Your message dated Mon, 18 Dec 2023 13:22:51 +0000
with message-id <[email protected]>
and subject line Bug#1056010: fixed in rsem 1.3.3+dfsg-3
has caused the Debian Bug report #1056010,
regarding rsem: FTBFS: boost1.83 transition
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1056010: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1056010
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: rsem
Version: 1.3.3+dfsg-2
Severity: normal
User: [email protected]
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 âvoid expand_data_size(bam1_t*)â:
sam_utils.h:34:17: warning: comparison of integer expressions of different
signedness: âuint32_tâ {aka âunsigned intâ} and âintâ
[-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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-boost183-transition&[email protected]&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.
--- End Message ---
--- Begin Message ---
Source: rsem
Source-Version: 1.3.3+dfsg-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
rsem, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated rsem package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 18 Dec 2023 13:58:36 +0100
Source: rsem
Architecture: source
Version: 1.3.3+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1056010
Changes:
rsem (1.3.3+dfsg-3) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Fix salca-ci since i386 is explicitly excluded by Build-Depends: bowtie2
.
[ Étienne Mollier ]
* stdgnu++11.patch: new: fix ftbfs with boost1.83.
boost1.83 looks to require building with gnu++11, but upstream
codebase is still at gnu++98 for now, hence the nature of the patch.
(Closes: #1056010)
* d/control: declare compliance to standards version 4.6.2.
* d/control: build depend on libncurses-dev.
This replaces the obsolete libncurses5-dev.
Checksums-Sha1:
b8d154ddc3af8e02d7c7a585c7853e9ad8b4dec6 2249 rsem_1.3.3+dfsg-3.dsc
05cea0dbf74cb2855055322ee7ec48f022ac1a9a 35660968
rsem_1.3.3+dfsg-3.debian.tar.xz
Checksums-Sha256:
ef9ae7d277c0f1ecc5daee18f4f26698575df18170047e63f365ae0228c93889 2249
rsem_1.3.3+dfsg-3.dsc
957be6fa620d1a09db0e41fe6207d56ee60a8e938f5a594176c068d78e063204 35660968
rsem_1.3.3+dfsg-3.debian.tar.xz
Files:
ad1d927d0d748bbe65d9cb0a7449d421 2249 science optional rsem_1.3.3+dfsg-3.dsc
4371920046ae5a0f654c8cae94a84c0c 35660968 science optional
rsem_1.3.3+dfsg-3.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=1XrR
-----END PGP SIGNATURE-----
--- End Message ---
