Bug#892222: seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta

[Andreas Tille]

Hi Aaron,

I had a quick look at this bug and realises that currently the source
code does not even build any more[1] thus not even reaching the test you
spotted as failing:

...
[  3%] Building CXX object 
apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o
cd /<>/obj-hppa-linux-gnu/apps/pair_align/lib && /usr/bin/c++ 
-DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK 
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 
-DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 
-DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 
-fdebug-prefix-map=/<>=. -Wformat -Werror=format-security -DNDEBUG 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2  -W -Wall -pedantic -fopenmp
-DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT 
apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o
 -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o 
CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c 
/<>/apps/pair_align/lib/pair_align_global.cpp
malloc(): unaligned tcache chunk detected
malloc(): unaligned tcache chunk detected
c++: internal compiler error: Aborted signal terminated program cc1plus
Please submit a full bug report,
with preprocessed source if appropriate.


Kind regards

 Andreas.


[1] 
https://buildd.debian.org/status/fetch.php?pkg=seqan2&arch=hppa&ver=2.4.0%2Bdfsg-14&stamp=1638150140&raw=0

-- 
http://fam-tille.de

Bug#892222: seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta

[Aaron M. Ucko]

Source: seqan2
Version: 2.4.0+dfsg-8
Severity: normal
Tags: upstream
User: debian-h...@lists.debian.org
Usertags: hppa

Greetings.

Builds of seqan2 for hppa (admittedly not a release architecture) have
been failing lately, per the below excerpts from [1].

Could you please take a look?

Thanks!

[1] 
https://buildd.debian.org/status/fetch.php?pkg=seqan2&arch=hppa&ver=2.4.0%2Bdfsg-8&stamp=1519074087&raw=0

--

392/401 Test #395: app_test_seqan_tcoffee 
***Failed   20.75 
sec
Comparing 
/<>/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/tests/2trx.mlcs.fasta 
against /tmp/tmp1bkmRo/2trx.mlcs.fasta
--- 

+++ 

@@ -1,24 +1,24 @@

 >1thx
-AE-QPVL---V--YFWA-S--WCGPCQ---LM---SPLIN--LA
-ANT-YSD-R---L---KV--V--KLE-IDP--NPTTVKKYK--VE---
-GV-PA--LRL--V-K-GEQILD-STE--
--G--V---IS--K--DKLLSFLDTH--LN---
---
+AE-QPVL---V--YFWA-S--WCGPCQL-MS--PLINLAANTY---SD
+-R---L---KV---VK--L-EI--DPNPTTVKKYK---V-
+-EG-V-PA-LRL--V-K---GE---Q-ILDSTE---
+-G--VI-SK---DKLLSF-LD---TH---LN-
+
 >1grx
---MQ---T--V-I-FG-RSG-C--P---
-YS-VRAKDLA-EK-L-SN---ER-D-DFQ--Y-QYV
--DIRA-EGITK-ED---LQQ--KAG-K--PVET-VPQIFVDQQH
-IG---GYTD-FAAWV-KEN--LD---A-
---
+--MQ---T--V-I-FG-RSG-C---PY---S-
+VRAKDL-AEKLSN---E-R-D-DFQY---Q-Y--VD
+-IRA-EGITKED---LQQ--KA--GKPV-ETVPQ-I---F
+VDQQHIGGYT--DF---AAW--VKEN-LDA--
+
 >1erv
-A-GDK-L---VVVDF---SATWCGPC-K---MIK--PFFH
--S--L-SEK--YSN--VIF-LE-VD--V-DDC
-QD---V--ASECE---V-KSMP--T-F---Q-
--FFKKGQKVG---EF--SG-A--NKE--KLE-A--T-I--NE--
-LV
+A-GDK-L---VVVDF---SATWCGPC--KM-IKP-FFHS-
+-LS-EK-YSNV-IFL-E--VDVDDCQ-DV---
+---ASEC---E---V-K-SM--P---TF
+QFFKKGQKV--G--E--FSG--A-N--KE-KL--EAT-I---NE
+--LV
 >2trcP
-KV-TTIV---VNIY---EDGVR-G-C--DAL---NSSL--ECLA
-A--EY-PMV--KFCKI-RASN--T
-GAGDRFSSDVLP--TL-L--VYK-
--G---G---ELISNF-IS-VAE-QFAEDF--FAADVESFLNEYG
-L-LPER
+KV-TTIV---VNIY---EDGVR-G-C--
+D--A--L-NSSLE-CLAAEYPMV--KFC
+KIRA---SNTG-AGDRFSSDVLP-TL-L--VYK---G---GELI-SNF
+-I-S-VAEQFAEDF--FAA--DV-E--SFLNE
+YGL-LPER
Executing test for seqan_tcoffee

[...]
==
 total tests: 66
failed tests: 1
successful tests: 65
==
[...]
99% tests passed, 1 tests failed out of 401

Total Test time (real) = 894.07 sec

The following tests FAILED:
395 - app_test_seqan_tcoffee (Failed)
Errors while running CTest

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu