Your message dated Sat, 05 Dec 2020 21:34:09 +0000
with message-id <[email protected]>
and subject line Bug#976525: fixed in plast 2.3.2+dfsg-4
has caused the Debian Bug report #976525,
regarding plast: FTBFS: SmallGapHitIteratorSSE8.cpp:294:5: error: ‘__m128i’ was
not declared in this scope
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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misconfiguration somewhere. Please contact [email protected]
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--
976525: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=976525
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: plast
Version: 2.3.2+dfsg-3
Severity: serious
Justification: FTBFS on arm64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201205 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on arm64 (I don't know if it also fails on amd64).
Relevant part (hopefully):
> /usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/include
> -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
> -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3
> -funroll-loops -fomit-frame-pointer -o
> CMakeFiles/plast.dir/src/algo/hits/hsp/HspExtensionCmd.cpp.o -c
> /<<PKGBUILDDIR>>/src/algo/hits/hsp/HspExtensionCmd.cpp
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp: In member
> function ‘void
> algo::hits::gapped::SmallGapHitIteratorSSE8::computeScores(size_t, const
> LETTER*, const LETTER*, int*)’:
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:294:5: error:
> ‘__m128i’ was not declared in this scope
> 294 | __m128i vscore_gap_col;
> | ^~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:295:12: error:
> expected ‘;’ before ‘vscore_gap_row’
> 295 | __m128i vscore_gap_row;
> | ^~~~~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:296:12: error:
> expected ‘;’ before ‘vnext_score’
> 296 | __m128i vnext_score;
> | ^~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:297:12: error:
> expected ‘;’ before ‘vscore’
> 297 | __m128i vscore;
> | ^~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:298:12: error:
> expected ‘;’ before ‘vbest_score’
> 298 | __m128i vbest_score;
> | ^~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:299:12: error:
> expected ‘;’ before ‘vbest_gap_arr’
> 299 | __m128i vbest_gap_arr[neighbourLength];
> | ^~~~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:300:12: error:
> expected ‘;’ before ‘vbest_arr’
> 300 | __m128i vbest_arr[neighbourLength];
> | ^~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:301:12: error:
> expected ‘;’ before ‘vgap_extend’
> 301 | __m128i vgap_extend;
> | ^~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:302:12: error:
> expected ‘;’ before ‘vgap_open’
> 302 | __m128i vgap_open;
> | ^~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:303:12: error:
> expected ‘;’ before ‘vgap_open_extend’
> 303 | __m128i vgap_open_extend;
> | ^~~~~~~~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:304:12: error:
> expected ‘;’ before ‘vscore_min’
> 304 | __m128i vscore_min;
> | ^~~~~~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:305:12: error:
> expected ‘;’ before ‘vtemp’
> 305 | __m128i vtemp;
> | ^~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:306:12: error:
> expected ‘;’ before ‘vtemp1’
> 306 | __m128i vtemp1;
> | ^~~~~~~
> | ;
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:309:5: error:
> ‘vgap_extend’ was not declared in this scope
> 309 | vgap_extend = _mm_set1_epi16 (-_parameters->extendGapCost);
> | ^~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:309:19: error:
> ‘_mm_set1_epi16’ was not declared in this scope
> 309 | vgap_extend = _mm_set1_epi16 (-_parameters->extendGapCost);
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:312:5: error:
> ‘vgap_open’ was not declared in this scope
> 312 | vgap_open = _mm_set1_epi16 (-_parameters->openGapCost);
> | ^~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:315:5: error:
> ‘vgap_open_extend’ was not declared in this scope
> 315 | vgap_open_extend = _mm_set1_epi16 (-(_parameters->openGapCost +
> _parameters->extendGapCost));
> | ^~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:318:5: error:
> ‘vscore_min’ was not declared in this scope
> 318 | vscore_min = _mm_set1_epi16 (-100);
> | ^~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:330:9: error:
> ‘vbest_arr’ was not declared in this scope
> 330 | vbest_arr[0] = _mm_set1_epi16(0);
> | ^~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:333:26: error:
> ‘vscore’ was not declared in this scope; did you mean ‘core’?
> 333 | _mm_store_si128(&vscore, vgap_open_extend);
> | ^~~~~~
> | core
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:333:9: error:
> ‘_mm_store_si128’ was not declared in this scope
> 333 | _mm_store_si128(&vscore, vgap_open_extend);
> | ^~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:336:26: error:
> ‘vbest_gap_arr’ was not declared in this scope
> 336 | _mm_store_si128 (vbest_gap_arr, vgap_open_extend);
> | ^~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:344:13: error:
> ‘vtemp’ was not declared in this scope; did you mean ‘mktemp’?
> 344 | vtemp = _mm_adds_epi16 (vscore, vgap_open_extend);
> | ^~~~~
> | mktemp
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:344:21: error:
> ‘_mm_adds_epi16’ was not declared in this scope
> 344 | vtemp = _mm_adds_epi16 (vscore, vgap_open_extend);
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:352:9: error:
> ‘vbest_score’ was not declared in this scope
> 352 | vbest_score = _mm_set1_epi16(0);
> | ^~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:363:31: error:
> ‘vscore_gap_row’ was not declared in this scope
> 363 | _mm_store_si128 (&vscore_gap_row, vscore_min);
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:371:35: error:
> ‘vscore_gap_col’ was not declared in this scope
> 371 | _mm_store_si128 (&vscore_gap_col, *(vbest_gap_arr+j));
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:389:17: error:
> ‘vtemp’ was not declared in this scope; did you mean ‘mktemp’?
> 389 | vtemp = _mm_set_epi16 (
> | ^~~~~
> | mktemp
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:389:25: error:
> ‘_mm_set_epi16’ was not declared in this scope
> 389 | vtemp = _mm_set_epi16 (
> | ^~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:395:25: error:
> ‘_mm_adds_epi16’ was not declared in this scope
> 395 | vtemp = _mm_adds_epi16 (vtemp,*(vbest_arr+j));
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:396:35: error:
> ‘vnext_score’ was not declared in this scope
> 396 | _mm_store_si128 (&vnext_score,vtemp);
> | ^~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:400:26: error:
> ‘_mm_max_epi16’ was not declared in this scope
> 400 | vscore = _mm_max_epi16 (vscore, vscore_gap_col);
> | ^~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:419:17: error:
> ‘vtemp1’ was not declared in this scope
> 419 | vtemp1 = _mm_max_epi16 (vtemp, vscore_gap_col);
> | ^~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:441:17: error:
> ‘vtemp’ was not declared in this scope; did you mean ‘mktemp’?
> 441 | vtemp = _mm_adds_epi16 (vscore_gap_row,
> vgap_open_extend);
> | ^~~~~
> | mktemp
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:441:25: error:
> ‘_mm_adds_epi16’ was not declared in this scope
> 441 | vtemp = _mm_adds_epi16 (vscore_gap_row,
> vgap_open_extend);
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:450:22: error:
> ‘_mm_extract_epi16’ was not declared in this scope
> 450 | scores[0] = _mm_extract_epi16 (vbest_score,0);
> | ^~~~~~~~~~~~~~~~~
> [ 8%] Building CXX object
> CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DefaultAlgoConfig.cpp.o
> /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__
> -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/include
> -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
> -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3
> -funroll-loops -fomit-frame-pointer -o
> CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DefaultAlgoConfig.cpp.o -c
> /<<PKGBUILDDIR>>/src/algo/core/impl/DefaultAlgoConfig.cpp
> make[3]: *** [CMakeFiles/plast.dir/build.make:280:
> CMakeFiles/plast.dir/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2020/12/05/plast_2.3.2+dfsg-3_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!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.
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: plast
Source-Version: 2.3.2+dfsg-4
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
plast, 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.
Andreas Tille <[email protected]> (supplier of updated plast 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: SHA256
Format: 1.8
Date: Sat, 05 Dec 2020 21:55:04 +0100
Source: plast
Architecture: source
Version: 2.3.2+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 976525
Changes:
plast (2.3.2+dfsg-4) unstable; urgency=medium
.
* Do nothing in dh_auto_configure and dh_auto_build for indep binaries
Closes: #976525
* Standards-Version: 4.5.1 (routine-update)
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Files:
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--- End Message ---
