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

h43kikqp  于 2022-11-30  发布在  Go
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我尝试在Amazon Lightsail示例(Amazon Linux 2017.09.1)上运行的R中安装rJava包。我一直收到gcc找不到libgomp.spec的错误
我在**/usr/lib/gcc/x86_64-amazon-linux/6.4.1/libgomp.spec**中找到了这个文件,并且尝试设置一个指向它的符号链接,但是我还没有能够找到符号链接的位置,这样gcc就可以找到它。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

有没有人知道把符号链接放在哪里,以便gcc可以找到它?在这个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’
cgvd09ve

cgvd09ve1#

很抱歉回答了我自己的问题,但添加这三个符号链接允许rJava安装在Amazon Linux 2017. 09. 1上:

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
anauzrmj

anauzrmj2#

我在Amazon Linux上安装rpy2时遇到了同样的问题。sudo yum install gcc64为我解决了这个问题。

ne5o7dgx

ne5o7dgx3#

Symlink对我很有效

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
vuv7lop3

vuv7lop34#

尝试安装libgomp和(libgomp-devlibgomp-devel

# void Linux
xbps-install -Sy libgomp libgomp-devel
# Arch
pacman -Sy libgomp libgomp-devel
# debian
apt install libgomp libgomp-dev

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