Your message dated Thu, 23 Apr 2020 10:36:27 +0000
with message-id <e1jrzdx-00059j...@fasolo.debian.org>
and subject line Bug#952102: fixed in salmon 1.2.1+ds1-1
has caused the Debian Bug report #952102,
regarding salmon: FTBFS: SalmonAlevin.cpp:780:6: error: ‘class
rapmap::utils::MappingConfig’ has no member named ‘maxSlack’
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 ow...@bugs.debian.org
immediately.)
--
952102: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=952102
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: salmon
Version: 0.12.0+ds1-1
Severity: serious
Justification: FTBFS on amd64
Tags: buster sid
Usertags: ftbfs-20200222 ftbfs-buster
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
> -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1
> -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<<PKGBUILDDIR>>/include
> -I/usr/include/eigen3 -I/<<PKGBUILDDIR>>/external
> -I/<<PKGBUILDDIR>>/external/cereal/include
> -I/<<PKGBUILDDIR>>/external/install/include -I/usr/include/rapmap
> -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o
> CMakeFiles/salmon.dir/WhiteList.cpp.o -c /<<PKGBUILDDIR>>/src/WhiteList.cpp
> In file included from /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:74:
> /usr/include/tbb/task_scheduler_init.h:21:154: note: #pragma message: TBB
> Warning: tbb/task_scheduler_init.h is deprecated. For details, please see
> Deprecated Features appendix in the TBB reference manual.
> 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is
> deprecated. For details, please see Deprecated Features appendix in the TBB
> reference manual.")
> |
>
> ^
> In file included from /<<PKGBUILDDIR>>/include/CollapsedCellOptimizer.hpp:9,
> from /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:91:
> /usr/include/tbb/atomic.h:21:141: note: #pragma message: TBB Warning:
> tbb/atomic.h is deprecated. For details, please see Deprecated Features
> appendix in the TBB reference manual.
> 21 | #pragma message("TBB Warning: tbb/atomic.h is deprecated. For
> details, please see Deprecated Features appendix in the TBB reference
> manual.")
> |
> ^
> In file included from /<<PKGBUILDDIR>>/src/WhiteList.cpp:2:
> /usr/include/tbb/task_scheduler_init.h:21:154: note: #pragma message: TBB
> Warning: tbb/task_scheduler_init.h is deprecated. For details, please see
> Deprecated Features appendix in the TBB reference manual.
> 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is
> deprecated. For details, please see Deprecated Features appendix in the TBB
> reference manual.")
> |
>
> ^
> /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp: In function ‘void
> processReadsQuasi(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&,
> alevin::AlnGroupVec<rapmap::utils::QuasiAlignment>&, std::atomic<long
> unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned
> int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&,
> std::atomic<unsigned int>&, RapMapIndexT*, std::vector<Transcript>&,
> ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&,
> BiasParams&, SalmonOpts&, std::mutex&, bool, std::atomic<bool>&, volatile
> bool&, AlevinOpts<ProtocolT>&, SoftMapT&,
> spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&)’:
> /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:780:6: error: ‘class
> rapmap::utils::MappingConfig’ has no member named ‘maxSlack’
> 780 | mc.maxSlack = salmonOpts.consensusSlack;
> | ^~~~~~~~
> make[4]: *** [src/CMakeFiles/salmon.dir/build.make:274:
> src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2020/02/22/salmon_0.12.0+ds1-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: salmon
Source-Version: 1.2.1+ds1-1
Done: michael.cru...@gmail.com (Michael R. Crusoe)
We believe that the bug you reported is fixed in the latest version of
salmon, 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 952...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <michael.cru...@gmail.com> (supplier of updated salmon
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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 23 Apr 2020 12:13:04 +0200
Source: salmon
Architecture: source
Version: 1.2.1+ds1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <michael.cru...@gmail.com>
Closes: 952102
Changes:
salmon (1.2.1+ds1-1) unstable; urgency=medium
.
* New upstream version (Closes: #952102)
* debhelper-compat 12
* Standards-Version: 4.5.0 (routine-update)
* Secure URI in copyright format (routine-update)
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
update)
* Set upstream metadata fields: Bug-Database, Bug-Submit.
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
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Checksums-Sha256:
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Files:
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