[med-svn] [Git][med-team/cufflinks][master] 7 commits: - Force -std=gnu11 when compiling the legacy locfit C code so that old-style...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / cufflinks


Commits:
f563355d by Andreas Tille at 2026-09-20T21:28:58+02:00
- Force -std=gnu11 when compiling the legacy locfit C code so that old-style "extern f();" declarations keep their pre-C23 meaning of "unspecified arguments" instead of "no arguments" - gcc15.patch: fix broken function signatures (prresp, compbandwid, wdexpand, compsda, widthsj, kdecri, ar_setfunction, extern INT fact[])

  - Force -std=gnu11 when compiling the legacy locfit C code so that
    old-style "extern f();" declarations keep their pre-C23 meaning of
    "unspecified arguments" instead of "no arguments"
  - gcc15.patch: fix broken function signatures (prresp, compbandwid,
    wdexpand, compsda, widthsj, kdecri, ar_setfunction, extern INT fact[])

- - - - -
26379120 by Andreas Tille at 2026-09-20T21:37:49+02:00
New upstream version 2.2.1+git20190706.dc3b0cb+dfsg
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0a0eb86a by Andreas Tille at 2026-09-20T21:37:51+02:00
Update upstream source from tag 'upstream/2.2.1+git20190706.dc3b0cb+dfsg'

Update to upstream version '2.2.1+git20190706.dc3b0cb+dfsg'
with Debian dir 36fc6f8f0df1245ea4560d9e5f16fe43d92ac4aa
- - - - -
bbfae3fd by Andreas Tille at 2026-09-20T21:39:46+02:00
Rebase patches to latest upstream version

- - - - -
83ee1154 by Andreas Tille at 2026-09-20T21:42:23+02:00
Build-Depends: libboost-filesystem-dev

- - - - -
7ce28965 by Andreas Tille at 2026-09-20T21:44:43+02:00
* Build-Depends:

   - libboost-filesystem-dev
   - s/dh-python/dh-sequence-python3/

- - - - -
bf2c642d by Andreas Tille at 2026-09-20T21:47:24+02:00
New upstream version (latest commit)

- - - - -


67 changed files:

- + .gitignore
- AUTHORS
- − README
- + README.md
- ax_bam.m4
- ax_boost_base.m4
- + ax_boost_filesystem.m4
- ax_boost_serialization.m4
- ax_boost_system.m4
- ax_boost_thread.m4
- ax_check_eigen.m4
- configure.ac
- debian/changelog
- debian/control
- debian/patches/0001-fix_spelling.patch
- debian/patches/0002-bam2samtools.patch
- debian/patches/0003-fix_includes_path.patch
- debian/patches/0004-fix-m64-usage-and-lfs.patch
- − debian/patches/boost1.65.patch
- debian/patches/byte.patch
- − debian/patches/fix_gcc-6.1_issue_in_liblemon_code_copy.patch
- debian/patches/fix_gcc-7_ftbfs.patch
- debian/patches/gcc15.patch
- debian/patches/lib_eigen.patch
- debian/patches/no_svnversion.patch
- debian/patches/py2to3.patch
- debian/patches/series
- debian/rules
- + index.md
- src/GArgs.cpp
- src/GArgs.h
- src/GBase.cpp
- src/GBase.h
- src/GFastaIndex.cpp
- src/GHash.hh
- src/GList.hh
- src/GVec.hh
- src/Makefile.am
- src/abundances.cpp
- src/biascorrection.cpp
- src/biascorrection.h
- src/bundles.cpp
- src/bundles.h
- src/clustering.h
- src/common.cpp
- src/common.h
- src/cuffcompare.cpp
- src/cuffdiff.cpp
- src/cuffdiff_to_gct.py
- src/cufflinks.cpp
- src/cuffmerge
- src/cuffnorm.cpp
- src/cuffquant.cpp
- src/differential.cpp
- src/differential.h
- src/filters.cpp
- src/gff.cpp
- src/gff.h
- src/gtf_reads.cpp
- src/gtf_tracking.h
- src/hits.cpp
- src/hits.h
- src/lemon/error.h
- src/replicates.cpp
- src/replicates.h
- src/transitive_closure.h
- src/update_check.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/c0672a03dcb9507d3185901e16131cb0c4a0ae28...bf2c642dd7e03713cbe73c9c4b3531c145853056

-- 
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/c0672a03dcb9507d3185901e16131cb0c4a0ae28...bf2c642dd7e03713cbe73c9c4b3531c145853056
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