[med-svn] [Git][med-team/kallisto][master] 4 commits: debputy lint --auto-fix (routine-update)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Oct 18 17:33:20 BST 2025
Andreas Tille pushed to branch master at Debian Med / kallisto
Commits:
f67318d9 by Andreas Tille at 2025-10-18T11:59:46+02:00
debputy lint --auto-fix (routine-update)
- - - - -
f5e28c2f by Andreas Tille at 2025-10-18T16:42:46+02:00
d/rules: work around gcc-15 build issue using std=gnu17
- - - - -
992ad77d by Andreas Tille at 2025-10-18T18:10:10+02:00
bifrost: Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE
- - - - -
fe0400cb by Andreas Tille at 2025-10-18T18:32:48+02:00
Fix typo in bifrost
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/bifrost_typo.patch
- + debian/patches/fix_bifrost_defines.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -12,6 +12,10 @@ kallisto (0.51.1+dfsg-1) UNRELEASED; urgency=medium
* d/watch: version=5
* Cleanup properly after build time test + fix clean target
Closes: #1047324
+ * debputy lint --auto-fix (routine-update)
+ * d/rules: work around gcc-15 build issue using std=gnu17
+ * bifrost: Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE
+ * Fix typo in bifrost
[ Michael R. Crusoe ]
* d/control: simplify architecture specifications by using provisions
=====================================
debian/control
=====================================
@@ -1,17 +1,19 @@
Source: kallisto
+Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- architecture-is-64-bit,
- catch2,
- cmake,
- libbifrost-dev,
- libhdf5-dev,
- libhts-dev,
- snakemake <!nocheck>,
-Standards-Version: 4.7.2
+Build-Depends:
+ debhelper-compat (= 13),
+ architecture-is-64-bit,
+ catch2,
+ cmake,
+ libbifrost-dev,
+ libhdf5-dev,
+ libhts-dev,
+ snakemake <!nocheck>,
Vcs-Browser: https://salsa.debian.org/med-team/kallisto
Vcs-Git: https://salsa.debian.org/med-team/kallisto.git
Homepage: https://pachterlab.github.io/kallisto
@@ -19,8 +21,9 @@ Rules-Requires-Root: no
Package: kallisto
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: near-optimal RNA-Seq quantification
Kallisto is a program for quantifying abundances of transcripts from
RNA-Seq data, or more generally of target sequences using high-throughput
@@ -38,10 +41,13 @@ Description: near-optimal RNA-Seq quantification
Package: kallisto-examples
Architecture: all
-Depends: ${misc:Depends}
-Recommends: kallisto
Multi-Arch: foreign
-Suggests: snakemake
+Depends:
+ ${misc:Depends},
+Recommends:
+ kallisto,
+Suggests:
+ snakemake,
Description: near-optimal RNA-Seq quantification (example data)
Kallisto is a program for quantifying abundances of transcripts from
RNA-Seq data, or more generally of target sequences using high-throughput
=====================================
debian/patches/bifrost_typo.patch
=====================================
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2025-10-18
+Description: Seems there is a typo
+ sz_link is a local variable in the constructor, not a class member which leads to
+
+In file included from /build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataManager.hpp:10:
+/build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataStorage.tcc: In copy constructor 'DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)':
+/build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataStorage.tcc:81:69: error: 'const class DataStorage<Unitig_data_t>' has no member named 'sz_link' [-Wtemplate-body]
+ 81 | for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
+ | ^~~~~~~
+
+--- a/ext/bifrost/src/DataStorage.tcc
++++ b/ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,7 @@ DataStorage<U>::DataStorage(const DataSt
+
+ unitig_cs_link = new atomic<uint64_t>[sz_link];
+
+- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+ }
+
+ if ((o.data != nullptr) && (o.sz_cs != 0)){
=====================================
debian/patches/fix_bifrost_defines.patch
=====================================
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2025-10-18
+Description: Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE
+ (Any hint how to inject these without patching welcome)
+
+--- a/ext/bifrost/CMakeLists.txt
++++ b/ext/bifrost/CMakeLists.txt
+@@ -5,7 +5,8 @@ project(Bifrost)
+ find_package(Threads REQUIRED)
+
+ # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
+-SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
++SET(MAX_KMER_SIZE "31" CACHE STRING "MAX_KMER_SIZE")
++SET(MAX_GMER_SIZE "63" CACHE STRING "MAX_GMER_SIZE")
+ # Enable architecture optimizations
+ SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
+ # Enable AVX2 instructions
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ htslib1.3
gcc11.patch
disable-failing-bustools-test.patch
#use_debian_packaged_bifrost.patch
+fix_bifrost_defines.patch
+bifrost_typo.patch
=====================================
debian/rules
=====================================
@@ -9,6 +9,8 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
-DBUILD_FUNCTESTING=1 -DUSE_BAM=1 \
-DCMAKE_POLICY_VERSION_MINIMUM=3.5
+export DEB_CFLAGS_MAINT_APPEND += -std=gnu17
+
%:
dh $@
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/096fd9a5934b5ee5f29ac66cd8b7c633d29ef97d...fe0400cbaf82390710e86ba5961dc943234f79ed
--
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/096fd9a5934b5ee5f29ac66cd8b7c633d29ef97d...fe0400cbaf82390710e86ba5961dc943234f79ed
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20251018/7e048936/attachment-0001.htm>
More information about the debian-med-commit
mailing list