Ok so we would add NLopt as a dependency in R easyconfig. Will this fix the installation for nloptr?
I would think we would also need NLopt for other toolchains like foss, intel so those could build also. Regards From: 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 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
