{bio}[GCCcore/14.3.0] hifiasm v0.25.0 #24459

Micket · 2025-11-05T09:35:02Z

(created using eb --new-pr)

github-actions · 2025-11-05T09:35:28Z

Updated software `hifiasm-0.25.0-GCCcore-14.3.0.eb`

Diff against hifiasm-0.23.0-GCCcore-13.2.0.eb

easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
index 6d9b52352a..ee84853bdf 100644
--- a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.23.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
@@ -1,31 +1,30 @@
-# Author: Jasper Grimm (UoY)
-# Update: Sebastien Moretti (SIB), Denis Kristak (Inuits)
-
 easyblock = 'MakeCp'
 
 name = 'hifiasm'
-version = '0.23.0'
+version = '0.25.0'
 
 homepage = 'https://github.com/chhylp123/hifiasm'
 description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads."""
 # software_license = 'LicenseMIT'
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
 toolchainopts = {'opt': True}
 
 github_account = 'chhylp123'
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['52b4b615c2d2938b3b10cca4890c7857750f4a5ee54d5eb78c49dc638c9f14e0']
+checksums = ['51633138865207a9d41630da9377d46e4921ad4fc5facaa1740ceccae8611f1f']
 
 builddependencies = [
-    ('binutils', '2.40'),
+    ('binutils', '2.44'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.13'),
+    ('zlib', '1.3.1'),
 ]
 
+# include guard name __ASSEMBLY__ interferes with pthread.h
+prebuildopts = 'sed -i "s/__ASSEMBLY__/__ASSEMBLY_H__/" Assembly.h && '
 buildopts = 'CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" CPPFLAGS="$CPPFLAGS"'
 
 files_to_copy = [

Diff against hifiasm-0.19.7-GCCcore-12.2.0.eb

easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.7-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
index 15f778b588..ee84853bdf 100644
--- a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.7-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
@@ -1,31 +1,31 @@
-# Author: Jasper Grimm (UoY)
-# Update: Sebastien Moretti (SIB), Denis Kristak (Inuits)
-
 easyblock = 'MakeCp'
 
 name = 'hifiasm'
-version = '0.19.7'
+version = '0.25.0'
 
 homepage = 'https://github.com/chhylp123/hifiasm'
 description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads."""
 # software_license = 'LicenseMIT'
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchainopts = {'opt': True}
 
 github_account = 'chhylp123'
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['16d6127c7efb2d450630f25402a05e7d691b411465b304950d84d8afd53d5ee6']
+checksums = ['51633138865207a9d41630da9377d46e4921ad4fc5facaa1740ceccae8611f1f']
 
 builddependencies = [
-    ('binutils', '2.39'),
+    ('binutils', '2.44'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.12'),
+    ('zlib', '1.3.1'),
 ]
 
-buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"'
+# include guard name __ASSEMBLY__ interferes with pthread.h
+prebuildopts = 'sed -i "s/__ASSEMBLY__/__ASSEMBLY_H__/" Assembly.h && '
+buildopts = 'CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" CPPFLAGS="$CPPFLAGS"'
 
 files_to_copy = [
     ([name], 'bin'),

Diff against hifiasm-0.19.5-GCCcore-11.2.0.eb

easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
index 8d271908c7..ee84853bdf 100644
--- a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.25.0-GCCcore-14.3.0.eb
@@ -1,31 +1,31 @@
-# Author: Jasper Grimm (UoY)
-# Update: Sebastien Moretti (SIB)
-
 easyblock = 'MakeCp'
 
 name = 'hifiasm'
-version = '0.19.5'
+version = '0.25.0'
 
 homepage = 'https://github.com/chhylp123/hifiasm'
 description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads."""
 # software_license = 'LicenseMIT'
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchainopts = {'opt': True}
 
 github_account = 'chhylp123'
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['18ed6889972e38d0088ccbdafee90756158977d6b1e1b6e56f522b870d71c072']
+checksums = ['51633138865207a9d41630da9377d46e4921ad4fc5facaa1740ceccae8611f1f']
 
 builddependencies = [
-    ('binutils', '2.37'),
+    ('binutils', '2.44'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.11'),
+    ('zlib', '1.3.1'),
 ]
 
-buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"'
+# include guard name __ASSEMBLY__ interferes with pthread.h
+prebuildopts = 'sed -i "s/__ASSEMBLY__/__ASSEMBLY_H__/" Assembly.h && '
+buildopts = 'CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" CPPFLAGS="$CPPFLAGS"'
 
 files_to_copy = [
     ([name], 'bin'),

Thyre · 2025-11-05T10:02:25Z

Test report by @Thyre
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/04da81f49eca15f1d9c7f6fc7a8d499b for a full test report.

Thyre · 2025-11-05T10:02:56Z

Test report by @Thyre
SUCCESS
Build succeeded for 1 out of 1 (total: 42 secs) (1 easyconfigs in total)
ZAM054 - Linux Zorin OS 18, x86_64, 12th Gen Intel(R) Core(TM) i7-1260P (skylake), 1 x NVIDIA NVIDIA GeForce MX550, 580.95.05, Python 3.12.3
See https://gist.github.com/Thyre/68a1131f758a5aa8cd6dc43812d6ea10 for a full test report.

Thyre · 2025-11-05T10:07:18Z

Test report by @Thyre
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/04da81f49eca15f1d9c7f6fc7a8d499b for a full test report.

That's a package simply broken with aarch64. LLVM provides a header for this, GCC doesn't.
Shouldn't be a blocker, but good to know...

Thyre · 2025-11-05T10:07:46Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-11-05T10:10:10Z

@Thyre: 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=24459 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24459 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8650

Test results coming soon (I hope)...

- notification for comment with ID 3490311540 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 · 2025-11-05T10:11:30Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (total: 1 min 2 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/b7c3ed08686e013302ba4b8172f1b912 for a full test report.

Micket · 2025-11-05T11:03:02Z

I just made this to test #24435 since I didn't have an old toolchain to test with.

Micket · 2025-11-06T15:10:06Z

#24435 (comment) I found the bug here

Micket · 2025-11-06T16:19:33Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-11-06T16:20:10Z

@Micket: 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=24459 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24459 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8668

Test results coming soon (I hope)...

- notification for comment with ID 3498163694 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).

Micket · 2025-11-06T16:20:54Z

Test report by @Micket
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
vera-zen4-build - Linux Rocky Linux 9.6 (Blue Onyx), x86_64, QEMU Virtual CPU version 2.5+, Python 3.9.21
See https://gist.github.com/Micket/773879e0a1d1a2748f403ed082131b02 for a full test report.

boegelbot · 2025-11-06T16:21:37Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 1 min 10 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/0375d4acf2f7d48304f4ea18904d276f for a full test report.

adding easyconfigs: hifiasm-0.25.0-GCCcore-14.3.0.eb

72680f8

Micket added the update label Nov 5, 2025

github-actions bot added the 2025b issues & PRs related to 2025b common toolchains label Nov 5, 2025

Fix include guard

81d3e39

Micket assigned smoors Nov 7, 2025

{bio}[GCCcore/14.3.0] hifiasm v0.25.0 #24459

Are you sure you want to change the base?

{bio}[GCCcore/14.3.0] hifiasm v0.25.0 #24459

Uh oh!

Conversation

Micket commented Nov 5, 2025

Uh oh!

github-actions bot commented Nov 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Updated software hifiasm-0.25.0-GCCcore-14.3.0.eb

Uh oh!

Thyre commented Nov 5, 2025

Uh oh!

Thyre commented Nov 5, 2025

Uh oh!

Thyre commented Nov 5, 2025

Uh oh!

Thyre commented Nov 5, 2025

Uh oh!

boegelbot commented Nov 5, 2025

Uh oh!

boegelbot commented Nov 5, 2025

Uh oh!

Micket commented Nov 5, 2025

Uh oh!

Micket commented Nov 6, 2025

Uh oh!

Micket commented Nov 6, 2025

Uh oh!

boegelbot commented Nov 6, 2025

Uh oh!

Micket commented Nov 6, 2025

Uh oh!

boegelbot commented Nov 6, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

github-actions bot commented Nov 5, 2025 •

edited

Loading

Updated software `hifiasm-0.25.0-GCCcore-14.3.0.eb`