Installation issue: openbabel #43556
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Comments
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Related to openbabel/openbabel#2533? |
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Can you please try to use the master branch and see if it works? 3.1.1 is quite old, unfortunately (from 2020). |
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It did not work :( |
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I attempted both 3.1.1 and master versions with gcc@11.4.0 but both failed. |
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I can't reproduce those issues unfortunately. Are you using Python as an external package? I am only using the compiler from the system, everything else is built with Spack. |
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#43612 should fix the original issue, can you please give it a try? Thanks |
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Closing since #43612 has been merged. Please feel free to re-open if this fix does not work for you. |
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Still not working for me :( I am using the systems python version as well. openbabel@master %gcc@11.4.0 openbabel %gcc@11.4.0 openbabel using gcc@13.2.0 |
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Right, looks like I solved a different issue with GCC12, which I had installed. I did not have GCC 13 installed. I just installed it, and I can indeed reproduce your issue. Looks like an Open Babel problem (see openbabel/openbabel#2688 (comment)) rather than a Spack-specific problem. I'd recommend to ping the developers there directly and see if they have a solution. I can't reproduce you issue with Python unfortunately, but as I said I'm not using the system Python (I installed everything but GCC with Spack). |
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Steps to reproduce the issue
Error message
Error message
$ spack install openbabel [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/bzip2-1.0.8-ss6qnnnb2jc3pzckctwa47vahnzezlsw [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/xz-5.4.1-nspysnil6toiugzgoq3pdkkjbrjunqg6 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5-wbwhp4spbwn2xsvuskhrr5dyw26o4g6k [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zstd-1.5.5-zvxveix5ngu4p2tvbch2zfejwxidvbc4 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/font-util-1.4.0-sfwat7he5ik7nzpgyofh3zczyrltfrd7 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libiconv-1.17-eh6wgi6gbbazprxuwraajo5ks27bxg5m [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/util-linux-uuid-2.38.1-6psym7biafovmin2y6g6j26dw7tzptj6 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/ncurses-6.4-yjlxwprperm4e7drp3sc5gloyjqpcg3k [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/pkgconf-1.9.5-56dlotyzsvlza33jf6bbszygmsshdkmp [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libffi-3.4.4-oswqmd6kjvhtuy6tepjjqbni53ny7jac [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/pcre2-10.42-rvx6bksym4ggklytsziep7n7nkgertpy [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/berkeley-db-18.1.40-sflltu6xbrssa3v62bjqpc2p67qaviio [+] /opt/ohpc/pub/apps/python3/3.9.16 (external python-3.9.16-4n5gh2n3f7phywrqqpslvbxpknszequb) [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/eigen-3.4.0-5x3dbwlmyoeuqtauzn7j7rqjolaasona [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/gmake-4.4.1-mnrolzjc5rx3pgvda2vhyzdxukkt7d6h [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/boost-1.83.0-plifjr6gknx7at4ad47nsykx2pzoh2wt [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/fribidi-1.0.12-vdrqbdmdawru6bhgijxhveufkoc2hmoi [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/xtrans-1.4.0-6yg7zxo7aviwiqkc5rcdn4hsxwoiqalb [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/nghttp2-1.57.0-wx4ck5dhzpdwbtd2d7q4owh7som2xt27 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/pigz-2.7-6dsbfkbb2m2pwfudam2gn6zetahswxno [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/readline-8.2-6xfnoyeiecwiasdvqycact7ga5sn3kmt [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/xproto-7.0.31-xkrhas2slhfa4wkyihstpodlgwlgtsky [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/swig-4.1.1-q4kn5ryuoqn6jd2yzy5djpvbaa4z6dy3 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/icu4c-67.1-kw4e7jstcyk4tzntvcxlfzsuoowggr3u [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/rapidjson-1.2.0-2022-03-09-2rtdtfqmgrwl2kbibqy2sdbs4htcyhh5 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libxml2-2.10.3-zp2t4dm2ugu7oui6rzeocbkkjfmx4u2q [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libpng-1.6.39-bfx7zoh3mwuzlszxoopdoxuisv4245dj [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/openssl-3.1.3-vocf6ejdr4cjsw3jsjzfatwsi72jzqys [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/tar-1.34-ob5weonjgh5q4ou4sjonss4c6llvalbq [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/gdbm-1.23-fz462h7hv6pagshhfmkuqpuo22oxlh6o [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libice-1.0.9-hlns3yctdjpv35v3rhtywn6iouevv7xw [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/pixman-0.42.2-qdxhrcccn7iimakvjxbkjtejfsxxbils [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/freetype-2.11.1-f3xcfauuyvne5lgbmhbmdvqjjwadhmok [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/curl-8.4.0-jaggwhwtazvibu4lt3bmfyuihupmnb6i [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/gettext-0.22.4-hyqbyassrylr724ohf7oqim5cmolt2pt [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/perl-5.38.0-z4z5di7d7y6aoclrw23atluy5rrk4qdf [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libsm-1.2.3-h7gj6ydx7egz7xaddvlbze6riwwidx3o [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/fontconfig-2.14.2-rk2tr7bigkujrxixaeoxx326iagoelmf [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/cmake-3.27.9-i3t3cdlrp5wdfv23ltq2lzbhoztyuhor [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/elfutils-0.190-kgtcjwmss7b66f43chorkotqewmkkaj3 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/glib-2.78.0-njmuf44uibpskg525diefdtnfqj3h6jr [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/cairo-1.16.0-alilhmqv3tof7nggq2h6di3lb5jyyvpi [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/gobject-introspection-1.76.1-x6nvtqtlnhmqifp5a5ip4ujkiyqu2sqg [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/harfbuzz-7.3.0-fkntulwn35mb5hpcdevvlywcneehwma5 [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/json-glib-1.6.6-sesiok6dt64oxkclrjt74gqoqubuhtbr [+] /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/pango-1.50.13-fsvis6aflyearchhwg5trdpxd2i463yi ==> Installing openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj [47/47] ==> No binary for openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj found: installing from source ==> Using cached archive: /opt/ohpc/pub/spack/var/spack/cache/_source-cache/git//openbabel/openbabel.git/cbd4db43f8908b874864280fdc03bf92569eebc1.tar.gz ==> Warning: Fetching from mirror without a checksum! This package is normally checked out from a version control system, but it has been archived on a spack mirror. This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure! ==> No patches needed for openbabel ==> openbabel: Executing phase: 'cmake' ==> openbabel: Executing phase: 'build' ==> Error: ProcessError: Command exited with status 2: 'make' '-j8' 6 errors found in build log: 1319 | ^~~~~~~~~~~~~~~ 1320 /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-9.4.0/gcc-13.2.0-amrg7qqakxemynqsg5y3h2pn3cy3xnzf/lib/gcc/x86_64-pc-linux-gnu/13.2.0/../../../../include/c++/13.2.0/bits/stl_function.h: 131:12: note: declared here 1321 131 | struct binary_function 1322 | ^~~~~~~~~~~~~~~ 1323 In file included from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/src/depict/asciipainter.cpp:18: 1324 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h: In member function 'void OpenBabel::OBStopwatch::Start()': >> 1325 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:65:14: error: 'clock' was not declared in this scope 1326 65 | start= clock(); 1327 | ^~~~~ 1328 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:40:1: note: 'clock' is defined in header ''; did you forget to '#include '? 1329 39 | #include 1330 +++ |+#include 1331 40 | 1332 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h: In member function 'double OpenBabel::OBStopwatch::Lap()': >> 1333 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:70:13: error: 'clock' was not declared in this scope 1334 70 | stop= clock(); 1335 | ^~~~~ 1336 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:70:13: note: 'clock' is defined in header ''; did you forget t o '#include '? >> 1337 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:71:40: error: 'CLOCKS_PER_SEC' was not declared in this scope 1338 71 | return((stop - start) / (double) CLOCKS_PER_SEC); 1339 | ^~~~~~~~~~~~~~ 1340 /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obutil.h:71:40: note: the macro 'CLOCKS_PER_SEC' had not yet been defined 1341 In file included from /usr/include/time.h:33, 1342 from /usr/include/pthread.h:24, 1343 from /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-9.4.0/gcc-13.2.0-amrg7qqakxemynqsg5y3h2pn3cy3xnzf/lib/gcc/x86_64-pc-linux-gnu/13.2.0/../../../../include/c++/13.2. 0/x86_64-pc-linux-gnu/bits/gthr-default.h:35, ... 1382 In file included from /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-9.4.0/gcc-13.2.0-amrg7qqakxemynqsg5y3h2pn3cy3xnzf/lib/gcc/x86_64-pc-linux-gnu/13.2.0/../../../../include/c++/13.2. 0/string:49, 1383 from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/dlhandler.h:24, 1384 from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/plugin.h:23: 1385 /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-9.4.0/gcc-13.2.0-amrg7qqakxemynqsg5y3h2pn3cy3xnzf/lib/gcc/x86_64-pc-linux-gnu/13.2.0/../../../../include/c++/13.2.0/bits/stl_function.h: 131:12: note: declared here 1386 131 | struct binary_function 1387 | ^~~~~~~~~~~~~~~ >> 1388 make[2]: *** [src/formats/CMakeFiles/asciiformat.dir/build.make:93: src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o] Error 1 1389 make[2]: *** Waiting for unfinished jobs.... 1390 make -f src/formats/CMakeFiles/MNAformat.dir/build.make src/formats/CMakeFiles/MNAformat.dir/depend 1391 make[2]: Entering directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' 1392 cd /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k && /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/cmake-3.27.9-i3t3cd lrp5wdfv23ltq2lzbhoztyuhor/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src /tmp/spack/spack-stage/sp ack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/src/formats /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k /tmp/ spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/src/formats /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fc ynuj/spack-build-drixo3k/src/formats/CMakeFiles/MNAformat.dir/DependInfo.cmake "--color=" 1393 make[2]: Leaving directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' 1394 make -f src/formats/CMakeFiles/MNAformat.dir/build.make src/formats/CMakeFiles/MNAformat.dir/build 1395 make[2]: Entering directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' 1396 [ 30%] Building CXX object src/formats/CMakeFiles/MNAformat.dir/MNAformat.cpp.o 1397 cd /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/src/formats && /opt/ohpc/pub/spack/lib/spack/env/gcc/g++ -DBUILD_LINK_AS_DLL -DHAVE _EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DMNAformat_EXPORTS -DUSING_DYNAMIC_LIBS -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5- wbwhp4spbwn2xsvuskhrr5dyw26o4g6k/include -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/include -I/tmp/spack/spack-stage/spack-stag e-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/data -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include -I/opt/ohpc/pub/spac k/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/eigen-3.4.0-5x3dbwlmyoeuqtauzn7j7rqjolaasona/include/eigen3 -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/boost-1.83.0-plifjr6gknx 7at4ad47nsykx2pzoh2wt/include -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/rapidjson-1.2.0-2022-03-09-2rtdtfqmgrwl2kbibqy2sdbs4htcyhh5/include -I/opt/ohpc/pub/spack/opt/spa ck/linux-rocky8-x86_64/gcc-13.2.0/cairo-1.16.0-alilhmqv3tof7nggq2h6di3lb5jyyvpi/include/cairo -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/ include/inchi -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/libxml2-2.10.3-zp2t4dm2ugu7oui6rzeocbkkjfmx4u2q/include/libxml2 -O3 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pth read -MD -MT src/formats/CMakeFiles/MNAformat.dir/MNAformat.cpp.o -MF CMakeFiles/MNAformat.dir/MNAformat.cpp.o.d -o CMakeFiles/MNAformat.dir/MNAformat.cpp.o -c /tmp/spack/spack-stage/spack-s tage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/src/formats/MNAformat.cpp 1398 make[2]: Leaving directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' >> 1399 make[1]: *** [CMakeFiles/Makefile2:1608: src/formats/CMakeFiles/asciiformat.dir/all] Error 2 1400 make[1]: *** Waiting for unfinished jobs.... 1401 [ 30%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o 1402 cd /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/src && /opt/ohpc/pub/spack/lib/spack/env/gcc/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_ LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DUSING_DYNAMIC_LIBS -Dplugin_charges_EXPORTS -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5-wbwhp4spbwn2xsvuskhrr5d yw26o4g6k/include -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/include -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo 3krctotza7prydmvit755fcynuj/spack-src/data -I/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include -I/opt/ohpc/pub/spack/opt/spack/linux-rocky 8-x86_64/gcc-13.2.0/eigen-3.4.0-5x3dbwlmyoeuqtauzn7j7rqjolaasona/include/eigen3 -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/boost-1.83.0-plifjr6gknx7at4ad47nsykx2pzoh2wt/i nclude -I/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/rapidjson-1.2.0-2022-03-09-2rtdtfqmgrwl2kbibqy2sdbs4htcyhh5/include -O3 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthrea d -MD -MT src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o -c /tmp/spack/spa ck-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/src/charges/qtpie.cpp 1403 In file included from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/format.h:22, 1404 from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/include/openbabel/obconversion.h:37, 1405 from /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-src/src/formats/copyformat.cpp:14: ... 1757 [ 35%] Linking CXX shared module ../lib/plugin_charges.so 1758 cd /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/src && /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/cmake-3.27.9-i3 t3cdlrp5wdfv23ltq2lzbhoztyuhor/bin/cmake -E cmake_link_script CMakeFiles/plugin_charges.dir/link.txt --verbose=1 1759 /opt/ohpc/pub/spack/lib/spack/env/gcc/g++ -fPIC -O3 -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -o ../lib/plugin _charges.so CMakeFiles/plugin_charges.dir/charges/eem.cpp.o CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o CMakeFiles/plugin_charges.dir/charges/none.cpp.o CMakeFiles/plugin_charges.d ir/charges/mmff94.cpp.o CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o CMakeFiles/plugi n_charges.dir/charges/qtpie.cpp.o -Wl,-rpath,/opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5-wbwhp4spbwn2xsvuskhrr5dyw26o4g6k/lib:/tmp/spack/spack-stage/spack-sta ge-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k/lib:::::: -lm -ldl /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5-wbwhp4spbwn2xsvuskhrr5dy w26o4g6k/lib/libz.so ../lib/libopenbabel.so.7.0.0 -lm -ldl /opt/ohpc/pub/spack/opt/spack/linux-rocky8-x86_64/gcc-13.2.0/zlib-ng-2.1.5-wbwhp4spbwn2xsvuskhrr5dyw26o4g6k/lib/libz.so -pthread 1760 make[2]: Leaving directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' 1761 [ 35%] Built target plugin_charges 1762 make[1]: Leaving directory '/tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-drixo3k' >> 1763 make: *** [Makefile:149: all] Error 2 See build log for details: /tmp/spack/spack-stage/spack-stage-openbabel-3.1.1-drixo3krctotza7prydmvit755fcynuj/spack-build-out.txtInformation on your system
Additional information
spack-build-env.txt
spack-build-out.txt
@RMeli
General information
spack debug reportand reported the version of Spack/Python/Platformspack maintainers <name-of-the-package>and @mentioned any maintainersThe text was updated successfully, but these errors were encountered: