r - gcc:错误:libgomp.spec:Amazon Linux 2017.09.1 没有此类文件或目录

Question

我正在尝试在 Amazon Lightsail 实例 (Amazon Linux 2017.09.1) 上运行的 R 中安装 rJava 软件包。我不断收到 gcc 找不到 libgomp.spec

的错误

我已在 /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec 找到该文件，并尝试设置指向它的符号链接(symbolic link)，但我无法弄清楚将符号链接(symbolic link)放在哪里以便 gcc 可以找到它。例如，这似乎不起作用:

ln -s /usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec /usr/local/lib64/libgomp.spec

有谁知道将符号链接(symbolic link)放在哪里以便 gcc 可以找到它？此输出中可能有一个我不明白的提示:

    * 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

很抱歉回答我自己的问题，但添加这三个符号链接(symbolic link)允许 rJava 在 Amazon Linux 2017.09.1 上安装:

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