Error in dyn.load(dynlib <- getDynlib(dir)) : ...... rgl.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv
icejean opened this issue · 3 comments
icejean commented
Hi, dmurdoch,
How do you do?
I'm trying to install rgl on my virtual machine that runs R-4.1.2 on CentOS 7.6 and Xvfb. I'v updated my gcc devtoolset to 11, and while trying to install rgl, it prompts the errors below:
installing to /usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
libgcc_s.so.1 must be installed for pthread_cancel to work
sh: 行 1: 2266 已放弃 R_TESTS= '/usr/lib64/R-4.1.2/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmptUxAmj/file3f063df2c82'
Error in dyn.load(dynlib <- getDynlib(dir)) :
无法载入共享目标对象‘/usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/libs/rgl.so’：:
/usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/libs/rgl.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv
Warning: Loading rgl's DLL failed.
Warning: Trying without OpenGL...
Error in dyn.load(dynlib <- getDynlib(dir)) :
无法载入共享目标对象‘/usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/useNULL/rgl.so’：:
/usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/useNULL/rgl.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv
Error: package or namespace load failed for ‘rgl’:
loadNamespace()里算'rgl'时.onLoad失败了，详细内容：
调用: fun(libname, pkgname)
错误: Loading failed.
错误: loading failed
停止执行
ERROR: loading failed
* removing ‘/usr/lib64/R-4.1.2/lib64/R/library/rgl’
I search around and find that the problem may be the version of my libstdc++.so is too low, the version of mine is libstdc++.so.6.0.28, and maybe you test rgl on libstdc++.so.6.0.29 and abbove.
difference between libstdc++.so.6.0.28 & 29:
GLIBCXX_3.4.29 _ZSt28__throw_bad_array_new_lengthv
(base) [root@VM-4-12-centos lib]# strings /usr/lib64/libstdc++.so.6.0.28 | grep throw_bad_array
__cxa_throw_bad_array_length
__cxa_throw_bad_array_new_length
__cxa_throw_bad_array_length
__cxa_throw_bad_array_new_length
__cxa_throw_bad_array_length
__cxa_throw_bad_array_new_length
(base) [root@VM-4-12-centos lib]# strings /usr/lib64/libstdc++.so.6.0.28 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_DEBUG_MESSAGE_LENGTH
My gcc version:
(base) [root@VM-4-12-centos lib]# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-11/root/usr/libexec/gcc/x86_64-redhat-linux/11/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-11/root/usr --mandir=/opt/rh/devtoolset-11/root/usr/share/man --infodir=/opt/rh/devtoolset-11/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-11.2.1-20220127/obj-x86_64-redhat-linux/isl-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.2.1 20220127 (Red Hat 11.2.1-9) (GCC)
Below is the latest binary devtoolsets available for CentOS 7.6, and I'v installed the highest:
(base) [root@VM-4-12-centos lib]# yum list | grep devtoolset-
devtoolset-11-binutils.x86_64 2.36.1-1.el7.2 @centos-sclo-rh
devtoolset-11-gcc.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-gcc-c++.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-gcc-gdb-plugin.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-gcc-gfortran.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-gcc-plugin-devel.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-libquadmath-devel.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-libstdc++-devel.x86_64 11.2.1-9.el7 @centos-sclo-rh
devtoolset-11-runtime.x86_64 11.1-2.el7 @centos-sclo-rh
devtoolset-8-binutils.x86_64 2.30-55.el7.2 @centos-sclo-rh
devtoolset-8-gcc.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-gcc-c++.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-gcc-gdb-plugin.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-gcc-gfortran.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-gcc-plugin-devel.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-libquadmath-devel.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-libstdc++-devel.x86_64 8.3.1-3.2.el7 @centos-sclo-rh
devtoolset-8-runtime.x86_64 8.1-1.el7 @centos-sclo-rh
devtoolset-10.x86_64 10.1-0.el7 centos-sclo-rh
devtoolset-10-annobin.x86_64 9.23-4.el7.1 centos-sclo-rh
devtoolset-10-annobin-annocheck.x86_64 9.23-4.el7.1 centos-sclo-rh
devtoolset-10-binutils.x86_64 2.35-5.el7.4 centos-sclo-rh
devtoolset-10-binutils-devel.x86_64 2.35-5.el7.4 centos-sclo-rh
devtoolset-10-build.x86_64 10.1-0.el7 centos-sclo-rh
devtoolset-10-dwz.x86_64 0.12-1.1.el7 centos-sclo-rh
devtoolset-10-dyninst.x86_64 10.2.1-1.el7 centos-sclo-rh
devtoolset-10-dyninst-devel.x86_64 10.2.1-1.el7 centos-sclo-rh
devtoolset-10-dyninst-doc.x86_64 10.2.1-1.el7 centos-sclo-rh
devtoolset-10-dyninst-static.x86_64 10.2.1-1.el7 centos-sclo-rh
devtoolset-10-dyninst-testsuite.x86_64 10.2.1-1.el7 centos-sclo-rh
devtoolset-10-elfutils.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-elfutils-debuginfod.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-elfutils-debuginfod-client.x86_64
devtoolset-10-elfutils-debuginfod-client-devel.x86_64
devtoolset-10-elfutils-devel.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-elfutils-libelf.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-elfutils-libelf-devel.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-elfutils-libs.x86_64 0.182-3.el7 centos-sclo-rh
devtoolset-10-gcc.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-gcc-c++.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-gcc-gdb-plugin.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-gcc-gfortran.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-gcc-plugin-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-gdb.x86_64 9.2-10.el7 centos-sclo-rh
devtoolset-10-gdb-doc.noarch 9.2-10.el7 centos-sclo-rh
devtoolset-10-gdb-gdbserver.x86_64 9.2-10.el7 centos-sclo-rh
devtoolset-10-libasan-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libatomic-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libgccjit.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libgccjit-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libgccjit-docs.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libitm-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-liblsan-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libquadmath-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libstdc++-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libstdc++-docs.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libtsan-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-libubsan-devel.x86_64 10.2.1-11.2.el7 centos-sclo-rh
devtoolset-10-ltrace.x86_64 0.7.91-1.el7 centos-sclo-rh
devtoolset-10-make.x86_64 1:4.2.1-1.el7 centos-sclo-rh
devtoolset-10-make-devel.x86_64 1:4.2.1-1.el7 centos-sclo-rh
devtoolset-10-memstomp.x86_64 0.1.5-6.el7 centos-sclo-rh
devtoolset-10-oprofile.x86_64 1.4.0-1.el7 centos-sclo-rh
devtoolset-10-oprofile-devel.x86_64 1.4.0-1.el7 centos-sclo-rh
devtoolset-10-oprofile-jit.x86_64 1.4.0-1.el7 centos-sclo-rh
devtoolset-10-perftools.x86_64 10.1-0.el7 centos-sclo-rh
devtoolset-10-runtime.x86_64 10.1-0.el7 centos-sclo-rh
devtoolset-10-strace.x86_64 5.7-3.el7 centos-sclo-rh
devtoolset-10-systemtap.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-client.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-devel.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-initscript.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-runtime.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-runtime-python2.x86_64
devtoolset-10-systemtap-sdt-devel.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-server.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-systemtap-testsuite.x86_64 4.4-6.el7 centos-sclo-rh
devtoolset-10-toolchain.x86_64 10.1-0.el7 centos-sclo-rh
devtoolset-10-valgrind.x86_64 1:3.16.1-5.el7 centos-sclo-rh
devtoolset-10-valgrind-devel.x86_64 1:3.16.1-5.el7 centos-sclo-rh
devtoolset-11.x86_64 11.1-2.el7 centos-sclo-rh
devtoolset-11-annobin-annocheck.x86_64 10.38-1.el7 centos-sclo-rh
devtoolset-11-annobin-docs.noarch 10.38-1.el7 centos-sclo-rh
devtoolset-11-annobin-plugin-gcc.x86_64 10.38-1.el7 centos-sclo-rh
devtoolset-11-binutils-devel.x86_64 2.36.1-1.el7.2 centos-sclo-rh
devtoolset-11-build.x86_64 11.1-2.el7 centos-sclo-rh
devtoolset-11-dwz.x86_64 0.14-2.el7 centos-sclo-rh
devtoolset-11-dyninst.x86_64 11.0.0-1.el7 centos-sclo-rh
devtoolset-11-dyninst-devel.x86_64 11.0.0-1.el7 centos-sclo-rh
devtoolset-11-dyninst-doc.x86_64 11.0.0-1.el7 centos-sclo-rh
devtoolset-11-dyninst-static.x86_64 11.0.0-1.el7 centos-sclo-rh
devtoolset-11-dyninst-testsuite.x86_64 11.0.0-1.el7 centos-sclo-rh
devtoolset-11-elfutils.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-elfutils-debuginfod.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-elfutils-debuginfod-client.x86_64
devtoolset-11-elfutils-debuginfod-client-devel.x86_64
devtoolset-11-elfutils-devel.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-elfutils-libelf.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-elfutils-libelf-devel.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-elfutils-libs.x86_64 0.185-2.el7 centos-sclo-rh
devtoolset-11-gdb.x86_64 10.2-6.el7 centos-sclo-rh
devtoolset-11-gdb-doc.noarch 10.2-6.el7 centos-sclo-rh
devtoolset-11-gdb-gdbserver.x86_64 10.2-6.el7 centos-sclo-rh
devtoolset-11-libasan-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libatomic-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libgccjit.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libgccjit-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libgccjit-docs.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libitm-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-liblsan-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libstdc++-docs.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libtsan-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-libubsan-devel.x86_64 11.2.1-9.el7 centos-sclo-rh
devtoolset-11-ltrace.x86_64 0.7.91-1.el7 centos-sclo-rh
devtoolset-11-make.x86_64 1:4.3-1.el7 centos-sclo-rh
devtoolset-11-make-devel.x86_64 1:4.3-1.el7 centos-sclo-rh
devtoolset-11-memstomp.x86_64 0.1.5-6.el7 centos-sclo-rh
devtoolset-11-oprofile.x86_64 1.4.0-2.el7 centos-sclo-rh
devtoolset-11-oprofile-devel.x86_64 1.4.0-2.el7 centos-sclo-rh
devtoolset-11-oprofile-jit.x86_64 1.4.0-2.el7 centos-sclo-rh
devtoolset-11-perftools.x86_64 11.1-2.el7 centos-sclo-rh
devtoolset-11-strace.x86_64 5.13-3.3.el7 centos-sclo-rh
devtoolset-11-systemtap.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-client.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-devel.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-initscript.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-runtime.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-sdt-devel.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-server.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-systemtap-testsuite.x86_64 4.5-7.el7 centos-sclo-rh
devtoolset-11-toolchain.x86_64 11.1-2.el7 centos-sclo-rh
devtoolset-11-valgrind.x86_64 1:3.17.0-4.el7 centos-sclo-rh
devtoolset-11-valgrind-devel.x86_64 1:3.17.0-4.el7 centos-sclo-rh
devtoolset-7.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-all.x86_64 7.0-5.el7 centos-sclo-rh
devtoolset-7-binutils.x86_64 2.28-11.el7 centos-sclo-rh
devtoolset-7-binutils-devel.x86_64 2.28-11.el7 centos-sclo-rh
devtoolset-7-build.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-dockerfiles.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-dwz.x86_64 0.12-1.1.el7 centos-sclo-rh
devtoolset-7-dyninst.x86_64 9.3.2-3.el7 centos-sclo-rh
devtoolset-7-dyninst-devel.x86_64 9.3.2-3.el7 centos-sclo-rh
devtoolset-7-dyninst-doc.x86_64 9.3.2-3.el7 centos-sclo-rh
devtoolset-7-dyninst-static.x86_64 9.3.2-3.el7 centos-sclo-rh
devtoolset-7-dyninst-testsuite.x86_64 9.3.2-3.el7 centos-sclo-rh
devtoolset-7-elfutils.x86_64 0.170-5.el7 centos-sclo-rh
devtoolset-7-elfutils-devel.x86_64 0.170-5.el7 centos-sclo-rh
devtoolset-7-elfutils-libelf.x86_64 0.170-5.el7 centos-sclo-rh
devtoolset-7-elfutils-libelf-devel.x86_64 0.170-5.el7 centos-sclo-rh
devtoolset-7-elfutils-libs.x86_64 0.170-5.el7 centos-sclo-rh
devtoolset-7-gcc.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-gcc-c++.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-gcc-gdb-plugin.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-gcc-gfortran.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-gcc-plugin-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-gdb.x86_64 8.0.1-36.el7 centos-sclo-rh
devtoolset-7-gdb-doc.noarch 8.0.1-36.el7 centos-sclo-rh
devtoolset-7-gdb-gdbserver.x86_64 8.0.1-36.el7 centos-sclo-rh
devtoolset-7-go.x86_64 7.0-5.el7 centos-sclo-rh
devtoolset-7-libasan-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libatomic-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libcilkrts-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libgccjit.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libgccjit-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libgccjit-docs.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libitm-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-liblsan-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libmpx-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libquadmath-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libstdc++-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libstdc++-docs.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libtsan-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-libubsan-devel.x86_64 7.3.1-5.16.el7 centos-sclo-rh
devtoolset-7-llvm.x86_64 7.0-5.el7 centos-sclo-rh
devtoolset-7-ltrace.x86_64 0.7.91-2.el7 centos-sclo-rh
devtoolset-7-make.x86_64 1:4.2.1-3.el7 centos-sclo-rh
devtoolset-7-memstomp.x86_64 0.1.5-5.1.el7 centos-sclo-rh
devtoolset-7-oprofile.x86_64 1.2.0-2.el7.1 centos-sclo-rh
devtoolset-7-oprofile-devel.x86_64 1.2.0-2.el7.1 centos-sclo-rh
devtoolset-7-oprofile-jit.x86_64 1.2.0-2.el7.1 centos-sclo-rh
devtoolset-7-perftools.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-runtime.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-rust.x86_64 7.0-5.el7 centos-sclo-rh
devtoolset-7-strace.x86_64 4.17-7.el7 centos-sclo-rh
devtoolset-7-systemtap.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-client.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-devel.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-initscript.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-runtime.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-sdt-devel.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-server.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-systemtap-testsuite.x86_64 3.1-4s.el7 centos-sclo-rh
devtoolset-7-toolchain.x86_64 7.1-4.el7 centos-sclo-rh
devtoolset-7-valgrind.x86_64 1:3.13.0-11.el7 centos-sclo-rh
devtoolset-7-valgrind-devel.x86_64 1:3.13.0-11.el7 centos-sclo-rh
devtoolset-8.x86_64 8.1-1.el7 centos-sclo-rh
devtoolset-8-binutils-devel.x86_64 2.30-55.el7.2 centos-sclo-rh
devtoolset-8-build.x86_64 8.1-1.el7 centos-sclo-rh
devtoolset-8-dockerfiles.x86_64 8.0-2.el7 centos-sclo-rh
devtoolset-8-dwz.x86_64 0.12-1.1.el7 centos-sclo-rh
devtoolset-8-dyninst.x86_64 9.3.2-6.el7 centos-sclo-rh
devtoolset-8-dyninst-devel.x86_64 9.3.2-6.el7 centos-sclo-rh
devtoolset-8-dyninst-doc.x86_64 9.3.2-6.el7 centos-sclo-rh
devtoolset-8-dyninst-static.x86_64 9.3.2-6.el7 centos-sclo-rh
devtoolset-8-dyninst-testsuite.x86_64 9.3.2-6.el7 centos-sclo-rh
devtoolset-8-elfutils.x86_64 0.176-1.el7 centos-sclo-rh
devtoolset-8-elfutils-devel.x86_64 0.176-1.el7 centos-sclo-rh
devtoolset-8-elfutils-libelf.x86_64 0.176-1.el7 centos-sclo-rh
devtoolset-8-elfutils-libelf-devel.x86_64 0.176-1.el7 centos-sclo-rh
devtoolset-8-elfutils-libs.x86_64 0.176-1.el7 centos-sclo-rh
devtoolset-8-gdb.x86_64 8.2-3.el7 centos-sclo-rh
devtoolset-8-gdb-doc.noarch 8.2-3.el7 centos-sclo-rh
devtoolset-8-gdb-gdbserver.x86_64 8.2-3.el7 centos-sclo-rh
devtoolset-8-libasan-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libatomic-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libgccjit.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libgccjit-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libgccjit-docs.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libitm-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-liblsan-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libstdc++-docs.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libtsan-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-libubsan-devel.x86_64 8.3.1-3.2.el7 centos-sclo-rh
devtoolset-8-ltrace.x86_64 0.7.91-1.el7 centos-sclo-rh
devtoolset-8-make.x86_64 1:4.2.1-4.el7 centos-sclo-rh
devtoolset-8-memstomp.x86_64 0.1.5-5.el7 centos-sclo-rh
devtoolset-8-oprofile.x86_64 1.3.0-2.el7 centos-sclo-rh
devtoolset-8-oprofile-devel.x86_64 1.3.0-2.el7 centos-sclo-rh
devtoolset-8-oprofile-jit.x86_64 1.3.0-2.el7 centos-sclo-rh
devtoolset-8-perftools.x86_64 8.1-1.el7 centos-sclo-rh
devtoolset-8-strace.x86_64 4.24-4.el7 centos-sclo-rh
devtoolset-8-systemtap.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-client.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-devel.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-initscript.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-runtime.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-sdt-devel.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-server.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-systemtap-testsuite.x86_64 3.3-2.el7 centos-sclo-rh
devtoolset-8-toolchain.x86_64 8.1-1.el7 centos-sclo-rh
devtoolset-8-valgrind.x86_64 1:3.14.0-16.el7 centos-sclo-rh
devtoolset-8-valgrind-devel.x86_64 1:3.14.0-16.el7 centos-sclo-rh
devtoolset-9.x86_64 9.1-0.el7 centos-sclo-rh
devtoolset-9-annobin.x86_64 8.79-2.el7 centos-sclo-rh
devtoolset-9-annobin-annocheck.x86_64 8.79-2.el7 centos-sclo-rh
devtoolset-9-binutils.x86_64 2.32-16.el7 centos-sclo-rh
devtoolset-9-binutils-devel.x86_64 2.32-16.el7 centos-sclo-rh
devtoolset-9-build.x86_64 9.1-0.el7 centos-sclo-rh
devtoolset-9-dwz.x86_64 0.12-1.1.el7 centos-sclo-rh
devtoolset-9-dyninst.x86_64 10.1.0-4.el7 centos-sclo-rh
devtoolset-9-dyninst-devel.x86_64 10.1.0-4.el7 centos-sclo-rh
devtoolset-9-dyninst-doc.x86_64 10.1.0-4.el7 centos-sclo-rh
devtoolset-9-dyninst-static.x86_64 10.1.0-4.el7 centos-sclo-rh
devtoolset-9-dyninst-testsuite.x86_64 10.1.0-4.el7 centos-sclo-rh
devtoolset-9-elfutils.x86_64 0.176-6.el7 centos-sclo-rh
devtoolset-9-elfutils-devel.x86_64 0.176-6.el7 centos-sclo-rh
devtoolset-9-elfutils-libelf.x86_64 0.176-6.el7 centos-sclo-rh
devtoolset-9-elfutils-libelf-devel.x86_64 0.176-6.el7 centos-sclo-rh
devtoolset-9-elfutils-libs.x86_64 0.176-6.el7 centos-sclo-rh
devtoolset-9-gcc.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-gcc-c++.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-gcc-gdb-plugin.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-gcc-gfortran.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-gcc-plugin-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-gdb.x86_64 8.3-3.el7 centos-sclo-rh
devtoolset-9-gdb-doc.noarch 8.3-3.el7 centos-sclo-rh
devtoolset-9-gdb-gdbserver.x86_64 8.3-3.el7 centos-sclo-rh
devtoolset-9-libasan-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libatomic-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libgccjit.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libgccjit-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libgccjit-docs.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libitm-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-liblsan-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libquadmath-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libstdc++-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libstdc++-docs.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libtsan-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-libubsan-devel.x86_64 9.3.1-2.2.el7 centos-sclo-rh
devtoolset-9-ltrace.x86_64 0.7.91-2.el7 centos-sclo-rh
devtoolset-9-make.x86_64 1:4.2.1-2.el7 centos-sclo-rh
devtoolset-9-memstomp.x86_64 0.1.5-5.el7 centos-sclo-rh
devtoolset-9-oprofile.x86_64 1.3.0-4.el7 centos-sclo-rh
devtoolset-9-oprofile-devel.x86_64 1.3.0-4.el7 centos-sclo-rh
devtoolset-9-oprofile-jit.x86_64 1.3.0-4.el7 centos-sclo-rh
devtoolset-9-perftools.x86_64 9.1-0.el7 centos-sclo-rh
devtoolset-9-runtime.x86_64 9.1-0.el7 centos-sclo-rh
devtoolset-9-strace.x86_64 5.1-7.el7 centos-sclo-rh
devtoolset-9-systemtap.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-client.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-devel.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-initscript.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-runtime.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-sdt-devel.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-server.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-systemtap-testsuite.x86_64 4.1-9.el7 centos-sclo-rh
devtoolset-9-toolchain.x86_64 9.1-0.el7 centos-sclo-rh
devtoolset-9-valgrind.x86_64 1:3.15.0-9.el7 centos-sclo-rh
devtoolset-9-valgrind-devel.x86_64 1:3.15.0-9.el7 centos-sclo-rh
Any idea without compiling gcc on my machine by my own? I haven't coded with C from many years, and there may be some difficulty to do it.
Thanks in advance.
Best
Regards
Jean
dmurdoch commented
I don't have any calls to that function in the code I wrote. From the sound of it, I'd guess it's automatically generated by your compiler. So this sounds like a problem in your tools, having a compiler that's not compatible with the libs on your system. I'd try re-installing the compiler or the libs --- but I don't really know anything about CentOS, so I don't know how difficult that would be.
icejean commented
I just built gcc-11.3.0 from source and get libstdc++.so.6.0.29, it took more than 2 and a half hours:
(base) [root@VM-4-12-centos lib64]# ls -l /usr/local/gcc-11.3.0/lib64/libstdc++.so.6.0.29
-rwxr-xr-x 1 root root 17961216 10月 22 20:42 /usr/local/gcc-11.3.0/lib64/libstdc++.so.6.0.29
(base) [root@VM-4-12-centos lib64]# strings /usr/local/gcc-11.3.0/lib64/libstdc++.so.6.0.29 | grep throw_bad_array
__cxa_throw_bad_array_length
__cxa_throw_bad_array_new_length
_ZSt28__throw_bad_array_new_lengthv
__cxa_throw_bad_array_length
__cxa_throw_bad_array_new_length
_ZSt28__throw_bad_array_new_lengthv
__throw_bad_array_new_length
__cxa_throw_bad_array_length
_ZSt28__throw_bad_array_new_lengthv
__cxa_throw_bad_array_new_length
(base) [root@VM-4-12-centos lib64]# strings /usr/local/gcc-11.3.0/lib64/libstdc++.so.6.0.29 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_3.4.29
GLIBCXX_DEBUG_MESSAGE_LENGTH
And link it to /usr/lib64/libstdc++.so.6
ln -s /usr/local/gcc-11.3.0/lib64/libstdc++.so.6.0.29 libstdc++.so.6
And start up and Xvfb server:
Xvfb :2 -screen 0 1280x960x24 &
Then start up R with setting the display to Xvfb server:
DISPLAY=:2 R
Then install rgl with install.packages("rgl"), it's O.K. now. :)
installing to /usr/lib64/R-4.1.2/lib64/R/library/00LOCK-rgl/00new/rgl/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rgl)
The downloaded source packages are in
‘/tmp/Rtmp3t3pvO/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
dmurdoch commented
Great news!