The only difference I see is I am using binutils 2.27. I copied the files from GCC-5.4.0-2.26 and renamed the version. This is an issue I had before. I had issues building libtool with GCCcore. I had this same problem with PCRE-8.38 and few other packages. I would like to build some stuff with GCCcore in order for me to use intel toolchain to pick up deps from GCCcore 5.4.0. If not then I have to rebuild everything from same toolchain.
The problem I am having is when build R I have deps from foss, GCC, and GCCcore. I have to carefully select which packages build with GCCcore. See error below. hpcswadm@hpcv18$eb libtool-2.4.6-GCC-5.4.0-2.27.eb --rebuild == temporary log file in case of crash /tmp/eb-Ut_pu7/easybuild-i3E3Be.log == processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/libtool/libtool-2.4.6-GCC-5.4.0-2.27.eb == building and installing Compiler/GCC/5.4.0-2.27/libtool/2.4.6... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == testing... == installing... == taking care of extensions... == postprocessing... == sanity checking... == cleaning up... == creating module... == permissions... == packaging... == COMPLETED: Installation ended successfully == Results of the build can be found in the log file(s) /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libtool/2.4.6/easybuild/easybuild-libtool-2.4.6-20170314.134924.log == Build succeeded for 1 out of 1 == Temporary log file(s) /tmp/eb-Ut_pu7/easybuild-i3E3Be.log* have been removed. == Temporary directory /tmp/eb-Ut_pu7 has been removed. hpcswadm@hpcv18$eb libtool-2.4.6-GCC-5.4.0-2.27.eb --try-toolchain=GCCcore,5.4.0 == temporary log file in case of crash /tmp/eb-smNLgN/easybuild-nF8gfe.log == processing EasyBuild easyconfig /tmp/eb-smNLgN/tweaked_easyconfigs/libtool-2.4.6-GCCcore-5.4.0.eb == building and installing Compiler/GCCcore/5.4.0/libtool/2.4.6... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /nfs/grid/software/RHEL7-BUILD/easybuild/build/libtool/2.4.6/GCCcore-5.4.0): build failed (first 300 chars): cmd " make -j 8 " exited with exitcode 2 and output: GEN libtoolize make all-recursive make[1]: Entering directory `/nfs/grid/software/RHEL7-BUILD/easybuild/build/libtool/2.4.6/GCCcore-5.4.0/libtool-2.4.6' Making all in . make[2]: Entering directory `/nfs/grid/software/RHEL7-BUILD/easybuild/ == Results of the build can be found in the log file(s) /tmp/eb-smNLgN/easybuild-libtool-2.4.6-20170314.134934.hwxza.log ERROR: Build of /tmp/eb-smNLgN/tweaked_easyconfigs/libtool-2.4.6-GCCcore-5.4.0.eb failed (err: 'build failed (first 300 chars): cmd " make -j 8 " exited with exitcode 2 and output:\n GEN libtoolize\nmake all-recursive\nmake[1]: Entering directory `/nfs/grid/software/RHEL7-BUILD/easybuild/build/libtool/2.4.6/GCCcore-5.4.0/libtool-2.4.6\'\nMaking all in .\nmake[2]: Entering directory `/nfs/grid/software/RHEL7-BUILD/easybuild/') hpcswadm@hpcv18$eb libtool-2.4.6-GCC-5.4.0-2.27.eb --try-toolchain=GCCcore,5.4.0 -D == temporary log file in case of crash /tmp/eb-XjigMM/easybuild-E9w1uP.log Dry run: printing build status of easyconfigs and dependencies * [x] /hpc/hpcswadm/easybuild/M4/M4-1.4.17.eb (module: Core | M4/.1.4.17) * [x] /hpc/hpcswadm/easybuild/Bison/Bison-3.0.4.eb (module: Core | Bison/.3.0.4) * [x] /hpc/hpcswadm/easybuild/flex/flex-2.6.0.eb (module: Core | flex/.2.6.0) * [x] /hpc/hpcswadm/easybuild/zlib/zlib-1.2.8.eb (module: Core | zlib/.1.2.8) * [x] /hpc/hpcswadm/easybuild/binutils/binutils-2.27.eb (module: Core | binutils/.2.27) * [x] /hpc/hpcswadm/easybuild/GCCcore/GCCcore-5.4.0.eb (module: Core | GCCcore/.5.4.0) * [x] /hpc/hpcswadm/easybuild/M4/M4-1.4.17-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | M4/.1.4.17) * [ ] /tmp/eb-XjigMM/tweaked_easyconfigs/libtool-2.4.6-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | libtool/2.4.6) == temporary log file in case of crash /tmp/eb-Xcd2jV/easybuild-4aukKE.log Dry run: printing build status of easyconfigs and dependencies CFGS=/hpc/hpcswadm/easybuild * [x] $CFGS/M4/M4-1.4.17.eb (module: Core | M4/.1.4.17) * [x] $CFGS/Bison/Bison-3.0.4.eb (module: Core | Bison/.3.0.4) * [x] $CFGS/flex/flex-2.6.0.eb (module: Core | flex/.2.6.0) * [x] $CFGS/zlib/zlib-1.2.8.eb (module: Core | zlib/.1.2.8) * [x] $CFGS/binutils/binutils-2.27.eb (module: Core | binutils/.2.27) * [x] $CFGS/GCCcore/GCCcore-5.4.0.eb (module: Core | GCCcore/.5.4.0) * [x] $CFGS/M4/M4-1.4.17-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | M4/.1.4.17) * [x] $CFGS/Bison/Bison-3.0.4-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | Bison/.3.0.4) * [x] $CFGS/flex/flex-2.6.0-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | flex/.2.6.0) * [x] $CFGS/zlib/zlib-1.2.8-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | zlib/.1.2.8) * [x] $CFGS/binutils/binutils-2.27-GCCcore-5.4.0.eb (module: Compiler/GCCcore/5.4.0 | binutils/.2.27) * [x] $CFGS/GCC/GCC-5.4.0-2.27.eb (module: Core | GCC/5.4.0-2.27) * [x] $CFGS/libtool/libtool-2.4.6-GCC-5.4.0-2.27.eb (module: Compiler/GCC/5.4.0-2.27 | libtool/2.4.6) From: easybuild-requ...@lists.ugent.be [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Tuesday, March 14, 2017 12:41 PM To: easybuild@lists.ugent.be Subject: Re: [easybuild] RE: R-3.3.1-foss build error Hi Shahzeb, On 14/03/2017 17:27, Siddiqui, Shahzeb wrote: I think the problem I am having is a mixture of dependencies using GCC and foss toolchain. I build LibTIFF with GCC while I build PROJ and GDAL with foss. They all build fine, but the rpackage doesn't work. I have run across this issue with numerous other packages. For instance Autotools bundle was able to build with GCCcore 5.4.0 except for libtools so I had to rebuild all of them with GCC-5.4.0 The error I am getting now when building with PROJ 4.8.0 is something to do with libtiff.so. I have the libraries and they are correct. I don't know if this is due to foss vs gcc toolchain issue. This sounds like it may have something to do with the binutils version you are using... When building things with GCCcore, you need to make sure you're using the same binutils version as included in the GCC bundle as a build dependency. regards, Kenneth checking for pj_init_plus in -lproj... yes ./proj_conf_test: /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/lib/libtiff.so.5: version `LIBTIFF_4.0' not found (required by /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/lib/libgdal.so.20) ./configure: line 3669: test: -eq: unary operator expected ./configure: line 3674: test: -ge: unary operator expected configure: PROJ.4 version: < 4.8.0 ./configure: line 3700: test: -ge: unary operator expected ./proj_conf_test: /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/lib/libtiff.so.5: version `LIBTIFF_4.0' not found (required by /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/lib/libgdal.so.20) checking PROJ.4: epsg found and readable... no Error: proj/epsg not found Either install missing proj support files, for example the proj-nad and proj-epsg RPMs on systems using RPMs, or if installed but not autodetected, set PROJ_LIB to the correct path, and if need be use the --with-proj-share= configure argument. ERROR: configuration failed for package 'rgdal' (at easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 in parse_cmd_output) == 2017-03-14 11:59:33,109 easyblock.py:2520 WARNING build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/rgdal_1.1-10.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source hpcswadm@hpcv18$strings /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/lib/libtiff.so.5 | grep 4.0 count<0x40000000 LIBTIFF, Version 4.0.6 GCC: (GNU) 5.4.0 module.5480 __PRETTY_FUNCTION__.4701 module.4809 module.5450 module.4804 __PRETTY_FUNCTION__.4903 module.4908 __PRETTY_FUNCTION__.4909 module.7460 __PRETTY_FUNCTION__.4901 module.4802 __PRETTY_FUNCTION__.4803 module.4703 module.4702 module.4705 From: easybuild-requ...@lists.ugent.be<mailto:easybuild-requ...@lists.ugent.be> [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Tuesday, March 14, 2017 11:54 AM To: easybuild@lists.ugent.be<mailto:easybuild@lists.ugent.be> Subject: Re: [easybuild] RE: R-3.3.1-foss build error On 13/03/2017 16:52, Siddiqui, Shahzeb wrote: Hi, So now I was able to get further into my R build, that's great but I now encounter an issue with rgdal which seems to be an issue with PROJ. I think current version of rgdal requires PROJ 4.8.0 or lower, I think this was not captured in the R-3.3.1 dependency. list. Should we fix version for PROJ? Are you sure the version of PROJ is the problem here? Using PROJ 4.9.3 with rgdal 1.1-10 worked fine for us... What are the problems with LibTIFF and GDAL about? That looks broken to me... regards, Kenneth == installing extension pheatmap 1.0.8 (317/414)... == installing extension openxlsx 3.0.0 (318/414)... == installing extension pvclust 2.0-0 (319/414)... == installing extension RCircos 1.1.3 (320/414)... == installing extension lambda.r 1.1.7 (321/414)... == installing extension futile.options 1.0.0 (322/414)... == installing extension futile.logger 1.4.1 (323/414)... == installing extension VennDiagram 1.6.17 (324/414)... == installing extension xlsxjars 0.6.1 (325/414)... == installing extension xlsx 0.5.7 (326/414)... == installing extension forecast 7.1 (327/414)... == installing extension fma 2.2 (328/414)... == installing extension expsmooth 2.3 (329/414)... == installing extension fpp 0.5 (330/414)... == installing extension maptools 0.8-39 (331/414)... == installing extension deldir 0.1-12 (332/414)... == installing extension tensor 1.5 (333/414)... == installing extension polyclip 1.5-6 (334/414)... == installing extension goftest 1.0-3 (335/414)... == installing extension spatstat 1.46-1 (336/414)... == installing extension rgdal 1.1-10 (337/414)... == FAILED: Installation ended unsuccessfully (build directory: /nfs/grid/software/RHEL7-BUILD/easybuild/build/R/3.3.1/foss-2016.03): build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/rgdal_1.1-10.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source == Results of the build can be found in the log file(s) /tmp/eb-OJyzIr/easybuild-R-3.3.1-20170313.110123.yASoa.log.1, /tmp/eb-OJyzIr/easybuild-R-3.3.1-20170313.110123.yASoa.log ERROR: Build of /hpc/hpcswadm/easybuild/R/R-3.3.1-foss-2016.03.eb failed (err: 'build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/rgdal_1.1-10.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output:\n* installing *source') checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -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/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 gdal.h usability... yes checking gdal.h presence... yes checking for gdal.h... yes checking gdal: linking with --libs only... yes checking GDAL: /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/share/gdal/pcs.csv readable... yes checking proj_api.h usability... yes checking proj_api.h presence... yes checking for proj_api.h... yes checking for pj_init_plus in -lproj... yes ./proj_conf_test: /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/lib/libtiff.so.5: version `LIBTIFF_4.0' not found (required by /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/lib/libgdal.so.20) ./configure: line 3669: test: -eq: unary operator expected ./configure: line 3674: test: -ge: unary operator expected configure: PROJ.4 version: < 4.8.0 ./configure: line 3700: test: -ge: unary operator expected proj_conf_test.c:3:7: error: conflicting types for 'pj_open_lib' FILE *pj_open_lib(const char *, const char *); ^ In file included from proj_conf_test.c:2:0: /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/PROJ/4.9.2/include/proj_api.h:148:8: note: previous declaration of 'pj_open_lib' was here PAFile pj_open_lib(projCtx, const char *, const char *); ^ ./proj_conf_test: /nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/lib/libtiff.so.5: version `LIBTIFF_4.0' not found (required by /nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/lib/libgdal.so.20) checking PROJ.4: epsg found and readable... no Error: proj/epsg not found Either install missing proj support files, for example the proj-nad and proj-epsg RPMs on systems using RPMs, or if installed but not autodetected, set PROJ_LIB to the correct path, and if need be use the --with-proj-share= configure argument. ERROR: configuration failed for package 'rgdal' (at easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 in parse_cmd_output) == 2017-03-13 11:41:37,416 easyblock.py:2520 WARNING build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/rgdal_1.1-10.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source == 2017-03-13 11:41:37,417 easyblock.py:276 INFO Closing log for application name R version 3.3.1 From: easybuild-requ...@lists.ugent.be<mailto:easybuild-requ...@lists.ugent.be> [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Saturday, March 11, 2017 12:47 PM To: easybuild@lists.ugent.be<mailto:easybuild@lists.ugent.be> Subject: Re: [easybuild] RE: R-3.3.1-foss build error Hi Shahzeb, I'm not sure why the download is failing, but it seems like we should be including NLopt as a dependency to prevent the nloptr package to download & compile NLopt by itself? Cfr. https://github.com/hpcugent/easybuild-easyconfigs/pull/1750<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hpcugent_easybuild-2Deasyconfigs_pull_1750&d=DwMD-g&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=v5g2JeJmmyOIaJFfII2nMBo_3-6t6pbdcWvsZNDLBkw&s=XZOuzfi7l-6vFS9P98NDTZP2ON5GT5IkSbwLhjlz27E&e=> regards, Kenneth On 11/03/2017 02:09, Siddiqui, Shahzeb wrote: Seems to be an issue with the nloptr package. It was not uncompressed properly. Any suggestions what to do? ython2.7/site-packages/vsc_base-2.5.7-py2.7.egg/vsc/utils/exceptions.py:124 in __init__): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/nloptr_1.0.4.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source* package 'nloptr' ... ** package 'nloptr' successfully unpacked and MD5 sums checked 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 g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for pkg-config... yes configure: Now testing for NLopt header file. 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/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 nlopt.h usability... no checking nlopt.h presence... no checking for nlopt.h... no configure: Need to download and build NLopt trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz<https://urldefense.proofpoint.com/v2/url?u=http-3A__ab-2Dinitio.mit.edu_nlopt_nlopt-2D2.4.2.tar.gz&d=DwMD-g&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=v5g2JeJmmyOIaJFfII2nMBo_3-6t6pbdcWvsZNDLBkw&s=eq3j6J299blyPUwWbdTUeBhYQmxFxqo8wbl2zXKF9y0&e=>' Content type 'application/x-gzip' length 2361992 bytes (2.3 MB) downloaded 13 KB Warning message: In download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz";<https://urldefense.proofpoint.com/v2/url?u=http-3A__ab-2Dinitio.mit.edu_nlopt_nlopt-2D2.4.2.tar.gz&d=DwMD-g&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=v5g2JeJmmyOIaJFfII2nMBo_3-6t6pbdcWvsZNDLBkw&s=eq3j6J299blyPUwWbdTUeBhYQmxFxqo8wbl2zXKF9y0&e=>, : downloaded length 14299 != reported length 2361992 gzip: stdin: unexpected end of file /bin/gtar: Unexpected EOF in archive /bin/gtar: Unexpected EOF in archive /bin/gtar: Error is not recoverable: exiting now Warning message: In untar(tarfile = "nlopt-2.4.2.tar.gz") : '/bin/gtar -zxf 'nlopt-2.4.2.tar.gz'' returned error code 2 configure: Starting to install library to /tmp/eb-xzY7sj/RtmpXxtxZL/R.INSTALL2f5e896ff82975/nloptr/nlopt-2.4.2 configure: Done installing library to /tmp/eb-xzY7sj/RtmpXxtxZL/R.INSTALL2f5e896ff82975/nloptr/nlopt-2.4.2 configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/include -DNDEBUG -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/OpenBLAS/0.2.19-LAPACK-3.6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/ScaLAPACK/2.0.2-OpenBLAS-0.2.19-LAPACK-3.6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/FFTW/3.3.4/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libreadline/6.3/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/ncurses/6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/bzip2/1.0.6/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/XZ/5.2.2/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/zlib/1.2.8/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/SQLite/3.13.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/PCRE/8.38/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libpng/1.6.23/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/libjpeg-turbo/1.5.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Core/Java/1.8.0_92/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/Tcl/8.6.5/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/Tk/8.6.5/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/cURL/7.49.1/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libxml2/2.9.4/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/PROJ/4.9.2/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/GMP/6.1.1/include -fpic -O2 -march=native -c dummy.cpp -o dummy.o gcc -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/include -DNDEBUG -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/OpenBLAS/0.2.19-LAPACK-3.6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/ScaLAPACK/2.0.2-OpenBLAS-0.2.19-LAPACK-3.6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/FFTW/3.3.4/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libreadline/6.3/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/ncurses/6.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/bzip2/1.0.6/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/XZ/5.2.2/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/zlib/1.2.8/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/SQLite/3.13.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/PCRE/8.38/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libpng/1.6.23/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/libjpeg-turbo/1.5.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/LibTIFF/4.0.6/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Core/Java/1.8.0_92/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/Tcl/8.6.5/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/Tk/8.6.5/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/cURL/7.49.1/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/libxml2/2.9.4/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/GDAL/2.1.0/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/PROJ/4.9.2/include -I/nfs/grid/software/testing/RHEL7/easybuild/software/Compiler/GCC/5.4.0-2.27/GMP/6.1.1/include -I/tmp/eb-xzY7sj/RtmpXxtxZL/R.INSTALL2f5e896ff82975/nloptr/nlopt-2.4.2/include -fpic -O2 -march=native -c nloptr.c -o nloptr.o nloptr.c:42:19: fatal error: nlopt.h: No such file or directory compilation terminated. make: *** [nloptr.o] Error 1 ERROR: compilation failed for package 'nloptr' (at easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 in parse_cmd_output) == 2017-03-10 18:30:22,017 easyblock.py:2520 WARNING build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/nloptr_1.0.4.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source == 2017-03-10 18:30:22,018 easyblock.py:276 INFO Closing log for application name R version 3.3.1 From: Siddiqui, Shahzeb Sent: Friday, March 10, 2017 8:07 PM To: easybuild@lists.ugent.be<mailto:easybuild@lists.ugent.be> Subject: R-3.3.1-foss build error I seem to be having an issue building nloptr during the R build. I am using the R-3.3.1 with foss 2016. Any ideas how to fix this problem. == installing extension GGally 1.2.0 (291/414)... == installing extension beanplot 1.2 (292/414)... == installing extension clValid 0.6-6 (293/414)... == installing extension matrixStats 0.50.2 (294/414)... == installing extension DiscriMiner 0.1-29 (295/414)... == installing extension ellipse 0.3-8 (296/414)... == installing extension leaps 2.9 (297/414)... == installing extension nloptr 1.0.4 (298/414)... == FAILED: Installation ended unsuccessfully (build directory: /nfs/grid/software/RHEL7-BUILD/easybuild/build/R/3.3.1/foss-2016.03): build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/nloptr_1.0.4.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source == Results of the build can be found in the log file(s) /tmp/eb-xzY7sj/easybuild-R-3.3.1-20170310.173552.YPJPA.log.1, /tmp/eb-xzY7sj/easybuild-R-3.3.1-20170310.173552.YPJPA.log ERROR: Build of /hpc/hpcswadm/easybuild/R/R-3.3.1-foss-2016.03.eb failed (err: 'build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/nloptr_1.0.4.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output:\n* installing *source') The log file suggest the following. e/Compiler/GCC/5.4.0-2.27/GMP/6.1.1/include -I/tmp/eb-xzY7sj/RtmpXxtxZL/R.INSTALL2f5e896ff82975/nloptr/nlopt-2.4.2/include -fpic -O2 -march=native -c nloptr.c -o nloptr.o nloptr.c:42:19: fatal error: nlopt.h: No such file or directory compilation terminated. make: *** [nloptr.o] Error 1 ERROR: compilation failed for package 'nloptr' (at easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 in parse_cmd_output) == 2017-03-10 18:30:22,017 easyblock.py:2520 WARNING build failed (first 300 chars): cmd "R CMD INSTALL /nfs/grid/software/RHEL7-BUILD/easybuild/sources/r/R/extensions/nloptr_1.0.4.tar.gz --library=/nfs/grid/software/testing/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/R/3.3.1/lib64/R/library --no-clean-on-error" exited with exitcode 1 and output: * installing *source == 2017-03-10 18:30:22,018 easyblock.py:276 INFO Closing log for application name R version 3.3.1 Shahzeb Siddiqui HPC Linux Engineer B2220-447.2 Groton, CT
