Source: mcmcpack Version: 1.3-6-1 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
Dear Maintainer,
mcmcpack fails to build from source in unstable/amd64:
[..]
Preparing to unpack .../51-gfortran-6_6.1.1-12_amd64.deb ...
Unpacking gfortran-6 (6.1.1-12) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../52-gfortran_4%3a6.1.1-1_amd64.deb ...
Unpacking gfortran (4:6.1.1-1) ...
Selecting previously unselected package libblas-dev.
Preparing to unpack .../53-libblas-dev_3.6.1-2_amd64.deb ...
Unpacking libblas-dev (3.6.1-2) ...
Selecting previously unselected package liblapack-dev.
Preparing to unpack .../54-liblapack-dev_3.6.1-2_amd64.deb ...
Unpacking liblapack-dev (3.6.1-2) ...
Selecting previously unselected package libtinfo-dev:amd64.
Preparing to unpack .../55-libtinfo-dev_6.0+20160625-1_amd64.deb ...
Unpacking libtinfo-dev:amd64 (6.0+20160625-1) ...
Selecting previously unselected package libncurses5-dev:amd64.
Preparing to unpack .../56-libncurses5-dev_6.0+20160625-1_amd64.deb ...
Unpacking libncurses5-dev:amd64 (6.0+20160625-1) ...
Selecting previously unselected package libreadline6-dev:amd64.
Preparing to unpack .../57-libreadline6-dev_6.3-8+b4_amd64.deb ...
Unpacking libreadline6-dev:amd64 (6.3-8+b4) ...
Selecting previously unselected package libreadline-dev:amd64.
Preparing to unpack .../58-libreadline-dev_6.3-8+b4_amd64.deb ...
Unpacking libreadline-dev:amd64 (6.3-8+b4) ...
Selecting previously unselected package libjpeg62-turbo-dev:amd64.
Preparing to unpack .../59-libjpeg62-turbo-dev_1%3a1.5.0-1_amd64.deb ...
Unpacking libjpeg62-turbo-dev:amd64 (1:1.5.0-1) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../60-libjpeg-dev_1%3a1.5.0-1_all.deb ...
Unpacking libjpeg-dev (1:1.5.0-1) ...
Selecting previously unselected package libpcre16-3:amd64.
Preparing to unpack .../61-libpcre16-3_2%3a8.39-1_amd64.deb ...
Unpacking libpcre16-3:amd64 (2:8.39-1) ...
Selecting previously unselected package libpcre32-3:amd64.
Preparing to unpack .../62-libpcre32-3_2%3a8.39-1_amd64.deb ...
Unpacking libpcre32-3:amd64 (2:8.39-1) ...
Selecting previously unselected package libpcrecpp0v5:amd64.
Preparing to unpack .../63-libpcrecpp0v5_2%3a8.39-1_amd64.deb ...
Unpacking libpcrecpp0v5:amd64 (2:8.39-1) ...
Selecting previously unselected package libpcre3-dev:amd64.
Preparing to unpack .../64-libpcre3-dev_2%3a8.39-1_amd64.deb ...
Unpacking libpcre3-dev:amd64 (2:8.39-1) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../65-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libpng-dev:amd64.
Preparing to unpack .../66-libpng-dev_1.6.24-2_amd64.deb ...
Unpacking libpng-dev:amd64 (1.6.24-2) ...
Selecting previously unselected package libbz2-dev:amd64.
Preparing to unpack .../67-libbz2-dev_1.0.6-8_amd64.deb ...
Unpacking libbz2-dev:amd64 (1.0.6-8) ...
Selecting previously unselected package liblzma-dev:amd64.
Preparing to unpack .../68-liblzma-dev_5.1.1alpha+20120614-2.1_amd64.deb ...
Unpacking liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../69-icu-devtools_57.1-2_amd64.deb ...
Unpacking icu-devtools (57.1-2) ...
Selecting previously unselected package libasan2:amd64.
Preparing to unpack .../70-libasan2_5.4.1-1_amd64.deb ...
Unpacking libasan2:amd64 (5.4.1-1) ...
Selecting previously unselected package libmpx0:amd64.
Preparing to unpack .../71-libmpx0_5.4.1-1_amd64.deb ...
Unpacking libmpx0:amd64 (5.4.1-1) ...
Selecting previously unselected package libgcc-5-dev:amd64.
Preparing to unpack .../72-libgcc-5-dev_5.4.1-1_amd64.deb ...
Unpacking libgcc-5-dev:amd64 (5.4.1-1) ...
Selecting previously unselected package libstdc++-5-dev:amd64.
Preparing to unpack .../73-libstdc++-5-dev_5.4.1-1_amd64.deb ...
Unpacking libstdc++-5-dev:amd64 (5.4.1-1) ...
Selecting previously unselected package libicu-dev.
Preparing to unpack .../74-libicu-dev_57.1-2_amd64.deb ...
Unpacking libicu-dev (57.1-2) ...
Selecting previously unselected package cdbs.
Preparing to unpack .../75-cdbs_0.4.142_all.deb ...
Unpacking cdbs (0.4.142) ...
Selecting previously unselected package r-base-dev.
Preparing to unpack .../76-r-base-dev_3.3.1-1_all.deb ...
Unpacking r-base-dev (3.3.1-1) ...
Selecting previously unselected package r-cran-lattice.
Preparing to unpack .../77-r-cran-lattice_0.20-33-1_amd64.deb ...
Unpacking r-cran-lattice (0.20-33-1) ...
Selecting previously unselected package r-cran-coda.
Preparing to unpack .../78-r-cran-coda_0.18-1-1_all.deb ...
Unpacking r-cran-coda (0.18-1-1) ...
Selecting previously unselected package r-cran-mass.
Preparing to unpack .../79-r-cran-mass_7.3-45-1_amd64.deb ...
Unpacking r-cran-mass (7.3-45-1) ...
Selecting previously unselected package r-cran-sparsem.
Preparing to unpack .../80-r-cran-sparsem_1.7-1_amd64.deb ...
Unpacking r-cran-sparsem (1.7-1) ...
Selecting previously unselected package r-cran-matrix.
Preparing to unpack .../81-r-cran-matrix_1.2-6-1_amd64.deb ...
Unpacking r-cran-matrix (1.2-6-1) ...
Selecting previously unselected package r-cran-matrixmodels.
Preparing to unpack .../82-r-cran-matrixmodels_0.4-1-1_all.deb ...
Unpacking r-cran-matrixmodels (0.4-1-1) ...
Selecting previously unselected package r-cran-quantreg.
Preparing to unpack .../83-r-cran-quantreg_5.26-1_amd64.deb ...
Unpacking r-cran-quantreg (5.26-1) ...
Selecting previously unselected package r-bioc-biocgenerics.
Preparing to unpack .../84-r-bioc-biocgenerics_0.18.0-1_all.deb ...
Unpacking r-bioc-biocgenerics (0.18.0-1) ...
Selecting previously unselected package r-cran-xml.
Preparing to unpack .../85-r-cran-xml_3.98-1.4-2_amd64.deb ...
Unpacking r-cran-xml (3.98-1.4-2) ...
Selecting previously unselected package r-bioc-graph.
Preparing to unpack .../86-r-bioc-graph_1.50.0-1_amd64.deb ...
Unpacking r-bioc-graph (1.50.0-1) ...
Setting up cdbs (0.4.142) ...
Setting up libbz2-dev:amd64 (1.0.6-8) ...
Setting up libjpeg62-turbo:amd64 (1:1.5.0-1) ...
Setting up libmpx0:amd64 (5.4.1-1) ...
Processing triggers for mime-support (3.60) ...
Setting up libpng16-16:amd64 (1.6.24-2) ...
Setting up libjbig0:amd64 (2.1-3.1) ...
Setting up libcurl3:amd64 (7.50.1-1) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libblas-common (3.6.1-2) ...
Setting up libgfortran3:amd64 (6.1.1-12) ...
Setting up libgfortran-6-dev:amd64 (6.1.1-12) ...
Setting up unzip (6.0-20) ...
Setting up libtinfo-dev:amd64 (6.0+20160625-1) ...
Setting up libasan2:amd64 (5.4.1-1) ...
Setting up libreadline6-dev:amd64 (6.3-8+b4) ...
Setting up libdatrie1:amd64 (0.2.10-2) ...
Setting up libtiff5:amd64 (4.0.6-2) ...
Setting up ucf (3.0036) ...
Setting up zip (3.0-11) ...
Setting up libfreetype6:amd64 (2.6.3-3+b1) ...
Setting up libgraphite2-3:amd64 (1.3.8-1) ...
Setting up libncurses5-dev:amd64 (6.0+20160625-1) ...
Setting up libpixman-1-0:amd64 (0.33.6-1) ...
Setting up libblas3 (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide
/usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Processing triggers for libc-bin (2.23-4) ...
Setting up libgcc-5-dev:amd64 (5.4.1-1) ...
Processing triggers for systemd (231-3) ...
Setting up openssl (1.0.2h-1) ...
Setting up libreadline-dev:amd64 (6.3-8+b4) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libpcrecpp0v5:amd64 (2:8.39-1) ...
Setting up libpcre32-3:amd64 (2:8.39-1) ...
Setting up icu-devtools (57.1-2) ...
Setting up libpcre16-3:amd64 (2:8.39-1) ...
Setting up libtcl8.6:amd64 (8.6.6+dfsg-1) ...
Setting up libthai-data (0.1.25-1) ...
Setting up libjpeg62-turbo-dev:amd64 (1:1.5.0-1) ...
Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ...
Setting up x11-common (1:7.7+16) ...
update-rc.d: warning: start and stop actions are no longer supported; falling
back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up xdg-utils (1.1.1-1) ...
Setting up ca-certificates (20160104) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libxau6:amd64 (1:1.0.8-1) ...
Setting up libstdc++-5-dev:amd64 (5.4.1-1) ...
Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Setting up libpaper1:amd64 (1.1.24+nmu4) ...
Creating config file /etc/papersize with new version
Setting up gfortran-6 (6.1.1-12) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre3-dev:amd64 (2:8.39-1) ...
Setting up fontconfig-config (2.11.0-6.5) ...
Setting up liblapack3 (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide
/usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libharfbuzz0b:amd64 (1.2.7-1+b1) ...
Setting up libthai0:amd64 (0.1.25-1) ...
Setting up libicu-dev (57.1-2) ...
Setting up libjpeg-dev (1:1.5.0-1) ...
Setting up libice6:amd64 (2:1.0.9-1+b1) ...
Setting up libpng-dev:amd64 (1.6.24-2) ...
Setting up libxcb1:amd64 (1.11.1-1.1) ...
Setting up gfortran (4:6.1.1-1) ...
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 libfontconfig1:amd64 (2.11.0-6.5) ...
Setting up libsm6:amd64 (2:1.2.2-1+b1) ...
Setting up libxcb-render0:amd64 (1.11.1-1.1) ...
Setting up libblas-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide
/usr/lib/libblas.so (libblas.so) in auto mode
Setting up libx11-6:amd64 (2:1.6.3-1) ...
Setting up libxcb-shm0:amd64 (1.11.1-1.1) ...
Setting up libxt6:amd64 (1:1.1.5-1) ...
Setting up libxrender1:amd64 (1:0.9.9-2) ...
Setting up libxft2:amd64 (2.3.2-1) ...
Setting up fontconfig (2.11.0-6.5) ...
Regenerating fonts cache... done.
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide
/usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxext6:amd64 (2:1.3.3-1) ...
Setting up libxss1:amd64 (1:1.2.2-1) ...
Setting up libpango-1.0-0:amd64 (1.40.1-1) ...
Setting up libcairo2:amd64 (1.14.6-1+b1) ...
Setting up libtk8.6:amd64 (8.6.6-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.40.1-1) ...
Setting up libpangocairo-1.0-0:amd64 (1.40.1-1) ...
Setting up r-base-core (3.3.1-1+b1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.3.1-1) ...
Setting up r-bioc-biocgenerics (0.18.0-1) ...
Setting up r-cran-sparsem (1.7-1) ...
Setting up r-cran-mass (7.3-45-1) ...
Setting up r-cran-xml (3.98-1.4-2) ...
Setting up r-bioc-graph (1.50.0-1) ...
Setting up r-cran-lattice (0.20-33-1) ...
Setting up r-cran-coda (0.18-1-1) ...
Setting up r-cran-matrix (1.2-6-1) ...
Setting up r-cran-matrixmodels (0.4-1-1) ...
Setting up r-cran-quantreg (5.26-1) ...
Setting up mcmcpack-build-deps (1.3-6-1) ...
Processing triggers for libc-bin (2.23-4) ...
Processing triggers for systemd (231-3) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
**************************************************************************************
** Environment
**
**************************************************************************************
PATH=/home/lamby/git/projects/dotfiles/dotfiles/..//bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
HOSTNAME=bae20ee1ce71
TERM=xterm
PAGER=more
DISPLAY=:0
DOCKER_IMAGE=lamby-debian-sid
DEB_BUILD_OPTIONS=parallel=9
PIP_DOWNLOAD_CACHE=/home/lamby/.cache/pip
HOME=/home/lamby
LOGNAME=lamby
SHLVL=1
PWD=/home/lamby/temp/cdt.20160817165739.rwqUq8LYwU.db.mcmcpack/mcmcpack-1.3-6
OLDPWD=/home/lamby/temp/cdt.20160817165739.rwqUq8LYwU.db.mcmcpack
GPG_TTY=/dev/console
QUILT_PATCHES=debian/patches
QUILT_NO_DIFF_INDEX=1
QUILT_REFRESH_ARGS=-p ab --no-timestamps --no-index
DEBEMAIL=la...@debian.org
DEBFULLNAME=Chris Lamb
EDITOR=vim
LESS=-cgiFx4M
GPG_KEY=1E953E27D4311E58
BLASTER=A220 I5 D1 H5 P330 T6
_=/usr/bin/env
**************************************************************************************
** Building mcmcpack 1.3-6-1 on amd64
**
**************************************************************************************
dpkg-buildpackage -rfakeroot -D -us -uc -b
dpkg-buildpackage: info: source package mcmcpack
dpkg-buildpackage: info: source version 1.3-6-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Chris Lawrence
<lawre...@debian.org>
dpkg-source --before-build mcmcpack-1.3-6
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh_listpackages: -s/--same-arch is deprecated; please use -a/--arch instead
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
rm -vf src/Makevars
debian/rules build
dh_listpackages: -s/--same-arch is deprecated; please use -a/--arch instead
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary
dh_listpackages: -s/--same-arch is deprecated; please use -a/--arch instead
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 (>= 3.3.1-1), r-api-3" >>
debian/r-cran-mcmcpack.substvars
if test -f /usr/bin/xvfb-run; then \
MAKEFLAGS="LDFLAGS=-Wl,-z,relro" xvfb-run -a
\
R CMD INSTALL -l
/home/lamby/temp/cdt.20160817165739.rwqUq8LYwU.db.mcmcpack/mcmcpack-1.3-6/debian/r-cran-mcmcpack/usr/lib/R/site-library
--clean \
. \
"--built-timestamp=\"Tue, 16 Aug 2016 20:45:12
-0400\"" \
; \
else \
MAKEFLAGS="LDFLAGS=-Wl,-z,relro" R CMD INSTALL -l
/home/lamby/temp/cdt.20160817165739.rwqUq8LYwU.db.mcmcpack/mcmcpack-1.3-6/debian/r-cran-mcmcpack/usr/lib/R/site-library
\
--clean . \
"--built-timestamp=\"Tue, 16 Aug 2016 20:45:12
-0400\"" \
; \
fi
ERROR: dependency 'mcmc' is not available for package 'MCMCpack'
* removing
'/home/lamby/temp/cdt.20160817165739.rwqUq8LYwU.db.mcmcpack/mcmcpack-1.3-6/debian/r-cran-mcmcpack/usr/lib/R/site-library/MCMCpack'
/usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
make: *** [R_any_arch] Error 1
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
mcmcpack.1.3-6-1.unstable.amd64.log.txt.gz
Description: Binary data
