I'm trying to install the rJava package in R running on an Amazon Lightsail instance (Amazon Linux 2017.09.1). I keep getting an error that gcc can't find libgomp.spec
I've located the file at /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec and I've tried setting up a symbolic link to it, but I haven't been able to figure out where to put the symbolic link so gcc can find it. For example, this doesn't seem to work:
ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec /usr/local/lib64/libgomp.specDoes anyone know where to put the symbolic link so gcc can find it? There is probably a hint in this output that I don't understand:
* installing *source* package ‘rJava’ ... ** package ‘rJava’ successfully unpacked and MD5 sums checked checking for gcc... gcc -m64 -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m64 -std=gnu99 -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 -m64 -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/bin/java' archiver : '/usr/bin/jar' compiler : '/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags : '-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux' java libs : '-L/usr/lib/jvm/jre/lib/amd64/server -ljvm' checking whether Java run-time works... yes checking whether -Xrs is supported... yes 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 headless init is enabled... 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/RtmphGxVwl/R.INSTALL1d971c944ee1/rJava/jri) configure: running /bin/sh ./configure --disable-option-checking '-- prefix=/usr/local' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc -m64 -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m64 -std=gnu99 -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 -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rglue.c -o Rglue.o Rglue.c:847:13: warning: ‘new_jrectRef’ defined but not used [-Wunused-function] static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) { ^~~~~~~~~~~~ gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrayc.c -o arrayc.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c callJNI.c -o callJNI.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c callback.c -o callback.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c fields.c -o fields.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c init.c -o init.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c jri_glue.c -o jri_glue.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c loader.c -o loader.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c otables.c -o otables.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rJava.c -o rJava.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c tools.c -o tools.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -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/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR (cd ../jri && make) make[1]: Entering directory `/tmp/RtmphGxVwl/R.INSTALL1d971c944ee1/rJava/jri' make -C src JRI.jar make[2]: Entering directory `/tmp/RtmphGxVwl/R.INSTALL1d971c944ee1/rJava/jri/src' /usr/bin/javac -target 1.6 -source 1.6 -d . ../RConsoleOutputStream.java ../RFactor.java ../REXP.java ../Rengine.java ../RList.java ../Mutex.java ../package-info.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.java warning: [options] bootstrap class path not set in conjunction with -source 1.6 Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 warning /usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine gcc -m64 -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux gcc -m64 -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux rjava.c: In function ‘RJava_request_lock’: rjava.c:22:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(ipcout, buf, sizeof(ptrlong)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function ‘RJava_clear_lock’: rjava.c:30:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(ipcout, buf, sizeof(ptrlong)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function ‘RJava_request_callback’: rjava.c:39:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(ipcout, buf, sizeof(ptrlong) * 3); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function ‘RJava_init_ctrl’: rjava.c:51:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(ipcout, buf, sizeof(ptrlong)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c:52:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(resin, buf, sizeof(ptrlong) * 2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -m64 -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/lib/jvm/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L/usr/lib64/R/lib -lR -ltre -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n gcc: error: libgomp.spec: No such file or directory make[2]: *** [libjri.so] Error 1 make[2]: Leaving directory `/tmp/RtmphGxVwl/R.INSTALL1d971c944ee1/rJava/jri/src' make[1]: *** [src/JRI.jar] Error 2 make[1]: Leaving directory `/tmp/RtmphGxVwl/R.INSTALL1d971c944ee1/rJava/jri' make: *** [jri] Error 2 ERROR: compilation failed for package ‘rJava’