Re: [easybuild] RE: R-3.3.1-foss build error

Tue, 14 Mar 2017 09:46:21 -0700 

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] *On Behalf Of *Kenneth Hoste

*Sent:* Tuesday, March 14, 2017 11:54 AM
*To:* 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

























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