On 13/03/2017 14:22, Siddiqui, Shahzeb wrote:
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.
We usually flesh out extensions that require additional dependencies
into a stand-alone module, but that's sort of site-specific choice...
So, in this case, I would look into an easyconfig file for nloptr that
depends on NLopt, or only an easyconfig for NLopt that installs nloptr
as extension as a part of it (since maybe using NLopt without nloptr
doesn't make much sense, I'm not sure).
regards,
Kenneth
Regards
*From:*[email protected]
[mailto:[email protected]] *On Behalf Of *Kenneth Hoste
*Sent:* Saturday, March 11, 2017 12:47 PM
*To:* [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
