Bug#805829: r-cran-gsl: Fails to build with GSL 2
Bas Couwenberg
sebastic at xs4all.nl
Sun Nov 22 21:06:33 UTC 2015
Source: r-cran-gsl
Version: 1.9-10-1
Severity: important
Tags: upstream
Dear Maintainer,
Your package fails to build with GSL 2:
configure: error: Need GSL version >= 1.12
ERROR: configuration failed for package 'gsl'
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
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I: using cowbuilder as pbuilder
dpkg-checkbuilddeps: Unmet build dependencies: libgsl-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package r-cran-gsl
dpkg-buildpackage: source version 1.9-10-1.1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Bas Couwenberg <sebastic at debian.org>
dpkg-source --before-build r-cran-gsl-1.9-10
dpkg-checkbuilddeps: Unmet build dependencies: libgsl-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
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
dpkg-source -b r-cran-gsl-1.9-10
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building r-cran-gsl using existing ./r-cran-gsl_1.9-10.orig.tar.gz
dpkg-source: info: building r-cran-gsl in r-cran-gsl_1.9-10-1.1.debian.tar.xz
dpkg-source: info: building r-cran-gsl in r-cran-gsl_1.9-10-1.1.dsc
dpkg-genchanges -S >../r-cran-gsl_1.9-10-1.1_source.changes
dpkg-genchanges: not including original source code in upload
dpkg-source --after-build r-cran-gsl-1.9-10
dpkg-buildpackage: binary and diff upload (original source NOT included)
-> Copying COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.29361
forking: cp -al /var/cache/pbuilder/base-sid.cow /var/cache/pbuilder/build//cow.29361
I: removed stale ilistfile /var/cache/pbuilder/build//cow.29361/.ilist
forking: chroot /var/cache/pbuilder/build//cow.29361 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.29361 --buildresult /var/cache/pbuilder/result/ --debbuildopts --no-targz --internal-chrootexec chroot /var/cache/pbuilder/build//cow.29361 cow-shell /home/bas/tmp/debian/r-cran-gsl_1.9-10-1.1.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 21:58:53 CET 2015
I: pbuilder-time-stamp: 1448225933
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-maint at 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 (>= 9.0), cdbs, r-base-dev, libgsl-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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dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper (>= 9.0); however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on cdbs; however:
Package cdbs is not installed.
pbuilder-satisfydepends-dummy depends on r-base-dev; however:
Package r-base-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
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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:
bsdmainutils{a} ca-certificates{a} cdbs{a} debhelper{a}
dh-strip-nondeterminism{a} file{a} fontconfig{a} fontconfig-config{a}
fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran{a} gfortran-5{a}
groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas-common{a}
libblas-dev{a} libblas3{a} libbz2-dev{a} libcairo2{a} libcroco3{a}
libcurl3{a} libdatrie1{a} libexpat1{a} libffi6{a}
libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a}
libgfortran-5-dev{a} libgfortran3{a} libglib2.0-0{a} libgnutls-deb0-28{a}
libgraphite2-3{a} libgsl-dev{a} libgsl2{a} libgssapi-krb5-2{a}
libharfbuzz0b{a} libhogweed4{a} libice6{a} libicu55{a} libidn11{a}
libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a}
libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a}
liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} liblzma-dev{a}
libmagic1{a} libncurses5-dev{a} libnettle6{a} libnghttp2-14{a}
libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a}
libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre16-3{a}
libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a}
libpixman-1-0{a} libpng12-0{a} libpng12-dev{a} libreadline-dev{a}
libreadline6-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a}
libsm6{a} libssh2-1{a} libssl1.0.2{a} libtasn1-6{a} libtcl8.6{a}
libthai-data{a} libthai0{a} libtiff5{a} libtinfo-dev{a} libtk8.6{a}
libunistring0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a}
libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a}
libxrender1{a} libxss1{a} libxt6{a} man-db{a} openssl{a} po-debconf{a}
r-base-core{a} r-base-dev{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a}
zip{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
autotools-dev bzip2-doc curl krb5-locales libfile-mimeinfo-perl
libglib2.0-data libmail-sendmail-perl libnet-dbus-perl libsasl2-modules
libx11-protocol-perl lynx-cur r-doc-html r-recommended shared-mime-info
wget x11-utils x11-xserver-utils xdg-user-dirs xml-core
0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded.
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Unpacking liblapack-dev (3.5.0-5) ...
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Unpacking liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ...
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Unpacking libtinfo-dev:amd64 (6.0+20151024-2) ...
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Unpacking libthai0:amd64 (0.1.23-1) ...
Selecting previously unselected package libpango-1.0-0:amd64.
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Unpacking libpango-1.0-0:amd64 (1.38.1-1) ...
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Unpacking libpangoft2-1.0-0:amd64 (1.38.1-1) ...
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Unpacking libpangocairo-1.0-0:amd64 (1.38.1-1) ...
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Unpacking libpaper-utils (1.1.24+nmu4) ...
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Unpacking libpcre16-3:amd64 (2:8.35-7.4) ...
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Unpacking libpcre32-3:amd64 (2:8.35-7.4) ...
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Unpacking libpcre3-dev:amd64 (2:8.35-7.4) ...
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Unpacking libreadline6-dev:amd64 (6.3-8+b3) ...
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Unpacking libreadline-dev:amd64 (6.3-8+b3) ...
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Unpacking libtcl8.6:amd64 (8.6.4+dfsg-2) ...
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Unpacking libtk8.6:amd64 (8.6.4+dfsg-2) ...
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Unpacking libxt6:amd64 (1:1.1.5-1) ...
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Unpacking zip (3.0-11) ...
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Unpacking xdg-utils (1.1.1-1) ...
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Unpacking r-base-core (3.2.2-1) ...
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Unpacking r-base-dev (3.2.2-1) ...
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 libexpat1:amd64 (2.1.0-7) ...
Setting up libpng12-0:amd64 (1.2.54-1) ...
Setting up libfreetype6:amd64 (2.6-2) ...
Setting up ucf (3.0031) ...
Setting up fonts-dejavu-core (2.35-1) ...
Setting up fontconfig-config (2.11.0-6.3) ...
Setting up libfontconfig1:amd64 (2.11.0-6.3) ...
Setting up fontconfig (2.11.0-6.3) ...
Regenerating fonts cache... done.
Setting up libffi6:amd64 (3.2.1-3) ...
Setting up x11-common (1:7.7+12) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
[....] Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix[?25l7[1G[[32m ok [39;49m8[?12l[?25h.
Setting up libice6:amd64 (2:1.0.9-1+b1) ...
Setting up libpaper1:amd64 (1.1.24+nmu4) ...
Creating config file /etc/papersize with new version
Setting up libpcrecpp0v5:amd64 (2:8.35-7.4) ...
Setting up libsm6:amd64 (2:1.2.2-1+b1) ...
Setting up libssh2-1:amd64 (1.5.0-2+b1) ...
Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
Setting up libxau6:amd64 (1:1.0.8-1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-1) ...
Setting up libxcb1:amd64 (1.11.1-1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:amd64 (2:1.6.3-1) ...
Setting up libxext6:amd64 (2:1.3.3-1) ...
Setting up libxrender1:amd64 (1:0.9.9-2) ...
Setting up libxft2:amd64 (2.3.2-1) ...
Setting up libxss1:amd64 (1:1.2.2-1) ...
Setting up libjbig0:amd64 (2.1-3.1) ...
Setting up libssl1.0.2:amd64 (1.0.2d-3) ...
Setting up libmagic1:amd64 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libnettle6:amd64 (3.1.1-4) ...
Setting up libhogweed4:amd64 (3.1.1-4) ...
Setting up libp11-kit0:amd64 (0.23.1-3) ...
Setting up libtasn1-6:amd64 (4.7-2) ...
Setting up libgnutls-deb0-28:amd64 (3.3.18-1) ...
Setting up libkeyutils1:amd64 (1.5.9-8) ...
Setting up libkrb5support0:amd64 (1.13.2+dfsg-4) ...
Setting up libk5crypto3:amd64 (1.13.2+dfsg-4) ...
Setting up libkrb5-3:amd64 (1.13.2+dfsg-4) ...
Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-4) ...
Setting up libidn11:amd64 (1.32-3) ...
Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14+b1) ...
Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14+b1) ...
Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2) ...
Setting up libicu55:amd64 (55.1-6) ...
Setting up libxml2:amd64 (2.9.2+zdfsg1-4) ...
Setting up openssl (1.0.2d-3) ...
Setting up ca-certificates (20150426) ...
Setting up cdbs (0.4.130) ...
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) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libgfortran3:amd64 (5.2.1-23) ...
Setting up libgfortran-5-dev:amd64 (5.2.1-23) ...
Setting up gfortran-5 (5.2.1-23) ...
Setting up gfortran (4:5.2.1-4) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libblas-common (1.2.20110419-11) ...
Setting up libblas3 (1.2.20110419-11) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-11) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:amd64 (1.0.6-8) ...
Setting up libpixman-1-0:amd64 (0.33.4-1) ...
Setting up libxcb-render0:amd64 (1.11.1-1) ...
Setting up libxcb-shm0:amd64 (1.11.1-1) ...
Setting up libcairo2:amd64 (1.14.4-1) ...
Setting up libnghttp2-14:amd64 (1.4.0-2) ...
Setting up librtmp1:amd64 (2.4+20150115.gita107cef-1+b2) ...
Setting up libcurl3:amd64 (7.45.0-1+b1) ...
Setting up libdatrie1:amd64 (0.2.10-1) ...
Setting up libgraphite2-3:amd64 (1.3.4-1) ...
Setting up libgsl2:amd64 (2.1+dfsg-1) ...
Setting up libgsl-dev (2.1+dfsg-1) ...
Setting up libharfbuzz0b:amd64 (1.0.1-1+b1) ...
Setting up libjpeg62-turbo:amd64 (1:1.4.1-2) ...
Setting up libjpeg62-turbo-dev:amd64 (1:1.4.1-2) ...
Setting up libjpeg-dev (1:1.4.1-2) ...
Setting up liblapack3 (3.5.0-5) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-5) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ...
Setting up libtinfo-dev:amd64 (6.0+20151024-2) ...
Setting up libncurses5-dev:amd64 (6.0+20151024-2) ...
Setting up libthai-data (0.1.23-1) ...
Setting up libthai0:amd64 (0.1.23-1) ...
Setting up libpango-1.0-0:amd64 (1.38.1-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.38.1-1) ...
Setting up libpangocairo-1.0-0:amd64 (1.38.1-1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre16-3:amd64 (2:8.35-7.4) ...
Setting up libpcre32-3:amd64 (2:8.35-7.4) ...
Setting up libpcre3-dev:amd64 (2:8.35-7.4) ...
Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Setting up libpng12-dev:amd64 (1.2.54-1) ...
Setting up libreadline6-dev:amd64 (6.3-8+b3) ...
Setting up libreadline-dev:amd64 (6.3-8+b3) ...
Setting up libtcl8.6:amd64 (8.6.4+dfsg-2) ...
Setting up libtiff5:amd64 (4.0.5-1) ...
Setting up libtk8.6:amd64 (8.6.4+dfsg-2) ...
Setting up libxt6:amd64 (1:1.1.5-1) ...
Setting up zip (3.0-11) ...
Setting up unzip (6.0-20) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up r-base-core (3.2.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.2.2-1) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Setting up debhelper (9.20151117) ...
Processing triggers for libc-bin (2.19-22) ...
Processing triggers for ca-certificates (20150426) ...
Updating certificates in /etc/ssl/certs...
180 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
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.
Selecting previously unselected package libfakeroot:amd64.
(Reading database ...
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(Reading database ... 25%
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(Reading database ... 100%
(Reading database ... 17349 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.20.2-1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.20.2-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.20.2-1_amd64.deb ...
Unpacking fakeroot (1.20.2-1) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libfakeroot:amd64 (1.20.2-1) ...
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/r-cran-gsl_1.9-10-1.1.dsc]
I: copying [/home/bas/tmp/debian/r-cran-gsl_1.9-10.orig.tar.gz]
I: copying [/home/bas/tmp/debian/r-cran-gsl_1.9-10-1.1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (r-cran-gsl_1.9-10-1.1.dsc)
dpkg-source: info: extracting r-cran-gsl in r-cran-gsl-1.9-10
dpkg-source: info: unpacking r-cran-gsl_1.9-10.orig.tar.gz
dpkg-source: info: unpacking r-cran-gsl_1.9-10-1.1.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 r-cran-gsl
dpkg-buildpackage: source version 1.9-10-1.1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Bas Couwenberg <sebastic at debian.org>
dpkg-source --before-build r-cran-gsl-1.9-10
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
dpkg-source -b r-cran-gsl-1.9-10
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-cran-gsl using existing ./r-cran-gsl_1.9-10.orig.tar.gz
dpkg-source: info: building r-cran-gsl in r-cran-gsl_1.9-10-1.1.debian.tar.xz
dpkg-source: info: building r-cran-gsl in r-cran-gsl_1.9-10-1.1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.2.2-1), r-api-3" >> debian/r-cran-gsl.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /tmp/buildd/r-cran-gsl-1.9-10/debian/r-cran-gsl/usr/lib/R/site-library --clean \
. \
"--built-timestamp=\"Sun, 22 Nov 2015 21:58:32 +0100\"" \
; \
else \
R CMD INSTALL -l /tmp/buildd/r-cran-gsl-1.9-10/debian/r-cran-gsl/usr/lib/R/site-library \
--clean . \
"--built-timestamp=\"Sun, 22 Nov 2015 21:58:32 +0100\"" \
; \
fi
* installing *source* package 'gsl' ...
** package 'gsl' successfully unpacked and MD5 sums checked
checking for gsl-config... /usr/bin/gsl-config
checking if GSL version >= 1.12... 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 ISO C89... none needed
configure: error: Need GSL version >= 1.12
ERROR: configuration failed for package 'gsl'
* removing '/tmp/buildd/r-cran-gsl-1.9-10/debian/r-cran-gsl/usr/lib/R/site-library/gsl'
/usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
make: *** [R_any_arch] Error 1
dpkg-buildpackage: error: fakeroot debian/rules binary 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.29361
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