{"action":"opened","issue":{"url":"https://api.github.com/repos/s-u/rJava/issues/82","repository_url":"https://api.github.com/repos/s-u/rJava","labels_url":"https://api.github.com/repos/s-u/rJava/issues/82/labels{/name}","comments_url":"https://api.github.com/repos/s-u/rJava/issues/82/comments","events_url":"https://api.github.com/repos/s-u/rJava/issues/82/events","html_url":"https://github.com/s-u/rJava/issues/82","id":168572748,"number":82,"title":"Error when installing rJava ","user":{"login":"ceste","id":8425054,"avatar_url":"https://avatars.githubusercontent.com/u/8425054?v=3","gravatar_id":"","url":"https://api.github.com/users/ceste","html_url":"https://github.com/ceste","followers_url":"https://api.github.com/users/ceste/followers","following_url":"https://api.github.com/users/ceste/following{/other_user}","gists_url":"https://api.github.com/users/ceste/gists{/gist_id}","starred_url":"https://api.github.com/users/ceste/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ceste/subscriptions","organizations_url":"https://api.github.com/users/ceste/orgs","repos_url":"https://api.github.com/users/ceste/repos","events_url":"https://api.github.com/users/ceste/events{/privacy}","received_events_url":"https://api.github.com/users/ceste/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-08-01T06:00:30Z","updated_at":"2016-08-01T06:00:30Z","closed_at":null,"body":"Hi, \r\n\r\nI try to install rJava on below specification :\r\n\r\n> version\r\n               _                           \r\nplatform       x86_64-pc-linux-gnu         \r\narch           x86_64                      \r\nos             linux-gnu                   \r\nsystem         x86_64, linux-gnu           \r\nstatus                                     \r\nmajor          3                           \r\nminor          3.1                         \r\nyear           2016                        \r\nmonth          06                          \r\nday            21                          \r\nsvn rev        70800                       \r\nlanguage       R                           \r\nversion.string R version 3.3.1 (2016-06-21)\r\nnickname       Bug in Your Hair            \r\n\r\nBut I always get the same error as below:\r\n\r\n> install.packages('rJava')\r\nInstalling package into ‘/usr/local/lib/R/site-library’\r\n(as ‘lib’ is unspecified)\r\ntrying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-8.tar.gz'\r\nContent type 'unknown' length 656615 bytes (641 KB)\r\n==================================================\r\ndownloaded 641 KB\r\n\r\n* installing *source* package ‘rJava’ ...\r\n** package ‘rJava’ successfully unpacked and MD5 sums checked\r\nchecking for gcc... gcc -std=gnu99\r\nchecking whether the C compiler works... yes\r\nchecking for C compiler default output file name... a.out\r\nchecking for suffix of executables... \r\nchecking whether we are cross compiling... no\r\nchecking for suffix of object files... o\r\nchecking whether we are using the GNU C compiler... yes\r\nchecking whether gcc -std=gnu99 accepts -g... yes\r\nchecking for gcc -std=gnu99 option to accept ISO C89... none needed\r\nchecking how to run the C preprocessor... gcc -std=gnu99 -E\r\nchecking for grep that handles long lines and -e... /bin/grep\r\nchecking for egrep... /bin/grep -E\r\nchecking for ANSI C header files... yes\r\nchecking for sys/wait.h that is POSIX.1 compatible... yes\r\nchecking for sys/types.h... yes\r\nchecking for sys/stat.h... yes\r\nchecking for stdlib.h... yes\r\nchecking for string.h... yes\r\nchecking for memory.h... yes\r\nchecking for strings.h... yes\r\nchecking for inttypes.h... yes\r\nchecking for stdint.h... yes\r\nchecking for unistd.h... yes\r\nchecking for string.h... (cached) yes\r\nchecking sys/time.h usability... yes\r\nchecking sys/time.h presence... yes\r\nchecking for sys/time.h... yes\r\nchecking for unistd.h... (cached) yes\r\nchecking for an ANSI C-conforming const... yes\r\nchecking whether time.h and sys/time.h may both be included... yes\r\nconfigure: checking whether gcc -std=gnu99 supports static inline...\r\nyes\r\nchecking whether setjmp.h is POSIX.1 compatible... yes\r\nchecking whether sigsetjmp is declared... yes\r\nchecking whether siglongjmp is declared... yes\r\nchecking Java support in R... present:\r\ninterpreter : '/usr/lib/jvm/default-java/jre/bin/java'\r\narchiver    : '/usr/lib/jvm/default-java/bin/jar'\r\ncompiler    : '/usr/lib/jvm/default-java/bin/javac'\r\nheader prep.: '/usr/lib/jvm/default-java/bin/javah'\r\ncpp flags   : '-I/usr/lib/jvm/default-java/include'\r\njava libs   : '-L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm'\r\nchecking whether Java run-time works... yes\r\nchecking whether -Xrs is supported... yes\r\nchecking whether JNI programs can be compiled... yes\r\nchecking JNI data types... ok\r\nchecking whether JRI should be compiled (autodetect)... yes\r\nchecking whether debugging output should be enabled... no\r\nchecking whether memory profiling is desired... no\r\nchecking whether threads support is requested... no\r\nchecking whether callbacks support is requested... no\r\nchecking whether JNI cache support is requested... no\r\nchecking whether headless init is enabled... no\r\nchecking whether JRI is requested... yes\r\nconfigure: creating ./config.status\r\nconfig.status: creating src/Makevars\r\nconfig.status: creating R/zzz.R\r\nconfig.status: creating src/config.h\r\n=== configuring in jri (/tmp/Rtmpc1bVU3/R.INSTALL28e94bb8043b/rJava/jri)\r\nconfigure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.\r\nchecking build system type... x86_64-unknown-linux-gnu\r\nchecking host system type... x86_64-unknown-linux-gnu\r\nchecking for gcc... gcc -std=gnu99\r\nchecking whether the C compiler works... yes\r\nchecking for C compiler default output file name... a.out\r\nchecking for suffix of executables... \r\nchecking whether we are cross compiling... no\r\nchecking for suffix of object files... o\r\nchecking whether we are using the GNU C compiler... yes\r\nchecking whether gcc -std=gnu99 accepts -g... yes\r\nchecking for gcc -std=gnu99 option to accept ISO C89... none needed\r\nchecking how to run the C preprocessor... gcc -std=gnu99 -E\r\nchecking for grep that handles long lines and -e... /bin/grep\r\nchecking for egrep... /bin/grep -E\r\nchecking for ANSI C header files... yes\r\nchecking whether Java interpreter works... checking whether JNI programs can be compiled... yes\r\nchecking whether JNI programs can be run... yes\r\nchecking JNI data types... ok\r\nchecking whether Rinterface.h exports R_CStackXXX variables... yes\r\nchecking whether Rinterface.h exports R_SignalHandlers... yes\r\nconfigure: creating ./config.status\r\nconfig.status: creating src/Makefile\r\nconfig.status: creating Makefile\r\nconfig.status: creating run\r\nconfig.status: creating src/config.h\r\n** libs\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Rglue.c -o Rglue.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c arrayc.c -o arrayc.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c callJNI.c -o callJNI.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c callback.c -o callback.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fields.c -o fields.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c jri_glue.c -o jri_glue.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c loader.c -o loader.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c otables.c -o otables.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c rJava.c -o rJava.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/default-java/include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c tools.c -o tools.o\r\ngcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR\r\n(cd ../jri && make)\r\nmake[1]: Entering directory `/tmp/Rtmpc1bVU3/R.INSTALL28e94bb8043b/rJava/jri'\r\nmake -C src JRI.jar\r\nmake[2]: Entering directory `/tmp/Rtmpc1bVU3/R.INSTALL28e94bb8043b/rJava/jri/src'\r\n/usr/lib/jvm/default-java/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\r\nwarning: [options] bootstrap class path not set in conjunction with -source 1.4\r\n1 warning\r\n/usr/lib/jvm/default-java/bin/javah -d . -classpath . org.rosuda.JRI.Rengine\r\ngcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/lib/jvm/default-java/include -I/usr/share/R/include -I/usr/share/R/include\r\ngcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/lib/jvm/default-java/include -I/usr/share/R/include -I/usr/share/R/include\r\ngcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/lib/jvm/default-java/include -I/usr/share/R/include -I/usr/share/R/include\r\ngcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/share/R/include -I/usr/share/R/include\r\ngcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/lib/jvm/default-java/include\r\ngcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include  -fpic -I/usr/lib/jvm/default-java/include\r\nrjava.c: In function ‘RJava_request_lock’:\r\nrjava.c:22:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]\r\n   write(ipcout, buf, sizeof(ptrlong));\r\n        ^\r\nrjava.c: In function ‘RJava_clear_lock’:\r\nrjava.c:30:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]\r\n   write(ipcout, buf, sizeof(ptrlong));\r\n        ^\r\nrjava.c: In function ‘RJava_request_callback’:\r\nrjava.c:39:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]\r\n   write(ipcout, buf, sizeof(ptrlong) * 3);\r\n        ^\r\nrjava.c: In function ‘RJava_init_ctrl’:\r\nrjava.c:51:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]\r\n   write(ipcout, buf, sizeof(ptrlong));\r\n        ^\r\nrjava.c:52:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]\r\n   read(resin, buf, sizeof(ptrlong) * 2);\r\n       ^\r\ngcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -shared -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp  -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm\r\n/usr/bin/ld: cannot find -lpcre\r\n/usr/bin/ld: cannot find -lbz2\r\ncollect2: error: ld returned 1 exit status\r\nmake[2]: *** [libjri.so] Error 1\r\nmake[2]: Leaving directory `/tmp/Rtmpc1bVU3/R.INSTALL28e94bb8043b/rJava/jri/src'\r\nmake[1]: Leaving directory `/tmp/Rtmpc1bVU3/R.INSTALL28e94bb8043b/rJava/jri'\r\nmake[1]: *** [src/JRI.jar] Error 2\r\nmake: *** [jri] Error 2\r\nERROR: compilation failed for package ‘rJava’\r\n* removing ‘/usr/local/lib/R/site-library/rJava’\r\nWarning in install.packages :\r\n  installation of package ‘rJava’ had non-zero exit status\r\n\r\nThe downloaded source packages are in\r\n\t‘/tmp/Rtmp00hxMw/downloaded_packages’\r\n\r\n\r\nHow can I fix this problem?"}}
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