gcc: error: libgomp.spec: No such file or director

Question

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’

Answer 1

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