[Debian-med-packaging] Bug#1056010: rsem: FTBFS: boost1.83 transition

[gladk at debian.org]

Source: rsem
Version: 1.3.3+dfsg-2
Severity: normal
User: gladk at debian.org
Usertags: boost183 ftbfs-boost183-transition

Hi,

we are preparing the transition of all libs on the new boost 1.83. During the
rebuild of packages against this library it was identified that probably your
package fails to build.

Relevant part (hopefully):

-----

g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp
In file included from SamParser.h:13,
                 from parseIt.cpp:27:
sam_utils.h: In function ‘void expand_data_size(bam1_t*)’:
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
   34 |   if (b->m_data < b->l_data) {
      |       ~~~~~~~~~~^~~~~~~~~~~
In file included from /usr/include/c++/13/type_traits:35,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:28,
                 from /usr/include/boost/math/special_functions/erf.hpp:13,
                 from /usr/include/boost/math/distributions/normal.hpp:19,
                 from LenDist.h:10,
                 from SingleModel.h:17,
                 from simulation.cpp:22:
/usr/include/c++/13/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
   32 | #error This file requires compiler and library support \
      |  ^~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~

-----

To reproduce this behavior, you can install  -dev Boost packages from the
experimental repository, as shown in the following command:

  apt install libboost-dev -t experimental


The full build log is available from:
http://qa-logs.debian.net/2023/10/27/rsem_1.3.3+dfsg-2_unstable_boost181.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-boost183-transition;users=gladk@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-boost183-transition&fusertaguser=gladk@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you are unable to reproduce this, please provide a build log and diff it
so that we can identify any relevant changes that may have occurred in the meantime.