Source: gbutils
Version: 5.6.7-1
Severity: important
Tags: upstream
Dear Maintainer,
Your package fails to build with GSL 2:
gbnlreg.c: In function 'ols_varcovar':
gbnlreg.c:185:28: error: 'gsl_multifit_fdfsolver {aka const struct
<anonymous>}' has no member named 'J'
gsl_multifit_covar (s->J, 1e-6, covar);
^
This needs to be fixed for the ongoing gsl transition (#804246).
The full build log is attached, as is a patch to update the build
dependencies for GSL 2 (changing libgsl0-dev to libgsl-dev).
Kind Regards,
Bas
I: using cowbuilder as pbuilder
dpkg-checkbuilddeps: Unmet build dependencies: libgsl-dev libmatheval-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package gbutils
dpkg-buildpackage: source version 5.6.7-1.1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Bas Couwenberg <sebas...@debian.org>
dpkg-source --before-build gbutils-5.6.7
dpkg-checkbuilddeps: Unmet build dependencies: libgsl-dev libmatheval-dev
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
dpkg-buildpackage: warning: this is currently a non-fatal warning with -S, but
will probably become fatal in the future
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
dpkg-source -b gbutils-5.6.7
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building gbutils using existing ./gbutils_5.6.7.orig.tar.gz
dpkg-source: info: building gbutils in gbutils_5.6.7-1.1.debian.tar.xz
dpkg-source: info: building gbutils in gbutils_5.6.7-1.1.dsc
dpkg-genchanges -S >../gbutils_5.6.7-1.1_source.changes
dpkg-genchanges: not including original source code in upload
dpkg-source --after-build gbutils-5.6.7
dpkg-buildpackage: binary and diff upload (original source NOT included)
-> Copying COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.21059
forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow
/var/cache/pbuilder/build//cow.21059
I: removed stale ilistfile /var/cache/pbuilder/build//cow.21059/.ilist
forking: chroot /var/cache/pbuilder/build//cow.21059 cowdancer-ilistcreate
/.ilist find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a
-links +1 -print0 \) | xargs -0 stat --format '%d %i '
-> Invoking pbuilder
forking: pbuilder build --debbuildopts --debbuildopts --buildplace
/var/cache/pbuilder/build//cow.21059 --buildresult /var/cache/pbuilder/result/
--debbuildopts --no-targz --internal-chrootexec chroot
/var/cache/pbuilder/build//cow.21059 cow-shell
/home/bas/tmp/debian/gbutils_5.6.7-1.1.dsc
I: Running in no-targz mode
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Nov 22 16:23:08 CET 2015
I: pbuilder-time-stamp: 1448205788
I: copying local configuration
I: mounting /proc filesystem
I: mounting /run/shm filesystem
I: mounting /dev/pts filesystem
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Installing the build-deps
W: no hooks of type D found -- ignoring
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-ma...@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by
pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper (>= 9), dh-autoreconf, help2man, libgsl-dev,
libmatheval-dev, zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in
'/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
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Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring
anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper (>= 9); however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on dh-autoreconf; however:
Package dh-autoreconf is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmatheval-dev; however:
Package libmatheval-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
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Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version
(0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version
(0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a}
debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} file{a}
gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a}
libarchive-zip-perl{a} libcroco3{a} libffi6{a}
libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a}
libgsl2{a} libicu55{a} libmagic1{a} libmatheval-dev{a} libmatheval1{a}
libpipeline1{a} libsigsegv2{a} libtool{a} libunistring0{a} libxml2{a}
m4{a} man-db{a} po-debconf{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx-cur
shared-mime-info wget xdg-user-dirs xml-core
0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/21.5 MB of archives. After unpacking 75.8 MB will be used.
Writing extended state information...
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.19-22) ...
Setting up groff-base (1.22.3-4) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in
auto mode
Setting up libpipeline1:amd64 (1.4.1-1) ...
Setting up man-db (2.7.5-1) ...
Building database of manual pages ...
Setting up libffi6:amd64 (3.2.1-3) ...
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Setting up libxml2:amd64 (2.9.2+zdfsg1-4) ...
Setting up m4 (1.4.17-4) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake
(automake) in auto mode
Setting up autopoint (0.19.6-1) ...
Setting up libglib2.0-0:amd64 (2.46.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3:amd64 (0.6.9-1) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
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Setting up libtool (2.4.2-1.11) ...
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Reading package lists...
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-> Finished parsing the build-deps
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Reading state information...
The following extra packages will be installed:
libfakeroot
The following NEW packages will be installed:
fakeroot libfakeroot
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/129 kB of archives.
After this operation, 434 kB of additional disk space will be used.
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Setting up fakeroot (1.20.2-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot
(fakeroot) in auto mode
I: Copying back the cached apt archive contents
I: Copying source file
I: copying [/home/bas/tmp/debian/gbutils_5.6.7-1.1.dsc]
I: copying [/home/bas/tmp/debian/gbutils_5.6.7.orig.tar.gz]
I: copying [/home/bas/tmp/debian/gbutils_5.6.7-1.1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (gbutils_5.6.7-1.1.dsc)
dpkg-source: info: extracting gbutils in gbutils-5.6.7
dpkg-source: info: unpacking gbutils_5.6.7.orig.tar.gz
dpkg-source: info: unpacking gbutils_5.6.7-1.1.debian.tar.xz
I: Building the package
W: no hooks of type A found -- ignoring
I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin"
dpkg-buildpackage -us -uc -rfakeroot
dpkg-buildpackage: source package gbutils
dpkg-buildpackage: source version 5.6.7-1.1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Bas Couwenberg <sebas...@debian.org>
dpkg-source --before-build gbutils-5.6.7
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
dpkg-source -b gbutils-5.6.7
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building gbutils using existing ./gbutils_5.6.7.orig.tar.gz
dpkg-source: info: building gbutils in gbutils_5.6.7-1.1.debian.tar.xz
dpkg-source: info: building gbutils in gbutils_5.6.7-1.1.dsc
debian/rules build
dh build --with autoreconf
dh_testdir
dh_autoreconf
dh_auto_configure
./configure --build=x86_64-linux-gnu --prefix=/usr
--includedir=\${prefix}/include --mandir=\${prefix}/share/man
--infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var
--disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu
--libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode
--disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether ln -s works... yes
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking for flex... no
checking for lex... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether getdelim is declared... yes
checking for getdelim... yes
checking whether getline is declared... yes
checking for getline... yes
checking for working getline function... yes
checking for getsubopt... yes
checking for strchrnul... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for ranlib... ranlib
checking for sin in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for evaluator_create in -lmatheval... yes
checking for gzopen in -lz... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strspn... yes
checking for memchr... yes
checking for strcspn... yes
checking for strtol... yes
checking for strtod... yes
checking for ANSI C header files... (cached) yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for help2man... /usr/bin/help2man
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
--------------------------------------------------------------------
| Congratulations! Configuration of ver. 5.6.7 is complete.
| Optional dependencies:
|
| Gnu Scientific Library (GSL) found
| GNU matheval library found
| zlib general purpose compression library found
| help2man automatic man pages generator found
|
| The utilities will be installed under /usr
| To compile and install the utilities in a different directory
| use the configure option --prefix, see the INSTALL file.
|
| Now you can type 'make' to compile GBUTILS and 'make install'
| to install it
| enjoy!
--------------------------------------------------------------------
dh_auto_build
make -j1
make[1]: Entering directory '/tmp/buildd/gbutils-5.6.7'
make all-recursive
make[2]: Entering directory '/tmp/buildd/gbutils-5.6.7'
Making all in lib
make[3]: Entering directory '/tmp/buildd/gbutils-5.6.7/lib'
make all-am
make[4]: Entering directory '/tmp/buildd/gbutils-5.6.7/lib'
rm -f libgnu.a
ar cru libgnu.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgnu.a
make[4]: Leaving directory '/tmp/buildd/gbutils-5.6.7/lib'
make[3]: Leaving directory '/tmp/buildd/gbutils-5.6.7/lib'
make[3]: Entering directory '/tmp/buildd/gbutils-5.6.7'
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbbin.o gbbin.c
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o tools.o tools.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbbin gbbin.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbdist.o
gbdist.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbdist gbdist.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbhisto.o
gbhisto.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbhisto gbhisto.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbmave.o
gbmave.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbmave gbmave.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbstat.o
gbstat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbstat gbstat.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbtest.o
gbtest.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbtest gbtest.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbnear.o
gbnear.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbnear gbnear.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbker2d.o
gbker2d.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbker2d gbker2d.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbhisto2d.o
gbhisto2d.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbhisto2d gbhisto2d.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbkreg2d.o
gbkreg2d.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbkreg2d gbkreg2d.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbquant.o
gbquant.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbquant gbquant.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbboot.o
gbboot.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbboot gbboot.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbenv.o gbenv.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbenv gbenv.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbgcorr.o
gbgcorr.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbgcorr gbgcorr.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbfilternear.o
gbfilternear.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbfilternear gbfilternear.o tools.o lib/libgnu.a -lz -lmatheval
-lgsl -lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbmstat.o
gbmstat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbmstat gbmstat.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbxcorr.o
gbxcorr.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbxcorr gbxcorr.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbget.o gbget.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbget gbget.o tools.o -lz -lmatheval -lgsl -lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbker.o gbker.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbker gbker.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbkreg.o
gbkreg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbkreg gbkreg.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbmodes.o
gbmodes.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbmodes gbmodes.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbinterp.o
gbinterp.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbinterp gbinterp.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbfun.o gbfun.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbfun gbfun.o tools.o -lz -lmatheval -lgsl -lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gblreg.o
gblreg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gblreg gblreg.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbgrid.o
gbgrid.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbgrid gbgrid.o tools.o -lz -lmatheval -lgsl -lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbglreg.o
gbglreg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o gbglreg gbglreg.o tools.o lib/libgnu.a -lz -lmatheval -lgsl
-lgslcblas -lm
gcc -DHAVE_CONFIG_H -I. -I./lib -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o gbnlreg.o
gbnlreg.c
gbnlreg.c: In function 'ols_varcovar':
gbnlreg.c:185:28: error: 'gsl_multifit_fdfsolver {aka const struct
<anonymous>}' has no member named 'J'
gsl_multifit_covar (s->J, 1e-6, covar);
^
Makefile:961: recipe for target 'gbnlreg.o' failed
make[3]: *** [gbnlreg.o] Error 1
make[3]: Leaving directory '/tmp/buildd/gbutils-5.6.7'
Makefile:1018: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/tmp/buildd/gbutils-5.6.7'
Makefile:638: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/tmp/buildd/gbutils-5.6.7'
dh_auto_build: make -j1 returned exit code 2
debian/rules:7: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
E: Failed autobuilding of package
W: no hooks of type C found -- ignoring
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
-> Cleaning COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.21059
diff -Nru gbutils-5.6.7/debian/changelog gbutils-5.6.7/debian/changelog
--- gbutils-5.6.7/debian/changelog 2015-09-16 14:58:08.000000000 +0200
+++ gbutils-5.6.7/debian/changelog 2015-11-22 16:22:49.000000000 +0100
@@ -1,3 +1,10 @@
+gbutils (5.6.7-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
+
+ -- Bas Couwenberg <sebas...@debian.org> Sun, 22 Nov 2015 16:22:46 +0100
+
gbutils (5.6.7-1) unstable; urgency=medium
* Imported Upstream version 5.6.7
diff -Nru gbutils-5.6.7/debian/control gbutils-5.6.7/debian/control
--- gbutils-5.6.7/debian/control 2015-09-14 14:20:33.000000000 +0200
+++ gbutils-5.6.7/debian/control 2015-11-22 16:22:44.000000000 +0100
@@ -5,7 +5,7 @@
Build-Depends: debhelper (>= 9),
dh-autoreconf,
help2man,
- libgsl0-dev,
+ libgsl-dev,
libmatheval-dev,
zlib1g-dev
Standards-Version: 3.9.6
