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Bug 741540

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 packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: UNCONFIRMED ---    
Severity: normal CC: jstein
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Attachments: build.log

Description Martin Mokrejš 2020-09-10 16:47:45 UTC
  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 \

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/
 * Fixing shebang in misc/
>>> 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.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

Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at
Comment 1 Martin Mokrejš 2020-09-10 16:48:37 UTC
Created attachment 659402 [details]