Re: ncbi-igblast - compiles so much redundant general NCBI bits - wrong source tree?
Hi Aaron,
Am Thu, May 07, 2020 at 10:36:55AM -0400 schrieb Aaron M. Ucko:
> Steffen Möller <steffen_moeller@gmx.de> writes:
>
> > This ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.15.0/ is
> > where I got the source tree. It is not the case that igblast also occurs
> > elsewhere, say together with the regular NCBI tools, and I am not aware
> > of it.
>
> ncbi-blast+ and ncbi-igblast are both offshoots of the unpackaged NCBI
> C++ Toolkit, albeit with their own release cycles. I'd suggest building
> the helper libraries statically here, by changing --with-dll to
> --without-dll. (The default is somewhere in between, producing PIC
> static libraries, whereas you want PIE if anything.)
I tried to follow your hint by
diff --git a/debian/rules b/debian/rules
index 9c8541d..b6617c2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,7 +10,7 @@ override_dh_auto_configure:
--without-ncbi-crypt \
--without-vdb \
--without-ngs \
- --with-dll --without-debug --with-strip \
+ --without-dll --without-debug --with-strip \
--without-openmp --without-mt --without-mesa --without-glut --without-orbacus --without-sp \
--without-local-lbsm --without-cppkafka --without-librdkafka --without-apache-arrow --without-hiredis --without-aws-sdk --without-msgsl --without-grpc --without-protobuf --without-libxlsxwriter --without-influxdb --without-h2o --without-nghttp2 --without-cassandra \
--without-libssh2 --without-libuv --without-lmdb --without-mongodb --without-leveldb --without-gmock --without-gsoap --without-avro --without-cereal --without-oechem --without-zorba --without-xalan --without-xerces --without-libexslt --without-sablot --without-icu --without-sybase \
but I get the same result as without this change:
...
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)
DIS -- [objtools/blast/seqdb_reader/test] scan_blastdb_mt
DIS -- [objtools/blast/seqdb_reader/test] scan_blastdb_st
DIS -- [objtools/blast/seqdb_reader/test] get_blastdb_metadata
Succeeded : 0
Timeout : 0
Failed : 7
Absent : 3
make[2]: *** [/build/ncbi-igblast-1.18.0/c++/src/build-system/Makefile.meta_r:46: check_r.real] Error 7
Kind regards
Andreas.
--
http://fam-tille.de
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