{lang}[foss/2020b] R v4.0.3 #11663

boegel · 2020-11-11T08:51:42Z

(created using eb --new-pr)

verdurin · 2020-11-11T16:25:39Z

Test report by @verdurin
FAILED
Build succeeded for 11 out of 13 (1 easyconfigs in total)
nuc.lan - Linux Fedora 32, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.8.6
See https://gist.github.com/fd47c69227f8f6fb3fdf47f289adc457 for a full test report.

verdurin · 2020-11-11T16:34:37Z

The error here was in nodejs/12.19.0-GCCcore-10.2.0:

== 2020-11-11 16:20:11,708 easyblock.py:3063 INFO Running method configure_step part of step configure
== 2020-11-11 16:20:11,708 run.py:203 DEBUG run_cmd: running cmd  ./configure --prefix=/mnt/ds918plus/eb/nuc-fedora32/software/nodejs/12.19.0-GCCcore-10.2.0 --with-intl=none (in /mnt/ds918plus/eb/nuc-fedora32/build/nodejs/12.19.0/GCCcore-10.2.0/node-v12.19.0)
== 2020-11-11 16:20:11,708 run.py:222 INFO running cmd:  ./configure --prefix=/mnt/ds918plus/eb/nuc-fedora32/software/nodejs/12.19.0-GCCcore-10.2.0 --with-intl=none
== 2020-11-11 16:20:11,825 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " ./configure --prefix=/mnt/ds918plus/eb/nuc-fedora32/software/nodejs/12.19.0-GCCcore-10.2.0 --with-intl=none" exited with exit code 1 and output:
which: no python2.7 in (/mnt/ds918plus/eb/nuc-fedora32/software/Python/3.8.6-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/XZ/5.2.5-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/SQLite/3.33.0-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/Tcl/8.6.10-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/ncurses/6.2-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/bzip2/1.0.8-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/binutils/2.35-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/GCCcore/10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/EasyBuild/20201110-dev/bin:/home/adam/.local/bin:/home/adam/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
which: no python2 in (/mnt/ds918plus/eb/nuc-fedora32/software/Python/3.8.6-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/XZ/5.2.5-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/SQLite/3.33.0-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/Tcl/8.6.10-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/ncurses/6.2-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/bzip2/1.0.8-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/binutils/2.35-GCCcore-10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/GCCcore/10.2.0/bin:/mnt/ds918plus/eb/nuc-fedora32/software/EasyBuild/20201110-dev/bin:/home/adam/.local/bin:/home/adam/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
Please use Python 2.7
 (at easybuild/tools/run.py:533 in parse_cmd_output)

boegel · 2020-11-11T19:51:47Z

@verdurin Nice catch! Fixed in #11679...

verdurin · 2020-11-12T00:21:43Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
nuc.lan - Linux Fedora 32, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.8.6
See https://gist.github.com/adb69e1f47bacbb6f602d6406bea48c8 for a full test report.

boegel · 2020-11-12T08:03:47Z

@boegelbot please test @ generoso

boegelbot · 2020-11-12T08:05:08Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11663 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11663 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9757

Test results coming soon (I hope)...

- notification for comment with ID 725911267 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2020-11-12T11:04:16Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/afffcaa52ac7f2ffba50ecd141449573 for a full test report.

boegel · 2020-11-12T14:48:46Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3134.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/5fa75a98536b9c00abe3507a146438b1 for a full test report.

terjekv · 2020-11-12T16:19:13Z

Test report by @terjekv
SUCCESS
Build succeeded for 94 out of 94 (1 easyconfigs in total)
arm1 - Linux ubuntu 18.04, AArch64, UNKNOWN (aarch64), Python 3.6.9
See https://gist.github.com/3dd9ccc87668c6546af9487059987570 for a full test report.

verdurin · 2020-11-13T18:21:09Z

This is the CentOS 8 failure from generoso:

* installing *source* package hdf5r ...
** package hdf5r successfully unpacked and MD5 sums checked
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for gawk... gawk
checking for grep that handles long lines and -e... /usr/bin/grep
checking for gcc... gcc
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 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 egrep... /usr/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 Using provided HDF5 C wrapper... /users/boegelbot/CentOS8/haswell/software/HDF5/1.10.7-gompi-2020b/bin/h5pcc
checking for HDF5 libraries... yes (version 1.10.7)
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fcreate in -lhdf5... yes
checking for hdf5_hl.h... yes
checking for H5LTpath_valid in -lhdf5_hl... yes
checking for main in -lhdf5_hl... yes
checking for matching HDF5 Fortran wrapper... /users/boegelbot/CentOS8/haswell/software/HDF5/1.10.7-gompi-2020b/bin/h5pfc
Found hdf5 with version: 1.10.7
checking for ggrep... /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
cp 1_10_3/*.c 1_10_3/*.h .

<snip>

installing to /users/boegelbot/CentOS8/haswell/software/R/4.0.3-foss-2020b/lib64/R/library/00LOCK-hdf5r/00new/hdf5r/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Error in base::serialize(base::as.list(base::getNamespace("hdf5r"), all.names = TRUE),  : 
  error writing to connection
Calls: <Anonymous> -> withCallingHandlers -> <Anonymous>
Execution halted
ERROR: loading failed
 (at easybuild/easybuild-framework/easybuild/tools/run.py:533 in parse_cmd_output)

dithwick · 2020-12-01T17:53:08Z

Pretty minor comment but in R-4.0.3-foss-2020b.eb:
# ('OpenSSL', '1.1.1e'),
should be
# ('OpenSSL', '1.1.1h'),

boegel · 2020-12-05T10:08:08Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3136.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/ceeef7250da2b785c661d77a3487c9c3 for a full test report.

boegel · 2020-12-06T12:57:42Z

@boegelbot please test @ generoso

boegelbot · 2020-12-06T13:00:22Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11663 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11663 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12206

Test results coming soon (I hope)...

- notification for comment with ID 739499176 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegel · 2020-12-09T21:54:14Z

@boegelbot please test @ generoso

boegelbot · 2020-12-09T21:55:43Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11663 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11663 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12268

Test results coming soon (I hope)...

- notification for comment with ID 742086789 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2020-12-10T01:00:42Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/5925d90f7cddfaee2bbe736ab0bce1ce for a full test report.

boegel · 2020-12-10T01:04:46Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3501.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/4c3420981f365b0a957abeda68ce97bf for a full test report.

boegel · 2020-12-10T15:47:40Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node2638.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/ea7c0a9e32a79a82c425da4714cbddf2 for a full test report.

zao · 2020-12-19T12:19:03Z

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
eb-u1604 - Linux ubuntu 16.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 2.7.12
See https://gist.github.com/04d624cfa9bc8fdfbed05c7d8a239905 for a full test report.

boegel · 2020-12-21T09:27:08Z

@boegelbot please test @ generoso

boegelbot · 2020-12-21T09:30:40Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11663 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11663 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12328

Test results coming soon (I hope)...

- notification for comment with ID 748870601 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

zao · 2020-12-21T11:57:20Z

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
eb-u2004 - Linux Ubuntu 20.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 3.8.5
See https://gist.github.com/a194bd1d715cb8d7c1c00c166dea5e83 for a full test report.

zao · 2020-12-21T11:58:18Z

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
eb-u1604 - Linux ubuntu 16.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 2.7.12
See https://gist.github.com/d3de1532b1c7c30f5046ff38f0af933a for a full test report.

zao · 2020-12-21T12:02:40Z

Test report by @zao
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
eb-u1804 - Linux ubuntu 18.04, x86_64, Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz, Python 2.7.17
See https://gist.github.com/d293e5916aeb125b285ae71f66d32e8e for a full test report.

boegelbot · 2020-12-21T13:17:44Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/3ad43045bf78e531f7f709ad187c4dce for a full test report.

boegel · 2020-12-21T13:46:35Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3575.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/03c62faf5f88b2e41806c5be11e342d4 for a full test report.

boegel · 2020-12-21T14:09:50Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2658.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/daefdf8398bdf2000a1431712a6c46cd for a full test report.

boegel · 2020-12-21T14:11:35Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3117.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/e04c4f8d5d37e33f9dcce03f3b1beca1 for a full test report.

lexming · 2020-12-21T17:27:15Z

Test report by @lexming
SUCCESS
Build succeeded for 31 out of 31 (1 easyconfigs in total)
node352.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/1e1c0e927c8d8109c762ec6b11637ba2 for a full test report.

branfosj · 2020-12-21T18:38:37Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0306u11a.bear.cluster - Linux RHEL 8.2, POWER, 8335-GTX (power9le), Python 3.6.8
See https://gist.github.com/f4197565e84c73b765f096cd7c8b838c for a full test report.

branfosj

lgtm

zao · 2020-12-21T19:51:22Z

@boegel I'd like to have the -a option added to xvfb-run as it makes the build pass on my 16.04 system (in conjunction with having the fonts package installed).

lexming

LGTM

lexming · 2020-12-21T20:59:44Z

@zao as discusses in Slack, we will merge this PR as it is and follow on that issue in #11917

lexming · 2020-12-21T20:59:55Z

Going in, thanks @boegel !

adding easyconfigs: R-4.0.3-foss-2020b.eb

e4c93c2

boegel added the update label Nov 11, 2020

boegel added this to the 4.3.2 milestone Nov 11, 2020

boegel added the 2020b issues & PRs related to 2020b label Nov 11, 2020

boegel added 2 commits November 11, 2020 09:54

fix date when extensions were last updated in R 4.0.3 easyconfig

c5a9fd2

add missing patch for HWxtest extension in R 4.0.3

0064b8b

easybuilders deleted a comment from boegelbot Nov 11, 2020

boegel mentioned this pull request Nov 11, 2020

{lang}[foss/2020a] R v4.0.3 #11455

Closed

boegel mentioned this pull request Nov 11, 2020

use Python 2 build dep for nodejs 12.19.0 #11679

Merged

boegel added 2 commits December 4, 2020 15:02

Merge branch 'develop' into 20201111095132_new_pr_R403

1fb83f2

fix version for (commented out) OpenSSL dep

12226f3

easybuilders deleted a comment from boegelbot Dec 4, 2020

include blavaan + required packages as extensions in R 4.0.3 easyconfig

a6ff177

boegel force-pushed the 20201111095132_new_pr_R403 branch from 3556930 to a6ff177 Compare December 4, 2020 14:16

easybuilders deleted a comment from boegelbot Dec 4, 2020

easybuilders deleted a comment from boegelbot Dec 6, 2020

boegel modified the milestones: 4.3.2 (next release), 4.4.0 Dec 8, 2020

add path to v8.h to $CPATH when installing V8 extension in R 4.0.3

1a5a2cb

zao mentioned this pull request Dec 21, 2020

segfault during installation of gWidgets2tcltk extension in R 4.0.x easyconfigs when fonts are missing on system #11917

Open

branfosj approved these changes Dec 21, 2020

View reviewed changes

lexming approved these changes Dec 21, 2020

View reviewed changes

lexming merged commit c635f7f into easybuilders:develop Dec 21, 2020

boegel deleted the 20201111095132_new_pr_R403 branch December 21, 2020 21:12

boegel mentioned this pull request Dec 21, 2020

add additional extensions to R v4.0.3 easyconfig #11922

Merged

boegel mentioned this pull request Dec 29, 2020

R 4.0.3 foss-2020b #11938

Closed

{lang}[foss/2020b] R v4.0.3 #11663

{lang}[foss/2020b] R v4.0.3 #11663

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