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?
== 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]] 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
