Re: What is the relation ncbi-magicblast and magicblast
Hi Aaron,
On Thu, Jun 18, 2020 at 03:54:19PM -0400, Aaron M. Ucko wrote:
> Please try adding --with-mbedtls to the configure command line to request
> use of system mbed TLS.
>
> Also, I found that c++/src/objtools/data_loaders/genbank/gicache/gicache.c
> ran afoul of -Werror=format-security, which this fresh upstream patch
> should address:
>
> https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B/src/objtools/data_loaders/genbank/gicache/gicache.c?r1=86537&r2=90486&view=patch
Thanks for these helpful hints which I implemented and pushed.
Unfortunately I'm now running into an error of the test suite:
Warning: non-existent sub-project "internal"
make[3]: Leaving directory
'/build/ncbi-magicblast-1.5.0/c++/GCC900-DebugMT64/build'
----------------------------------------------------------------------
Building check script...
SKIP -- objtools/blast/seqdb_reader/test/seqdb_perf (unmet CHECK_REQUIRES)
SKIP -- objtools/blast/seqdb_reader/test/seqdb_perf (unmet CHECK_REQUIRES)
SKIP -- objtools/blast/seqdb_reader/test/seqdb_perf (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/sra_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/sra_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/sra_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/sra_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/vdb_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/vdb_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/vdb_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/vdb_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/wgs_test (unmet CHECK_REQUIRES)
SKIP -- sra/readers/sra/test/graph_test (unmet CHECK_REQUIRES)
Done.
Testing, please wait...
ERR [127] -- [util/lmdb] lmdb_test.sh 1 (unparsable timing stats)
ERR [127] -- [util/lmdb] lmdb_test.sh 2 (unparsable timing stats)
ERR [127] -- [util/lmdb] lmdb_test.sh 3 (unparsable timing stats)
ERR [127] -- [util/lmdb] lmdb_test.sh 4 (unparsable timing stats)
ERR [127] -- [util/lmdb] lmdb_test.sh 5 (unparsable timing stats)
ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing
stats)
ERR [127] -- [objects/genomecoll/gc_cli] test_gencoll_svc_ASSM
(unparsable timing stats)
ERR [127] -- [objects/genomecoll/gc_cli] test_gencoll_svc_ASSM_BY_SEQ
(unparsable timing stats)
ERR [127] -- [objects/genomecoll/gc_cli] test_gencoll_svc_TYPELOC
(unparsable timing stats)
Succeeded : 0
Timeout : 0
Failed : 10
Absent : 0
make[2]: ***
[/build/ncbi-magicblast-1.5.0/c++/src/build-system/Makefile.meta_r:46:
check_r.real] Error 7
make[2]: Leaving directory
'/build/ncbi-magicblast-1.5.0/c++/GCC900-DebugMT64/build'
make[1]: *** [Makefile:33: check] Error 2
make[1]: Leaving directory '/build/ncbi-magicblast-1.5.0/c++'
dh_auto_test: error: cd c\+\+ && make -j4 check VERBOSE=1 returned exit
code 2
Any idea what to do next?
Moreover I've added unixodbc-dev to Build-Depends but I have no idea
how to get rid of the code copy in
c++/include/dbapi/driver/odbc/unix_odbc
Any hint (or even an upload of yours) would be really welcome.
Kind regards
Andreas.
--
http://fam-tille.de
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