Debian Patches

Status for cufflinks/2.2.1+git20190706.dc3b0cb+dfsg-1

Patch Description Author Forwarded Bugs Origin Last update
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
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
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
0001-fix_spelling.patch Fix spelling Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> no 2017-09-05
0002-bam2samtools.patch Make sure bam.h will be found Debian's libbam-dev installs the (legacy) samtools headers under
/usr/include/samtools/ rather than /usr/include/bam/. Adapt the configure
test and the library detection loop so that a plain -lbam is linked.		 Andreas Tille <tille@debian.org> no 2026-09-21
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
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
no_svnversion.patch Prevent that AM_INIT_AUTOMAKE is called twice Andreas Tille <tille@debian.org> no debian 2021-11-02
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
gcc15.patch Build with gcc-15 It might make actually sense to provide a separate locfit library under the
new free license which was used in the r-cran-locfit package.

diff --git a/src/locfit/adap.c b/src/locfit/adap.c
index eb1b48c..82cbd62 100644		 Andreas Tille <tille@debian.org> no debian 2026-09-20
cxxstandard.patch Force a sane C++ standard instead of upstream's -std=c++03 The upstream configure forced the C++ compiler to C++03, which is no longer
accepted by the system headers shipped with GCC 16 (libstdc++ requires
C++11), Boost 1.90 and Eigen 5. Compiling with the compiler default
(C++23 on GCC 16) on the other hand breaks the bundled LEMON graph
library, which still uses std::allocator::construct/destroy (removed in
C++20). Force -std=gnu++17, which satisfies all the requirements and
matches what the previous Debian versions were built with.
assisted by https://inference.debian.net/ Model DeepSeek V4 Flash 0731		 Andreas Tille <tille@debian.org> no debian 2026-09-21
byte.patch Fix build with GCC 16 (C++17): use uint8_t instead of bare 'byte' Upstream defines 'typedef unsigned char byte;' in GBase.h, which collides
with std::byte from <cstddef> under the newer C++ standards used by the
GCC 16 toolchain. Drop the typedef and use uint8_t instead. Also fix a
few old-style declarations in the bundled locfit C code.
assisted by https://inference.debian.net/ Model DeepSeek V4 Flash 0731		 Andreas Tille <tille@debian.org> no debian 2026-09-21

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