Shahzeb, Whenever you build something with GCCcore, you need to make sure that the same binutils that was used to build GCCcore is listed as a build dependency. Thus, '--try-toolchain' won't work in this case. I don't think there is currently a good way to handle this other than modifying the easyconfig file by hand...
Autoconf and Automake work, as they are pure shell and Perl scripts, but libtool really builds a library. Hth, Markus On 03/16/2017 05:22 PM, Siddiqui, Shahzeb wrote: > Has anyone else encountered this issue with GCCcore. I’d like to simply > by builds to use GCCcore for as many of my deps but I was not able to > get this resolved. The issue with rgdal seems to be an issue with > LibTIFF and I am not sure whether to build it and its dependencies with > foss, GCC, or GCCcore. > > > > > > > > *From:*Siddiqui, Shahzeb > *Sent:* Tuesday, March 14, 2017 1:55 PM > *To:* [email protected] > *Subject:* RE: [easybuild] RE: R-3.3.1-foss build error > > > > 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:*[email protected] > <mailto:[email protected]> > [mailto:[email protected]] *On Behalf Of *Kenneth Hoste > *Sent:* Tuesday, March 14, 2017 12:41 PM > *To:* [email protected] <mailto:[email protected]> > *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:*[email protected] > <mailto:[email protected]> > [mailto:[email protected]] *On Behalf Of *Kenneth Hoste > *Sent:* Tuesday, March 14, 2017 11:54 AM > *To:* [email protected] <mailto:[email protected]> > *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:*[email protected] > <mailto:[email protected]> > [mailto:[email protected]] *On Behalf Of *Kenneth Hoste > *Sent:* Saturday, March 11, 2017 12:47 PM > *To:* [email protected] <mailto:[email protected]> > *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:* [email protected] <mailto:[email protected]> > *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 > > > > > > > > > -- Dr. Markus Geimer Juelich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49-2461-61-1773 Fax: +49-2461-61-6656 E-Mail: [email protected] Web: http://www.fz-juelich.de/jsc ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
