rjava on FreeBSD
Locked
rjava on FreeBSD
 
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Trying to install Rjava on FreeBSD 9 and am getting the following error:
> install.packages('rJava') trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz' Content type 'application/x-gzip' length 537153 bytes (524 Kb) opened URL ================================================== downloaded 524 Kb * installing *source* package 'rJava' ... ** package 'rJava' successfully unpacked and MD5 sums checked checking for gcc... gcc46 -std=gnu99 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 gcc46 -std=gnu99 accepts -g... yes checking for gcc46 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc46 -std=gnu99 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 gcc46 -std=gnu99 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/local/bin/java' archiver : '/usr/local/bin/jar' compiler : '/usr/local/bin/javac' header prep.: '/usr/local/bin/javah' cpp flags : '-I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd' java libs : '-L/usr/local/jdk1.6.0/jre/lib/i386/server -L/usr/local/jdk1.6.0/jre/lib/i386 -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -L/usr/local/lib -ljvm' checking whether JNI programs can be compiled... yes checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this. ERROR: configuration failed for package 'rJava' * removing '/usr/local/lib/R/library/rJava' * removing '/usr/local/lib/R/library/rJava' The downloaded packages are in '/tmp/RtmpWtRfKe/downloaded_packages' Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages("rJava") : installation of package 'rJava' had non-zero exit status 2: In file.create(f.tg) : cannot create file '/usr/local/share/doc/R/html/packages.html', reason 'Permission denied' 3: In make.packages.html(.Library) : cannot update HTML package index > Ok, so I tried doing so as root, because it would solve the 'Permissions denied' issue and was rewarded with: > install.packages('rJava') trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz' Content type 'application/x-gzip' length 537153 bytes (524 Kb) opened URL ================================================== downloaded 524 Kb * installing *source* package 'rJava' ... ** package 'rJava' successfully unpacked and MD5 sums checked checking for gcc... gcc46 -std=gnu99 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 gcc46 -std=gnu99 accepts -g... yes checking for gcc46 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc46 -std=gnu99 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 gcc46 -std=gnu99 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/local/bin/java' archiver : '/usr/local/bin/jar' compiler : '/usr/local/bin/javac' header prep.: '/usr/local/bin/javah' cpp flags : '-I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd' java libs : '-L/usr/local/jdk1.6.0/jre/lib/i386/server -L/usr/local/jdk1.6.0/jre/lib/i386 -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -L/usr/local/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/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri) configure: running /bin/sh ./configure '--prefix=/usr/local' --cache-file=/dev/null --srcdir=. checking build system type... i386-unknown-freebsd9.0 checking host system type... i386-unknown-freebsd9.0 checking for gcc... gcc46 -std=gnu99 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 gcc46 -std=gnu99 accepts -g... yes checking for gcc46 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c Rglue.c -o Rglue.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c arrayc.c -o arrayc.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callJNI.c -o callJNI.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callback.c -o callback.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c fields.c -o fields.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c init.c -o init.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c jri_glue.c -o jri_glue.o jri_glue.c: In function 'PushToREXP': jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] jri_glue.c: In function 'RReleaseREXP': jri_glue.c:52:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c loader.c -o loader.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c otables.c -o otables.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c rJava.c -o rJava.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. -I/usr/local/jdk1.6.0/jre/../include -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tools.c -o tools.o gcc46 -std=gnu99 -fpic -shared -Wl,-rpath=/usr/local/lib/gcc46 -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/local/jdk1.6.0/jre/lib/i386/server -L/usr/local/jdk1.6.0/jre/lib/i386 -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -L/usr/local/lib -ljvm -L/usr/local/lib/R/lib -lR (cd ../jri && make) make -C src JRI.jar /usr/local/bin/javac -target 1.4 -source 1.4 -d . realpath: : No such file or directory javac: no source files Usage: javac <options> <source files> use -help for a list of possible options *** Error code 2 Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri/src. *** Error code 1 Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri. *** Error code 1 Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/src. ERROR: compilation failed for package 'rJava' * removing '/usr/local/lib/R/library/rJava' The downloaded packages are in '/tmp/Rtmp5Eg6iF/downloaded_packages' Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages("rJava") : installation of package 'rJava' had non-zero exit status > ... and I'm now at a loss... Any ideas? Many thanks! -- Sent from my mobile device Envoyait de mon portable ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: rjava on FreeBSD
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On 11.01.2012 22:51 (UTC+1), Hasan Diwan wrote:
> Trying to install Rjava on FreeBSD 9 and am getting the following error: >> install.packages('rJava') > trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz' > Content type 'application/x-gzip' length 537153 bytes (524 Kb) > opened URL > ================================================== > downloaded 524 Kb > > * installing *source* package 'rJava' ... > ** package 'rJava' successfully unpacked and MD5 sums checked > checking for gcc... gcc46 -std=gnu99 > 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 gcc46 -std=gnu99 accepts -g... yes > checking for gcc46 -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc46 -std=gnu99 -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/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 gcc46 -std=gnu99 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/local/bin/java' > archiver : '/usr/local/bin/jar' > compiler : '/usr/local/bin/javac' > header prep.: '/usr/local/bin/javah' > cpp flags : '-I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd' > java libs : '-L/usr/local/jdk1.6.0/jre/lib/i386/server > -L/usr/local/jdk1.6.0/jre/lib/i386 > -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 > -L/lib -L/usr/lib -L/usr/local/lib -ljvm' > checking whether JNI programs can be compiled... yes > checking JNI data types... configure: error: One or more JNI types > differ from the corresponding native type. You may need to use > non-standard compiler flags or a different compiler in order to fix > this. > ERROR: configuration failed for package 'rJava' > * removing '/usr/local/lib/R/library/rJava' > * removing '/usr/local/lib/R/library/rJava' > > The downloaded packages are in > '/tmp/RtmpWtRfKe/downloaded_packages' > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages("rJava") : > installation of package 'rJava' had non-zero exit status > 2: In file.create(f.tg) : > cannot create file '/usr/local/share/doc/R/html/packages.html', > reason 'Permission denied' > 3: In make.packages.html(.Library) : cannot update HTML package index >> > > Ok, so I tried doing so as root, because it would solve the > 'Permissions denied' issue and was rewarded with: >> install.packages('rJava') > trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz' > Content type 'application/x-gzip' length 537153 bytes (524 Kb) > opened URL > ================================================== > downloaded 524 Kb > > * installing *source* package 'rJava' ... > ** package 'rJava' successfully unpacked and MD5 sums checked > checking for gcc... gcc46 -std=gnu99 > 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 gcc46 -std=gnu99 accepts -g... yes > checking for gcc46 -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc46 -std=gnu99 -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/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 gcc46 -std=gnu99 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/local/bin/java' > archiver : '/usr/local/bin/jar' > compiler : '/usr/local/bin/javac' > header prep.: '/usr/local/bin/javah' > cpp flags : '-I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd' > java libs : '-L/usr/local/jdk1.6.0/jre/lib/i386/server > -L/usr/local/jdk1.6.0/jre/lib/i386 > -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 > -L/lib -L/usr/lib -L/usr/local/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/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri) > configure: running /bin/sh ./configure '--prefix=/usr/local' > --cache-file=/dev/null --srcdir=. > checking build system type... i386-unknown-freebsd9.0 > checking host system type... i386-unknown-freebsd9.0 > checking for gcc... gcc46 -std=gnu99 > 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 gcc46 -std=gnu99 accepts -g... yes > checking for gcc46 -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... cpp > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/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 > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c Rglue.c -o > Rglue.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c arrayc.c -o > arrayc.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callJNI.c -o > callJNI.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callback.c -o > callback.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c fields.c -o > fields.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c init.c -o > init.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c jri_glue.c -o > jri_glue.o > jri_glue.c: In function 'PushToREXP': > jri_glue.c:24:15: warning: cast from pointer to integer of different > size [-Wpointer-to-int-cast] > jri_glue.c: In function 'RReleaseREXP': > jri_glue.c:52:11: warning: cast to pointer from integer of different > size [-Wint-to-pointer-cast] > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c loader.c -o > loader.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c otables.c -o > otables.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c rJava.c -o > rJava.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I. > -I/usr/local/jdk1.6.0/jre/../include > -I/usr/local/jdk1.6.0/jre/../include/freebsd -fpic -O2 -pipe > -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tools.c -o > tools.o > gcc46 -std=gnu99 -fpic -shared -Wl,-rpath=/usr/local/lib/gcc46 -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/local/jdk1.6.0/jre/lib/i386/server > -L/usr/local/jdk1.6.0/jre/lib/i386 > -L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 > -L/lib -L/usr/lib -L/usr/local/lib -ljvm -L/usr/local/lib/R/lib -lR > (cd ../jri&& make) > make -C src JRI.jar > /usr/local/bin/javac -target 1.4 -source 1.4 -d . > realpath: : No such file or directory > javac: no source files > Usage: javac<options> <source files> > use -help for a list of possible options > *** Error code 2 > > Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri/src. > *** Error code 1 > > Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri. > *** Error code 1 > > Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/src. > ERROR: compilation failed for package 'rJava' > * removing '/usr/local/lib/R/library/rJava' > > The downloaded packages are in > '/tmp/Rtmp5Eg6iF/downloaded_packages' > Updating HTML index of packages in '.Library' > Making packages.html ... done > Warning message: > In install.packages("rJava") : > installation of package 'rJava' had non-zero exit status >> > > ... and I'm now at a loss... Any ideas? Many thanks! > Hi Hasan, because FreeBSD uses BSD make instead of GNU make (gmake) like Linux you have to build packages like rJava at the shell (command prompt). I personally prefer to write a small script for packages like this. So I am able to repeat the build and install, if needed. For rJava this could be for example: --script begins-- #!/bin/sh export MAKE=gmake R CMD INSTALL rJava_0.9-3.tar.gz --script ends-- Please be aware of the math/R OPTION 'LIBR', which builds and installs a shared library version of R. If not, JRI has to be disabled and for that your rJava script has to be customized like this: R CMD INSTALL --configure-args='--enable-jri=no' rJava_0.9-3.tar.gz Hope this helps, Rainer ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
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