Your message dated Mon, 26 May 2025 20:39:27 +0000
with message-id <e1ujebx-00aanu...@fasolo.debian.org>
and subject line Bug#1105544: fixed in ncbi-tools6 6.1.20170106+dfsg2-6
has caused the Debian Bug report #1105544,
regarding ncbi-tools6: FTBFS with make --shuffle=reverse: mv: cannot stat
'algorend.o': No such file or directory
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
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--
1105544: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105544
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ncbi-tools6
Version: 6.1.20170106+dfsg2-5
Severity: minor
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-shuffle
Hi,
GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/
This package fails to build with make --shuffle=reverse.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.
More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle
Relevant part (hopefully):
> ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o
> blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o
> blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o
> blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o
> gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o
> ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o
> blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o
> blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o
> blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o
> blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o
> gencode_singleton.o index_ungapped.o hspfilter_collector.o
> blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.o
> ar: `u' modifier ignored since `D' is the default (see `U')
> cp -p libblast.a ../lib
> ranlib ../lib/libblast.a
> makefile:517: update target 'algorend.glo' due to: target does not exist
> mv algorend.o algorend.tmp
> mv: cannot stat 'algorend.o': No such file or directory
> make[3]: *** [makefile:517: algorend.glo] Error 1 shuffle=reverse
The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/ncbi-tools6_6.1.20170106+dfsg2-5_unstable_reverse.log
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
--- End Message ---
--- Begin Message ---
Source: ncbi-tools6
Source-Version: 6.1.20170106+dfsg2-6
Done: Aaron M. Ucko <u...@debian.org>
We believe that the bug you reported is fixed in the latest version of
ncbi-tools6, 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 1105...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-tools6 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: Mon, 26 May 2025 15:40:41 -0400
Source: ncbi-tools6
Architecture: source
Version: 6.1.20170106+dfsg2-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <u...@debian.org>
Closes: 1105544
Changes:
ncbi-tools6 (6.1.20170106+dfsg2-6) unstable; urgency=medium
.
* Fix or work around build-order assumptions caught by
make --shuffle=reverse. (Closes: #1105544.)
- debian/rules: Explicitly invoke copy targets before compilation.
- make/makeall.unx: Build *.glo directly; GCC's on board with it, and
the current logic breaks when corresponding *.o files don't yet exist.
- make/makenet.unx: Explicitly build all static libraries encompassed
by nocopy or given as extra goals before any shared libraries.
* debian/copyright: Substitute a URL for the FSF's postal address.
(See #1080497.)
* Standards-Version: 4.7.2 (routine-update)
Checksums-Sha1:
c11e74bc97b30b32c4d100b843799d7e831f8cbd 2905
ncbi-tools6_6.1.20170106+dfsg2-6.dsc
0950edd06062c2b2832b158b27d370521629d95e 1516256
ncbi-tools6_6.1.20170106+dfsg2-6.debian.tar.xz
Checksums-Sha256:
b85ea6f2da138b3442e065ccf077cacc0f36e8aa3594c5fd8a89ad8c63251bd6 2905
ncbi-tools6_6.1.20170106+dfsg2-6.dsc
4542a00c84c449931cf43611d60ee2f8e8120b65c2e329dd885d523efc6cb12e 1516256
ncbi-tools6_6.1.20170106+dfsg2-6.debian.tar.xz
Files:
ed436840b49bce08536680d21e8b9180 2905 libdevel optional
ncbi-tools6_6.1.20170106+dfsg2-6.dsc
d846a83917bc20619566980083b9ef30 1516256 libdevel optional
ncbi-tools6_6.1.20170106+dfsg2-6.debian.tar.xz
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