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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.spec
Does 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’
303
Sorry for answering my own question, but adding these three symbolic links allowed rJava to install on Amazon Linux 2017.09.1:
ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec /usr/lib64/libgomp.spec
ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.a /usr/lib64/libgomp.a
ln -s /usr/lib64/libgomp.so.1.0.0 /usr/lib64/libgomp.so
I had the same issue on Amazon Linux when installing rpy2.
sudo yum install gcc64 solved it for me.
3
Symlink works for me
ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec /usr/lib64/libgomp.spec
ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.a /usr/lib64/libgomp.a
ln -s /usr/lib64/libgomp.so.1.0.0 /usr/lib64/libgomp.so
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