar org libjri.so
make[2]: Verlasse Verzeichnis '/tmp/RtmpgMykck/R.INSTALL16e07da8/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest.java
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
/usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest2.java
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
make[1]: Verlasse Verzeichnis '/tmp/RtmpgMykck/R.INSTALL16e07da8/rJava/jri'
installiert nach /home/kat/R/i486-pc-linux-gnu-library/2.12/rJava/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rJava)
* installing *source* package ‘JavaGD’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc -I/usr/share/R/include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -Iinclude -fpic -std=gnu99 -O3 -pipe -g -c jGDtalk.c -o jGDtalk.o
gcc -I/usr/share/R/include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -Iinclude -fpic -std=gnu99 -O3 -pipe -g -c javaGD.c -o javaGD.o
gcc -I/usr/share/R/include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../include/linux -Iinclude -fpic -std=gnu99 -O3 -pipe -g -c s2u.c -o s2u.o
gcc -shared -o JavaGD.so jGDtalk.o javaGD.o s2u.o -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.22/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm -L/usr/lib/R/lib -lR
installiert nach /home/kat/R/i486-pc-linux-gnu-library/2.12/JavaGD/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (JavaGD)
* installing *source* package ‘iplots’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (iplots)
* installing *source* package ‘JGR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update JGR.
* DONE (JGR)
The downloaded packages are in
‘/tmp/RtmplvLuPZ/downloaded_packages’
> JGR()
Starting JGR run script. This can be done from the shell as well, just run
/home/kat/R/i486-pc-linux-gnu-library/2.12/JGR/scripts/run
==> problem persists - i ran the code from inside JGR...
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00000000, pid=8371, tid=3010485104
#
# JRE version: 6.0_22-b04
# Java VM: Java HotSpot(TM) Client VM (17.1-b03 mixed mode, sharing linux-x86 )
# Problematic frame:
# C 0x00000000
#
# An error report file with more information is saved as:
# /root/hs_err_pid8371.log
#
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted
________________________________________
Von: Paul Johnson [pauljohn32 at gmail.com]
Gesendet: Mittwoch, 8. Dezember 2010 21:14
An: Manderscheid Katharina
Cc: R-SIG-DEBIAN
Betreff: Re: [R-sig-Debian] R crashes when making graphs
On Tue, Dec 7, 2010 at 3:00 AM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> here is the example i am using to test if it works.
>> data(airquality)
>> plot(airquality$Temp)
>
I have just tested this code and it works perfectly in the JGR on
Ubuntu 10.10. I have the Sun JDK installed.
I started JGR inside a terminal, after starting R manuall, so I could
track everything. If you do the same, maybe you will see a difference.
I install the JGR from "scratch" on CRAN, not with the deb package on
cran2deb. I do that because I'm a crabby old man, trying to make sure
all library versions match on my system. I suggest you try that too.
For general bug shooting, in Ubuntu note problem that you can get
several versions of package installed, under /usr/lib/R,
/usr/local/lib/R, and ~/R/. So try to make sure you have only one,
consider removing all.
Then as root run
$ R CMD javareconf
And then
$ install.packages("JGR", dep=T, lib="/usr/local/lib/R/site-library")
Here's the terminal output from starting R and then JGR:
pauljohn at pols124:~$ R
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(JGR)
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update JGR.
> JGR()
Please consider running JGR() as root to create a start script in
/usr/local/lib/R/site-library/JGR/scripts/run automatically.
Starting JGR ...
Warning message:
In file(con, "w") :
cannot open file '/usr/local/lib/R/site-library/JGR/scripts/run':
Permission denied
====================
Inside the JGR window, I type commands you listed and a graph popped out.
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=en_US.utf8
[9] LC_ADDRESS=en_US.utf8 LC_TELEPHONE=en_US.utf8
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=en_US.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] JGR_1.7-3 iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7
loaded via a namespace (and not attached):
[1] tools_2.12.0
>
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas
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