[Debian-med-packaging] Bug#976525: plast: FTBFS: SmallGapHitIteratorSSE8.cpp:294:5: error: ‘__m128i’ was not declared in this scope
Lucas Nussbaum
lucas at debian.org
Sat Dec 5 12:26:10 GMT 2020
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.
More information about the Debian-med-packaging
mailing list