| Summary: | sci-biology/bcftools-1.10.2 - support for extra features is disabled without a USE flag | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | UNCONFIRMED --- | ||
| Severity: | normal | CC: | jstein, mmokrejs |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | build.log | ||
Created attachment 659402 [details]
build.log
At least if the plugins were enabled because without them many addons are simply not available, e.g. "bcftools plugin fill-tags" and "bcftools plugin split-vep", etc. |
Hi, I realized that mysteriously by default on gentoo are forced the following args to configure: --disable-bcftools-plugins --disable-libgsl Please make by default --enable-bcftools-plugins \ --enable-libgsl \ --enable-perl-filters \ --with-htslib=system Enabling --enable-libgsl changes the resyulting binary licensing from MIT to GNU GPL license. Was that the reason somebody disabled support for gsl altogether? >>> Emerging (1 of 1) sci-biology/bcftools-1.10.2::gentoo * bcftools-1.10.2.tar.bz2 BLAKE2B SHA512 size ;-) ... [ ok ] * Using python3.6 to build >>> Unpacking source... >>> Unpacking bcftools-1.10.2.tar.bz2 to /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work >>> Source unpacked in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work >>> Preparing source in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work/bcftools-1.10.2 ... * Fixing shebang in misc/guess-ploidy.py. * Fixing shebang in misc/plot-roh.py. >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work/bcftools-1.10.2 ... ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/bcftools-1.10.2 --htmldir=/usr/share/doc/bcftools-1.10.2/html --libdir=/usr/lib64 --enable-bcftools-plugins --enable-libgsl --enable-perl-filters --with-htslib=system checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/