Re: igblast accepted - how can it be used to test igdiscover
Hi Aaron,
Am Wed, Aug 03, 2022 at 04:14:53PM -0400 schrieb Aaron M. Ucko:
> >> --with-vdb=/usr VDB_INCLUDE=-I/usr/include/ncbi-vdb
> >
> > Hmmm, this was running into an error which I tried to fix with
>
> Do you happen to remember what the error was? It worked for me, albeit
> in a rather non-minimal build environment.
Hmmmm, very strange. I "simply" pushed and wanted to show you in Salsa-CI
to show you the problem ... but there is no such error as here:
...
checking for Zorba... no
checking for libsqlite3... no
checking for ncbi-vdb in //usr... no
configure: error: --with-vdb explicitly specified, but no usable version found.
make[1]: *** [debian/rules:7: override_dh_auto_configure] Error 1
make[1]: Leaving directory '/build/ncbi-igblast-1.19.0'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
In any case I think it makes sense to fix all those
...
checking for libssl... no
checking for krb5-config... no
checking for libgssapi_krb5... no
checking for libcurl... no
checking for reentrant Sybase libraries... no
checking for Sybase... no
checking for FreeTDS... no
checking for mysql_config... no
checking for Berkeley DB libraries... no
checking for python... no
checking for python2.5... no
checking for python2.6... no
checking for python2.7... no
checking for python3... no
checking for perl... /usr/bin/perl
checking for usable Perl libraries... no
checking Boost version...
checking for Boost library name tag... -gcc121-mt-d-x64- (autodetected)
checking for Boost.Regex... no
checking for Boost.Spirit... no
checking for Boost.System... no
checking for Boost.Chrono... no
checking for Boost.Filesystem... no
checking for Boost.Iostreams... no
checking for Boost.Program-Options... no
checking for Boost.Serialization... no
checking for Boost.Test... no
checking for Boost.Thread... no
checking for the NCBI C toolkit... no
...
"no"s by the according Build-Depends if we have the actual library (not
sure yet what is checked by NCBI C toolkit but others are clear, thought.
> > I've cleared most of the --without options and added --with-openmp with
> > the according Build-Depends.
>
> Thanks! However, please note that OpenMP is a compiler feature and
> doesn't require any special build dependencies; OpenMPI, meanwhile, is a
> third-party library that doesn't come into play here.
OK, I removed libopenmpi-dev from Build-Depends.
Kind regards
Andreas.
--
http://fam-tille.de
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