Package Details: ncbi-toolkit 12.0.0-1

Git Clone URL: https://aur.archlinux.org/ncbi-toolkit.git (read-only)
Package Base: ncbi-toolkit
Description: Applications, scripts and C++ libraries for the analysis of biological data
Upstream URL: http://www.ncbi.nlm.nih.gov/books/NBK7160/
Licenses: custom
Conflicts: blast+-bin
Provides: blast+-bin
Submitter: None
Maintainer: mschu
Last Packager: mschu
Votes: 1
Popularity: 0.000000
First Submitted: 2009-04-01 07:27
Last Updated: 2016-02-02 20:23

Latest Comments

m.gruenstaeudl commented on 2015-12-10 10:29

The package doesn't compile with the latest gcc compiler (i.e., gcc 5.3.0).

==> Starting build()...
configure: loading site script ./src/build-system/config.site
configure: creating cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C compiler: /usr/bin/gcc
adjusted C++ compiler: /usr/bin/g++
configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++ 5.3.0

Upon removing flag "--with-mt" from PKGBUILD:

==> Starting build()...
configure: loading site script ./src/build-system/config.site
configure: creating cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C compiler: /usr/bin/gcc
adjusted C++ compiler: /usr/bin/g++
Compiler /usr/bin/g++ 5.3.0 is not fully supported.
Consult doc/config.html\#ref_Compilers for the list of
fully supported platforms/compilers.
Do you still want to proceed (at your own risk)? [y/N] y
configure: WARNING: Proceeding at your own risk...
configure: error: Do not know how to compile 64-bit with compiler /usr/bin/g++ 5.3.0 x86_64-unknown-linux-gnu:UNKNOWN

mschu commented on 2013-05-19 13:47

This is a giflib issue that the devs introduced in version 4.2. There is a patch available for giflib=4.2 but it is not used in the Archlinux package.

For the moment, try using giflib<4.2 or >=5.

balwierz commented on 2013-05-18 14:10

Does not compile (anymore):

/tmp/yaourt-tmp/aur-ncbi-toolkit/src/ncbi_cxx--9_0_0/src/util/image/image_io_gif.cpp: In member function ‘virtual void ncbi::CImageIOGif::WriteImage(const ncbi::CImage&, ncbi::CNcbiOstream&, ncbi::CImageIO::ECompress)’:
/tmp/yaourt-tmp/aur-ncbi-toolkit/src/ncbi_cxx--9_0_0/src/util/image/image_io_gif.cpp:351:51: error: ‘QuantizeBuffer’ was not declared in this scope
qdata_ptr, cmap->Colors) == GIF_ERROR) {
^