Debian Patches

Status for cufflinks/2.2.1+dfsg.1-10

Patch Description Author Forwarded Bugs Origin Last update
gcc14.patch fix build failure with gcc 14. This change fixes the following failure, now appearing with the new
warnings gone fatal with gcc 14:
.
locfit/c_plot.c:470:14: error: passing argument 1 of 'setvarname' from incompatible pointer type [-Wincompatible-pointer-types]
470 | setvarname(curstr,tname);
| ^~~~~~
| |
| char *
In file included from locfit/lffuns.h:214,
from locfit/local.h:106,
from locfit/c_plot.c:6:
locfit/vari.hpp:16:27: note: expected 'vari *' but argument is of type 'char *'
16 | void setvarname(vari* v, varname name);
| ~~~~~~^		 Étienne Mollier <emollier@debian.org> no debian 2024-08-27
py2to3.patch Convert cuffmerge to py3, thanks to Cheng H. Lee,see https://github.com/biobuilds/cufflinks/issues/1 Alex Mestiashvili <amestia@rsh2.donotuse.de> no
0002-bam2samtools.patch bam2samtools Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> no 2011-12-02
boost1.65.patch Fix FTBFS, boost::tr1 no longer exists. Dimitri John Ledkov <xnox@ubuntu.com> no
fix_gcc-6.1_issue_in_liblemon_code_copy.patch Fix a build issue caused by an unmaintained code copy of liblemon.
Remark: Cufflinks does not build with the current Debian packaged liblemon.
If you want to try you can use the branch use_debian_packaged_liblemon
in the packaging Git		 Graham Inggs <ginggs@debian.org> no debian 2016-08-15
0004-fix-m64-usage-and-lfs.patch Update configure.ac to not force -m64.Just because the compiler supports it, doesn't mean it can compile
natively to it (e.g. on powerpc, you can compile -m64, but there are
no headers for it plus it cannot run on 32-bit systems).		 Ben Collins <bcollins@ubuntu.com> no
gcc10.patch Fix FTBFS with GCC 10 curwin is declared in different source file. declare it as extern
to fix multiple definition linker error.		 Reiner Herrmann <reiner@reiner-h.de> no debian
fix_gcc-7_ftbfs.patch Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net> Alex Mestiashvili <mailatgoogl@gmail.com> no debian https://lists.debian.org/debian-med/2017/09/msg00021.html
0001-fix_spelling.patch Fix spelling Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> no 2017-09-05
0003-fix_includes_path.patch fix_includes_path.patch Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> no 2011-12-02
format-security.patch When building with --format-security (Debhelper 9 hardening) this patch is needed to build successfully Andreas Tille <tille@debian.org> no 2013-05-22
lib_eigen.patch For some reason Eigen thinks that v.colwise().sum() cannot be treated as a one-dimensional vector, which smells like a bug in Eigen.
https://github.com/cole-trapnell-lab/cufflinks/issues/61		 Jakub Wilk <jwilk@debian.org> no 2016-07-12
no_svnversion.patch Prevent that AM_INIT_AUTOMAKE is called twice Andreas Tille <tille@debian.org> no debian 2021-11-02

All known versions for source package 'cufflinks'

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