Easyconfig for R-3.4.1 with updated packages by jdemeul · Pull Request #5090 · easybuilders/easybuild-easyconfigs

jdemeul · 2017-09-03T09:21:18Z

Added easyconfig for current R-3.4.1 release and updated package versions as well as order

verdurin · 2017-09-04T10:39:11Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
ca003.camp.thecrick.org - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/aeb529b040f31787dabd80035a47c62e for a full test report.

jdemeul · 2017-09-04T15:50:03Z

@verdurin, I'll give compilation a go again as well.
RWekajars (and RWeka) have previously compiled successfully here multiple times, so not really sure what's going on. Hope the source is still the same. If it still fails, I'm inclined to remove both packages, as nothing else seems to depend on them (also from the Bioconductor packages).

verdurin · 2017-09-05T07:36:40Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
ca005.camp.thecrick.org - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/942af0b1aff872ab652a550cfd8baa5c for a full test report.

boegel · 2017-09-05T07:49:00Z

@jdemeul @verdurin You're probably hitting a recent kernel bug, see #4833

jdemeul · 2017-09-06T13:46:23Z

Seems to be fixed/fine on a CentOS 7.3.1611 instance (kernel release: 3.10.0-514.16.1.el7.x86_64):

Test result

Successfully built /home/centos/easyconfigs/R-3.4.1-foss-2016b-X11-20160819.eb

Overview of tested easyconfigs (in order)

SUCCESS R-3.4.1-foss-2016b-X11-20160819.eb

Time info

start: Tue, 05 Sep 2017 13:51:58 +0000 (UTC)
end: Tue, 05 Sep 2017 19:01:22 +0000 (UTC)

EasyBuild info

easybuild-framework version: 3.3.1
easybuild-easyblocks version: 3.3.1
command line:

eb R-3.4.1-foss-2016b-X11-20160819.eb -r --robot-paths :/home/centos/easyconfigs/

full configuration (includes defaults):

--add-dummy-to-minimal-toolchains
--allow-loaded-modules='EasyBuild'
--buildpath='/tmp'
--check-ebroot-env-vars='warn'
--cleanup-builddir
--cleanup-easyconfigs
--cleanup-tmpdir
--color='auto'
--configfiles='/etc/easybuild.cfg'
--default-opt-level='defaultopt'
--detect-loaded-modules='warn'
--disable-allow-modules-tool-mismatch
--disable-allow-use-as-root-and-accept-consequences
--disable-avail-cfgfile-constants
--disable-avail-easyconfig-constants
--disable-avail-easyconfig-licenses
--disable-avail-easyconfig-params
--disable-avail-easyconfig-templates
--disable-avail-module-naming-schemes
--disable-avail-modules-tools
--disable-avail-repositories
--disable-check-conflicts
--disable-check-github
--disable-check-style
--disable-consider-archived-easyconfigs
--disable-debug
--disable-debug-lmod
--disable-devel
--disable-dry-run
--disable-dry-run-short
--disable-dump-autopep8
--disable-dump-env-script
--disable-enforce-checksums
--disable-experimental
--disable-extended-dry-run
--disable-fixed-installdir-naming-scheme
--disable-force
--disable-hidden
--disable-ignore-osdeps
--disable-info
--disable-install-github-token
--disable-install-latest-eb-release
--disable-job
--disable-last-log
--disable-list-toolchains
--disable-logtostdout
--disable-minimal-toolchains
--disable-module-only
--disable-new-pr
--disable-package
--disable-pretend
--disable-quiet
--disable-read-only-installdir
--disable-rebuild
--disable-recursive-module-unload
--disable-regtest
--disable-rpath
--disable-sequential
--disable-set-default-module
--disable-show-config
--disable-show-default-configfiles
--disable-show-default-moduleclasses
--disable-show-full-config
--disable-skip
--disable-skip-test-cases
--disable-sticky-bit
--disable-terse
--disable-update-modules-tool-cache
--disable-upload-test-report
--disable-use-existing-modules
--disable-verify-easyconfig-filenames
--extended-dry-run-ignore-errors
--group-writable-installdir
--group='easybuild'
--ignore-dirs='.git,.svn'
--include-easyblocks=''
--include-module-naming-schemes=''
--include-toolchains=''
--installpath='/srv/sw/eb'
--job-backend='GC3Pie'
--job-max-walltime='24'
--job-output-dir='/home/centos'
--job-polling-interval='30.0'
--logfile-format='easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log'
--max-fail-ratio-adjust-permissions='0.5'
--module-naming-scheme='EasyBuildMNS'
--module-syntax='Lua'
--moduleclasses='base,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,phys,system,toolchain,tools,vis'
--modules-tool='Lmod'
--mpi-tests
--optarch='GENERIC'
--output-format='txt'
--package-naming-scheme='EasyBuildPNS'
--package-release='1'
--package-tool-options=''
--package-tool='fpm'
--package-type='rpm'
--packagepath='/home/centos/.local/easybuild/packages'
--pr-target-account='easybuilders'
--pr-target-branch='develop'
--pr-target-repo='easybuild-easyconfigs'
--repository='FileRepository'
--repositorypath='/srv/sw/eb/ebfiles'
--robot-paths=':/home/centos/easyconfigs'
--robot='/srv/sw/eb/software/EasyBuild/3.3.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.3.1-py2.7.egg/easybuild/easyconfigs:/home/centos/easyconfigs'
--set-gid-bit
--sourcepath='/srv/sw/eb/sources'
--strict='warn'
--subdir-modules='modules'
--subdir-software='software'
--suffix-modules-path='all'
--umask='002'
--use-ccache='False'
--use-f90cache='False'

System info

core count: 8
cpu model: Intel Xeon E3-12xx v2 (Ivy Bridge)
cpu speed: 2399.998
cpu vendor: Intel
gcc version: Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) ;
glibc version: 2.17
hostname: frontend001
os name: centos linux
os type: Linux
os version: 7.3.1611
platform name: x86_64-unknown-linux
python version: 2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]
system gcc path: /usr/bin/gcc
system python path: /usr/bin/python
total memory: 48140

List of loaded modules

EasyBuild/3.3.1

Environment

BASH_ENV = /opt/lmod/lmod/init/bash
BASH_FUNC_ml() = () {  eval $($LMOD_DIR/ml_cmd "$@")
}
BASH_FUNC_module() = () {  eval $($LMOD_CMD bash "$@");
 [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
CPATH = /usr/include/x86_64-linux-gnu
EASYBUILD_CONFIGFILES = /etc/easybuild.cfg
EBDEVELEASYBUILD = /srv/sw/eb/software/EasyBuild/3.3.1/easybuild/EasyBuild-3.3.1-easybuild-devel
EBROOTEASYBUILD = /srv/sw/eb/software/EasyBuild/3.3.1
EBVERSIONEASYBUILD = 3.3.1
FANCYLOGGER_IGNORE_MPI4PY = 1
HOME = /home/centos
LANG = en_GB.UTF-8
LC_CTYPE = en_GB.UTF-8
LESSOPEN = ||/usr/bin/lesspipe.sh %s
LMOD_CMD = /opt/lmod/lmod/libexec/lmod
LMOD_COLORIZE = yes
LMOD_DIR = /opt/lmod/lmod/libexec
LMOD_FULL_SETTARG_SUPPORT = no
LMOD_PKG = /opt/lmod/lmod
LMOD_PREPEND_BLOCK = normal
LMOD_SETTARG_CMD = :
LMOD_SYSTEM_DEFAULT_MODULES = EasyBuild
LMOD_VERSION = 7.0
LMOD_arch = x86_64
LMOD_sys = Linux
LOADEDMODULES = EasyBuild/3.3.1
LOGNAME = centos
LUA_CPATH = /usr/lib/lua/5.1/?.so;;
LUA_PATH = /usr/share/lua/5.1/?.so;;
MAIL = /var/mail/centos
MANPATH = /opt/lmod/lmod/share/man::
MODULEPATH = /srv/sw/eb/modules/all:/etc/modulefiles/Linux:/etc/modulefiles/Core:/opt/lmod/lmod/modulefiles/Core
MODULEPATH_ROOT = /etc/modulefiles
MODULESHOME = /opt/lmod/lmod
PATH = /srv/sw/eb/software/EasyBuild/3.3.1/bin:/usr/local/bin:/usr/bin
PDSH_RCMD_TYPE = ssh
PWD = /home/centos
PYTHONOPTIMIZE = 1
PYTHONPATH = /srv/sw/eb/software/EasyBuild/3.3.1/lib/python2.7/site-packages
SELINUX_LEVEL_REQUESTED =
SELINUX_ROLE_REQUESTED =
SELINUX_USE_CURRENT_RANGE =
SHELL = /bin/bash
SHLVL = 3
SSH_CLIENT = 192.168.24.10 46968 22
SSH_CONNECTION = 192.168.24.10 46968 192.168.24.26 22
USER = centos
XDG_RUNTIME_DIR = /run/user/1000
XDG_SESSION_ID = 4
_ = /usr/bin/python2
_LMFILES_ = /srv/sw/eb/modules/all/EasyBuild/3.3.1.lua
_ModuleTable001_ = X01vZHVsZVRhYmxlXz17WyJNVHZlcnNpb24iXT0zLFsiY19yZWJ1aWxkVGltZSJdPWZhbHNlLFsiY19zaG9ydFRpbWUiXT1mYWxzZSxkZXB0aFQ9e30sZmFtaWx5PXt9LG1UPXtFYXN5QnVpbGQ9e1siZm4iXT0iL3Nydi9zdy9lYi9tb2R1bGVzL2FsbC9FYXN5QnVpbGQvMy4zLjEubHVhIixbImZ1bGxOYW1lIl09IkVhc3lCdWlsZC8zLjMuMSIsWyJsb2FkT3JkZXIiXT0xLHByb3BUPXt9LFsic3RhdHVzIl09ImFjdGl2ZSIsWyJ1c2VyTmFtZSJdPSJFYXN5QnVpbGQiLH0sfSxtcGF0aEE9eyIvc3J2L3N3L2ViL21vZHVsZXMvYWxsIiwiL2V0Yy9tb2R1bGVmaWxlcy9MaW51eCIsIi9ldGMvbW9kdWxlZmlsZXMvQ29yZSIsIi9vcHQvbG1vZC9sbW9kL21vZHVsZWZpbGVzL0NvcmUi
_ModuleTable002_ = LH0sWyJzeXN0ZW1CYXNlTVBBVEgiXT0iL3Nydi9zdy9lYi9tb2R1bGVzL2FsbDovZXRjL21vZHVsZWZpbGVzL0xpbnV4Oi9ldGMvbW9kdWxlZmlsZXMvQ29yZTovb3B0L2xtb2QvbG1vZC9tb2R1bGVmaWxlcy9Db3JlIix9
_ModuleTable_Sz_ = 2
__Lmod_Init_Default_Modules = 1

verdurin · 2017-09-06T14:03:01Z

@jdemeul Yes, I think that's an earlier kernel. If you update then re-run the build, you'll encounter the same problem I saw.

boegel · 2017-11-17T21:42:36Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2047.delcatty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/532bd90804b8ac48049946e61d48dec1 for a full test report.

boegel · 2017-11-18T00:44:16Z

Test report by @boegel
SUCCESS
Build succeeded for 37 out of 37 (1 easyconfigs in this PR)
node2605.swalot.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/d4b8a33ae69489c8d24b21fbdae529ba for a full test report.

boegel

lgtm

boegel · 2017-11-18T07:27:49Z

Going in, thanks @jdemeul!

jdemeul · 2017-11-18T10:27:31Z

Great, thanks for following up @boegel!

jdemeul added 2 commits September 3, 2017 11:13

Added R-3.4.1 + updated packages for foss2016b

f39dc55

Added checksum for R-3.4.1

6f72dfd

boegel added this to the 3.5.0 milestone Nov 17, 2017

boegel added the update label Nov 17, 2017

boegel approved these changes Nov 18, 2017

View reviewed changes

boegel merged commit 22d3889 into easybuilders:develop Nov 18, 2017

boegel mentioned this pull request Nov 21, 2017

correctly configure R for BLAS/LAPACK & check configure output easybuilders/easybuild-easyblocks#1292

Merged

jdemeul deleted the R3.4.1_easyconfigs_jd branch August 9, 2018 15:24

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Easyconfig for R-3.4.1 with updated packages#5090

Easyconfig for R-3.4.1 with updated packages#5090
boegel merged 2 commits intoeasybuilders:developfrom
jdemeul:R3.4.1_easyconfigs_jd

jdemeul commented Sep 3, 2017

Uh oh!

verdurin commented Sep 4, 2017

Uh oh!

jdemeul commented Sep 4, 2017

Uh oh!

verdurin commented Sep 5, 2017

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boegel commented Sep 5, 2017

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jdemeul commented Sep 6, 2017

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verdurin commented Sep 6, 2017

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boegel commented Nov 17, 2017

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jdemeul commented Sep 3, 2017

Uh oh!

verdurin commented Sep 4, 2017

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jdemeul commented Sep 4, 2017

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verdurin commented Sep 5, 2017

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boegel commented Sep 5, 2017

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jdemeul commented Sep 6, 2017

Test result

Overview of tested easyconfigs (in order)

Time info

EasyBuild info

System info

List of loaded modules

Environment

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verdurin commented Sep 6, 2017

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