[Reproducible-builds] Bug#834631: mcmcpack: FTBFS: ERROR: dependency 'mcmc' is not available for package 'MCMCpack'

Chris Lamb lamby at debian.org
Wed Aug 17 17:07:26 UTC 2016 

Source: mcmcpack
Version: 1.3-6-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at 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=lamby at 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 <lawrencc at 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
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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