[Debian-med-packaging] Bug#835400: libminc: FTBFS: convert.c:13:18: fatal error: hdf5.h: No such file or directory

Thu Aug 25 10:26:43 UTC 2016

Source: libminc
Version: 2.3.00-2
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,

libminc fails to build from source in unstable/amd64:

  [..]

  Get:15 http://httpredir.debian.org/debian sid/main amd64 libjpeg-dev all 1:1.5.0-1 [54.8 kB]
  Get:16 http://httpredir.debian.org/debian sid/main amd64 libaec-dev amd64 0.3.2-1 [17.4 kB]
  Get:17 http://httpredir.debian.org/debian sid/main amd64 hdf5-helpers amd64 1.8.16+docs-8 [35.4 kB]
  Get:18 http://httpredir.debian.org/debian sid/main amd64 libhdf5-cpp-11 amd64 1.8.16+docs-8 [126 kB]
  Get:19 http://httpredir.debian.org/debian sid/main amd64 libhdf5-dev amd64 1.8.16+docs-8 [5032 kB]
  Get:20 http://httpredir.debian.org/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.50.1-1 [360 kB]
  Get:21 http://httpredir.debian.org/debian sid/main amd64 libnetcdf-dev amd64 1:4.4.1-1 [76.5 kB]
  Get:22 http://httpredir.debian.org/debian sid/main amd64 libnifti2 amd64 2.0.0-2 [107 kB]
  Get:23 http://httpredir.debian.org/debian sid/main amd64 libnifti-dev amd64 2.0.0-2 [138 kB]
  Fetched 12.7 MB in 0s (75.7 MB/s)
  Selecting previously unselected package cmake-data.
  (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 23248 files and directories currently installed.)
  Preparing to unpack .../00-cmake-data_3.6.1-1_all.deb ...
  Unpacking cmake-data (3.6.1-1) ...
  Selecting previously unselected package liblzo2-2:amd64.
  Preparing to unpack .../01-liblzo2-2_2.08-1.2_amd64.deb ...
  Unpacking liblzo2-2:amd64 (2.08-1.2) ...
  Selecting previously unselected package libarchive13:amd64.
  Preparing to unpack .../02-libarchive13_3.2.1-2_amd64.deb ...
  Unpacking libarchive13:amd64 (3.2.1-2) ...
  Selecting previously unselected package libcurl3:amd64.
  Preparing to unpack .../03-libcurl3_7.50.1-1_amd64.deb ...
  Unpacking libcurl3:amd64 (7.50.1-1) ...
  Selecting previously unselected package libjsoncpp1:amd64.
  Preparing to unpack .../04-libjsoncpp1_1.7.4-3_amd64.deb ...
  Unpacking libjsoncpp1:amd64 (1.7.4-3) ...
  Selecting previously unselected package cmake.
  Preparing to unpack .../05-cmake_3.6.1-1_amd64.deb ...
  Unpacking cmake (3.6.1-1) ...
  Selecting previously unselected package libgfortran3:amd64.
  Preparing to unpack .../06-libgfortran3_6.2.0-1_amd64.deb ...
  Unpacking libgfortran3:amd64 (6.2.0-1) ...
  Selecting previously unselected package libaec0:amd64.
  Preparing to unpack .../07-libaec0_0.3.2-1_amd64.deb ...
  Unpacking libaec0:amd64 (0.3.2-1) ...
  Selecting previously unselected package libsz2:amd64.
  Preparing to unpack .../08-libsz2_0.3.2-1_amd64.deb ...
  Unpacking libsz2:amd64 (0.3.2-1) ...
  Selecting previously unselected package libhdf5-10:amd64.
  Preparing to unpack .../09-libhdf5-10_1.8.16+docs-8_amd64.deb ...
  Unpacking libhdf5-10:amd64 (1.8.16+docs-8) ...
  Selecting previously unselected package libnetcdf11.
  Preparing to unpack .../10-libnetcdf11_1%3a4.4.1-1_amd64.deb ...
  Unpacking libnetcdf11 (1:4.4.1-1) ...
  Selecting previously unselected package zlib1g-dev:amd64.
  Preparing to unpack .../11-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 libjpeg62-turbo:amd64.
  Preparing to unpack .../12-libjpeg62-turbo_1%3a1.5.0-1_amd64.deb ...
  Unpacking libjpeg62-turbo:amd64 (1:1.5.0-1) ...
  Selecting previously unselected package libjpeg62-turbo-dev:amd64.
  Preparing to unpack .../13-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 .../14-libjpeg-dev_1%3a1.5.0-1_all.deb ...
  Unpacking libjpeg-dev (1:1.5.0-1) ...
  Selecting previously unselected package libaec-dev:amd64.
  Preparing to unpack .../15-libaec-dev_0.3.2-1_amd64.deb ...
  Unpacking libaec-dev:amd64 (0.3.2-1) ...
  Selecting previously unselected package hdf5-helpers.
  Preparing to unpack .../16-hdf5-helpers_1.8.16+docs-8_amd64.deb ...
  Unpacking hdf5-helpers (1.8.16+docs-8) ...
  Selecting previously unselected package libhdf5-cpp-11:amd64.
  Preparing to unpack .../17-libhdf5-cpp-11_1.8.16+docs-8_amd64.deb ...
  Unpacking libhdf5-cpp-11:amd64 (1.8.16+docs-8) ...
  Selecting previously unselected package libhdf5-dev.
  Preparing to unpack .../18-libhdf5-dev_1.8.16+docs-8_amd64.deb ...
  Unpacking libhdf5-dev (1.8.16+docs-8) ...
  Selecting previously unselected package libcurl4-gnutls-dev:amd64.
  Preparing to unpack .../19-libcurl4-gnutls-dev_7.50.1-1_amd64.deb ...
  Unpacking libcurl4-gnutls-dev:amd64 (7.50.1-1) ...
  Selecting previously unselected package libnetcdf-dev.
  Preparing to unpack .../20-libnetcdf-dev_1%3a4.4.1-1_amd64.deb ...
  Unpacking libnetcdf-dev (1:4.4.1-1) ...
  Selecting previously unselected package libnifti2.
  Preparing to unpack .../21-libnifti2_2.0.0-2_amd64.deb ...
  Unpacking libnifti2 (2.0.0-2) ...
  Selecting previously unselected package libnifti-dev.
  Preparing to unpack .../22-libnifti-dev_2.0.0-2_amd64.deb ...
  Unpacking libnifti-dev (2.0.0-2) ...
  Setting up libaec0:amd64 (0.3.2-1) ...
  Setting up libnifti2 (2.0.0-2) ...
  Setting up libjpeg62-turbo:amd64 (1:1.5.0-1) ...
  Setting up libcurl3:amd64 (7.50.1-1) ...
  Setting up libgfortran3:amd64 (6.2.0-1) ...
  Setting up cmake-data (3.6.1-1) ...
  Setting up libnifti-dev (2.0.0-2) ...
  Processing triggers for libc-bin (2.23-5) ...
  Processing triggers for man-db (2.7.5-1) ...
  Setting up libjpeg62-turbo-dev:amd64 (1:1.5.0-1) ...
  Setting up libcurl4-gnutls-dev:amd64 (7.50.1-1) ...
  Setting up hdf5-helpers (1.8.16+docs-8) ...
  Setting up liblzo2-2:amd64 (2.08-1.2) ...
  Setting up libsz2:amd64 (0.3.2-1) ...
  Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
  Setting up libjsoncpp1:amd64 (1.7.4-3) ...
  Setting up libhdf5-10:amd64 (1.8.16+docs-8) ...
  Setting up libhdf5-cpp-11:amd64 (1.8.16+docs-8) ...
  Setting up libarchive13:amd64 (3.2.1-2) ...
  Setting up libaec-dev:amd64 (0.3.2-1) ...
  Setting up libhdf5-dev (1.8.16+docs-8) ...
  update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
  Setting up libjpeg-dev (1:1.5.0-1) ...
  Setting up cmake (3.6.1-1) ...
  Setting up libnetcdf11 (1:4.4.1-1) ...
  Setting up libnetcdf-dev (1:4.4.1-1) ...
  Setting up libminc-build-deps (2.3.00-2) ...
  Processing triggers for libc-bin (2.23-5) ...

  **************************************************************************************
  ** Environment                                                                      **
  **************************************************************************************

  PATH=/home/lamby/git/projects/dotfiles/dotfiles/..//bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
  HOSTNAME=ff03e8606951
  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.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00
  OLDPWD=/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc
  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 libminc 2.3.00-2 on amd64                                               **
  **************************************************************************************

   dpkg-buildpackage -rfakeroot -D -us -uc -b
  dpkg-buildpackage: info: source package libminc
  dpkg-buildpackage: info: source version 2.3.00-2
  dpkg-buildpackage: info: source distribution unstable
  dpkg-buildpackage: info: source changed by Steve M. Robbins <smr at debian.org>
   dpkg-source --before-build libminc-2.3.00
  dpkg-buildpackage: info: host architecture amd64
   fakeroot debian/rules clean
  dh clean
     dh_testdir
     dh_auto_clean
     dh_clean
   debian/rules build
  dh build
     dh_testdir
     dh_update_autotools_config
     debian/rules override_dh_auto_configure
  make[1]: Entering directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00'
  rm -f cmake-modules/*HDF5*
  dh_auto_configure -- -DLIB_SUFFIX=/x86_64-linux-gnu -DBUILD_TESTING:BOOL=ON -DLIBMINC_BUILD_EZMINC_EXAMPLES:BOOL=ON -DLIBMINC_BUILD_SHARED_LIBS:BOOL=ON -DLIBMINC_MINC1_SUPPORT:BOOL=ON
  	cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DLIB_SUFFIX=/x86_64-linux-gnu -DBUILD_TESTING:BOOL=ON -DLIBMINC_BUILD_EZMINC_EXAMPLES:BOOL=ON -DLIBMINC_BUILD_SHARED_LIBS:BOOL=ON -DLIBMINC_MINC1_SUPPORT:BOOL=ON
  -- The C compiler identification is GNU 6.2.0
  -- The CXX compiler identification is GNU 6.2.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Found NetCDF headers: /usr/include
  -- Found NetCDF library: /usr/lib/x86_64-linux-gnu/libnetcdf.so
  -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
  -- HDF5: Using hdf5 compiler wrapper to determine C configuration
  -- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
  -- Found HDF5: /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16")  
  -- Looking for mkstemp
  -- Looking for mkstemp - found
  -- Looking for tmpnam
  -- Looking for tmpnam - found
  -- Looking for tempnam
  -- Looking for tempnam - found
  -- Looking for strerror
  -- Looking for strerror - found
  -- Looking for popen
  -- Looking for popen - found
  -- Looking for fork
  -- Looking for fork - found
  -- Looking for vfork
  -- Looking for vfork - found
  -- Looking for fdopen
  -- Looking for fdopen - found
  -- Looking for strdup
  -- Looking for strdup - found
  -- Looking for getpwnam
  -- Looking for getpwnam - found
  -- Looking for select
  -- Looking for select - found
  -- Looking for sysconf
  -- Looking for sysconf - found
  -- Looking for system
  -- Looking for system - found
  -- Looking for srand48
  -- Looking for srand48 - found
  -- Looking for drand48
  -- Looking for drand48 - found
  -- Looking for sleep
  -- Looking for sleep - found
  -- Looking for gettimeofday
  -- Looking for gettimeofday - found
  -- Looking for clock_gettime in rt
  -- Looking for clock_gettime in rt - found
  -- Looking for include file float.h
  -- Looking for include file float.h - found
  -- Looking for include file sys/dir.h
  -- Looking for include file sys/dir.h - found
  -- Looking for include file sys/ndir.h
  -- Looking for include file sys/ndir.h - not found
  -- Looking for include file sys/stat.h
  -- Looking for include file sys/stat.h - found
  -- Looking for include file sys/types.h
  -- Looking for include file sys/types.h - found
  -- Looking for include file sys/wait.h
  -- Looking for include file sys/wait.h - found
  -- Looking for include file sys/time.h
  -- Looking for include file sys/time.h - found
  -- Looking for include file values.h
  -- Looking for include file values.h - found
  -- Looking for include file unistd.h
  -- Looking for include file unistd.h - found
  -- Looking for include file dirent.h
  -- Looking for include file dirent.h - found
  -- Looking for include file memory.h
  -- Looking for include file memory.h - found
  -- Looking for include file stdlib.h
  -- Looking for include file stdlib.h - found
  -- Looking for include file fcntl.h
  -- Looking for include file fcntl.h - found
  -- Looking for include file dlfcn.h
  -- Looking for include file dlfcn.h - found
  -- Looking for include file vfork.h
  -- Looking for include file vfork.h - not found
  -- Looking for include file inttypes.h
  -- Looking for include file inttypes.h - found
  -- Looking for include file string.h
  -- Looking for include file string.h - found
  -- Looking for include file strings.h
  -- Looking for include file strings.h - found
  -- Looking for include file pwd.h
  -- Looking for include file pwd.h - found
  -- Configuring done
  -- Generating done
  CMake Warning:
    Manually-specified variables were not used by the project:

      CMAKE_INSTALL_LOCALSTATEDIR
      CMAKE_INSTALL_SYSCONFDIR

  -- Build files have been written to: /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu
  make[1]: Leaving directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00'
     dh_auto_build
  	make -j1
  make[1]: Entering directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  /usr/bin/cmake -H/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00 -B/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
  /usr/bin/cmake -E cmake_progress_start /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu/CMakeFiles /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu/CMakeFiles/progress.marks
  make -f CMakeFiles/Makefile2 all
  make[2]: Entering directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  make -f CMakeFiles/minc2_static.dir/build.make CMakeFiles/minc2_static.dir/depend
  make[3]: Entering directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  cd /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00 /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00 /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu/CMakeFiles/minc2_static.dir/DependInfo.cmake --color=
  Scanning dependencies of target minc2_static
  make[3]: Leaving directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  make -f CMakeFiles/minc2_static.dir/build.make CMakeFiles/minc2_static.dir/build
  make[3]: Entering directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  [  1%] Building C object CMakeFiles/minc2_static.dir/libsrc2/convert.c.o
  /usr/bin/cc  -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DMINC2=1 -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00 -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/libsrc2 -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/libsrc -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/volume_io/Include -I/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/ezminc -I/usr/include/nifti  -g -O2 -fdebug-prefix-map=/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2    -fPIC   -o CMakeFiles/minc2_static.dir/libsrc2/convert.c.o   -c /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/libsrc2/convert.c
  /home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/libsrc2/convert.c:13:18: fatal error: hdf5.h: No such file or directory
   #include <hdf5.h>
                    ^
  compilation terminated.
  CMakeFiles/minc2_static.dir/build.make:65: recipe for target 'CMakeFiles/minc2_static.dir/libsrc2/convert.c.o' failed
  make[3]: *** [CMakeFiles/minc2_static.dir/libsrc2/convert.c.o] Error 1
  make[3]: Leaving directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  CMakeFiles/Makefile2:70: recipe for target 'CMakeFiles/minc2_static.dir/all' failed
  make[2]: *** [CMakeFiles/minc2_static.dir/all] Error 2
  make[2]: Leaving directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  Makefile:163: recipe for target 'all' failed
  make[1]: *** [all] Error 2
  make[1]: Leaving directory '/home/lamby/temp/cdt.20160825112354.7wJltpfGDK.db.libminc/libminc-2.3.00/obj-x86_64-linux-gnu'
  dh_auto_build: make -j1 returned exit code 2
  debian/rules:14: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.

Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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