{bio}[GCCcore/13.3.0] tbl2asn v20230713 #21803

laraPPr · 2024-11-07T16:07:27Z

(created using eb --new-pr)

github-actions · 2024-11-07T16:07:58Z

Updated software `tbl2asn-20230713-GCCcore-13.3.0.eb`

Diff against tbl2asn-20230713-GCCcore-12.3.0.eb

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
index dcf4c39e8d..12b79ddde0 100644
--- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
@@ -13,9 +13,9 @@ homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
 description = """Tbl2asn is a command-line program that automates the creation of
  sequence records for submission to GenBank"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 builddependencies = [
-    ('binutils', '2.40'),
+    ('binutils', '2.42'),
     ('patchelf', '0.18.0'),
 ]

Diff against tbl2asn-20230713-linux64.eb

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb

diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
index 71b750650b..12b79ddde0 100644
--- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb
+++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
@@ -8,17 +8,20 @@ easyblock = 'Bundle'
 
 name = 'tbl2asn'
 version = '20230713'
-versionsuffix = '-linux64'
 
 homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
 description = """Tbl2asn is a command-line program that automates the creation of
  sequence records for submission to GenBank"""
 
-toolchain = SYSTEM
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 builddependencies = [
-    ('binutils', '2.35'),
+    ('binutils', '2.42'),
+    ('patchelf', '0.18.0'),
 ]
 
+# libraries that are copied to installdir need to be patched to have an RPATH section
+# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);
+
 default_easyblock = 'CmdCp'
 
 # It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions,
@@ -36,7 +39,7 @@ components = [
     (name, version, {
         'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' %
                         (version[:4] + '-' + version[4:6] + '-' + version[6:])],
-        'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:],
+        'sources': [{'download_filename': 'tbl2asn.linux64.gz',
                     'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}],
         'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'],
         'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")],
@@ -44,7 +47,12 @@ components = [
     }),
 ]
 
-postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"]
+postinstallcmds = [
+    "if %(rpath_enabled)s; then "
+    "  patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;"
+    "fi",
+    "chmod +x %(installdir)s/bin/tbl2asn",
+]
 
 sanity_check_paths = {
     'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT],

Diff against tbl2asn-20220427-linux64.eb

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb

diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
index c1d2f495db..12b79ddde0 100644
--- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb
+++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.3.0.eb
@@ -7,18 +7,21 @@
 easyblock = 'Bundle'
 
 name = 'tbl2asn'
-version = '20220427'
-versionsuffix = '-linux64'
+version = '20230713'
 
 homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
 description = """Tbl2asn is a command-line program that automates the creation of
  sequence records for submission to GenBank"""
 
-toolchain = SYSTEM
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 builddependencies = [
-    ('binutils', '2.35'),
+    ('binutils', '2.42'),
+    ('patchelf', '0.18.0'),
 ]
 
+# libraries that are copied to installdir need to be patched to have an RPATH section
+# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);
+
 default_easyblock = 'CmdCp'
 
 # It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions,
@@ -36,15 +39,20 @@ components = [
     (name, version, {
         'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' %
                         (version[:4] + '-' + version[4:6] + '-' + version[6:])],
-        'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:],
+        'sources': [{'download_filename': 'tbl2asn.linux64.gz',
                     'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}],
-        'checksums': ['c76481700e196ebd98a83f4174e0146569db9d6fe5753ac18691e9836d5c6a75'],
+        'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'],
         'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")],
         'files_to_copy': [(['tbl2asn'], 'bin')],
     }),
 ]
 
-postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"]
+postinstallcmds = [
+    "if %(rpath_enabled)s; then "
+    "  patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;"
+    "fi",
+    "chmod +x %(installdir)s/bin/tbl2asn",
+]
 
 sanity_check_paths = {
     'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT],

laraPPr · 2024-11-07T16:13:57Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4006.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/laraPPr/968bcf22e579684b56142313fda1e0c8 for a full test report.

boegel

lgtm

boegel · 2024-11-07T17:06:53Z

@boegelbot please test @ generoso

boegelbot · 2024-11-07T17:10:12Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=21803 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21803 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14655

Test results coming soon (I hope)...

- notification for comment with ID 2462785072 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).

laraPPr · 2024-11-07T17:10:50Z

Test report by @laraPPr
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3108.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.11.3
See https://gist.github.com/laraPPr/6c0fc38e9e787dd9d8a4963f5b0f6147 for a full test report.

boegelbot · 2024-11-07T17:11:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/1f9e815d01709d392ac60eafb31d811a for a full test report.

laraPPr · 2024-11-07T17:15:33Z

Test report by @laraPPr
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3108.skitty.os - Linux RHEL 9.4 (Plow), x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.9.18
See https://gist.github.com/laraPPr/4bf9cc6687e9b427a4257e92572c5d53 for a full test report.

laraPPr · 2024-11-07T17:16:16Z

Test report by @laraPPr FAILED Build succeeded for 0 out of 1 (1 easyconfigs in total) node3108.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.11.3 See https://gist.github.com/laraPPr/6c0fc38e9e787dd9d8a4963f5b0f6147 for a full test report.

Need to use develop of the easybuild framework. I've just retriggered the build.

boegel · 2024-11-07T19:30:10Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-07T19:30:14Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21803 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21803 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5221

Test results coming soon (I hope)...

- notification for comment with ID 2463050889 processed

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-07T19:31:10Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/7b9ec61c372cf90d066220c51218da3f for a full test report.

boegel · 2024-11-07T19:49:43Z

@laraPPr Hmm, this looks like a missing dependency, perhaps?

tbl2asn: error while loading shared libraries: libidn.so.11: cannot open shared object file: No such file or directory

laraPPr · 2024-11-08T10:18:54Z

I picked a newer version of libidn and now it has this library libidn.so.12 Not sure though what it is looking for the libidn.so.11 if it is tbl2asn than I'll fall back to the older version

laraPPr · 2024-11-08T11:00:15Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3163.skitty.os - Linux RHEL 9.4 (Plow), x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.9.18
See https://gist.github.com/laraPPr/c3f8a58adb87e332f3bde0093727fe55 for a full test report.

laraPPr · 2024-11-08T11:17:18Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/laraPPr/07ba04bc8a5710073065538d58f0f548 for a full test report.

laraPPr · 2024-11-08T14:49:25Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-08T14:50:13Z

@laraPPr: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21803 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21803 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5237

Test results coming soon (I hope)...

- notification for comment with ID 2464947613 processed

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-08T14:51:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/a51b5606714e246d71fce49c83ab6d17 for a full test report.

laraPPr · 2024-11-08T14:57:25Z

@boegelbot please test @ generoso

boegelbot · 2024-11-08T15:00:11Z

@laraPPr: Request for testing this PR well received on login1

PR test command 'EB_PR=21803 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21803 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14668

Test results coming soon (I hope)...

- notification for comment with ID 2464967910 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 · 2024-11-08T15:01:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/40011fae8402c76e172a23dadeaf81fa for a full test report.

verdurin · 2024-11-11T09:20:38Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/be2bc6fb794565d5b646bb3760c13b83 for a full test report.

verdurin

Looks fine.

verdurin · 2024-11-11T09:24:25Z

Going in, thanks @laraPPr!

adding easyconfigs: tbl2asn-20230713-GCCcore-13.3.0.eb

340a88a

laraPPr added the update label Nov 7, 2024

laraPPr mentioned this pull request Nov 7, 2024

Funnannotate vscentrum/vsc-software-stack#426

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boegel added this to the 4.x milestone Nov 7, 2024

boegel previously approved these changes Nov 7, 2024

View reviewed changes

use version 1.34 for libidn

704118d

laraPPr dismissed boegel’s stale review via 704118d November 8, 2024 10:54

verdurin approved these changes Nov 11, 2024

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verdurin modified the milestones: 4.x, release after 4.9.4 Nov 11, 2024

verdurin merged commit a12c3e8 into easybuilders:develop Nov 11, 2024
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{bio}[GCCcore/13.3.0] tbl2asn v20230713 #21803

{bio}[GCCcore/13.3.0] tbl2asn v20230713 #21803

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{bio}[GCCcore/13.3.0] tbl2asn v20230713 #21803

{bio}[GCCcore/13.3.0] tbl2asn v20230713 #21803

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Updated software tbl2asn-20230713-GCCcore-13.3.0.eb

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Updated software `tbl2asn-20230713-GCCcore-13.3.0.eb`