Bug#793902: ncview: FTBFS with netcdf in experimental

Bas Couwenberg sebastic at xs4all.nl
Tue Jul 28 19:16:16 UTC 2015


Package: ncview
Version: 2.1.5+ds1-1
Severity: normal
Tags: upstream
User: debian-gis at lists.debian.org
Usertags: netcdf-split-c-f-cxx

Dear Maintainer,

Your package FTBFS with the new netcdf packages in experimental due to
not accepting the mpicc compiler used to build netcdf.

It looks like AC_PROG_CC in configure.in doesn't check the alternative
properly:

    debian/rules override_dh_auto_configure
 make[1]: Entering directory '/tmp/buildd/ncview-2.1.5+ds1'
 ls -l /usr/bin/mpicc* /etc/alternatives/mpicc* /usr/bin/opal_wrapper
 lrwxrwxrwx 1 root root    22 Jul 28 18:53 /etc/alternatives/mpicc -> /usr/bin/mpicc.openmpi
 lrwxrwxrwx 1 root root    38 Jul 28 18:53 /etc/alternatives/mpicc.1.gz -> /usr/share/man/man1/mpicc.openmpi.1.gz
 lrwxrwxrwx 1 root root    23 Jul 28 18:53 /usr/bin/mpicc -> /etc/alternatives/mpicc
 lrwxrwxrwx 1 root root    12 Jun 25 09:47 /usr/bin/mpicc.openmpi -> opal_wrapper
 -rwxr-xr-x 1 root root 18856 Jun 25 09:47 /usr/bin/opal_wrapper
 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 nc-config... yes
 Netcdf library version: netCDF 4.4.0-rc2
 Netcdf library has version 4 interface present: yes
 Netcdf library was compiled with C compiler: /usr/bin/mpicc
 checking for /usr/bin/mpicc... no
 configure: error: in `/tmp/buildd/ncview-2.1.5+ds1':
 configure: error: no acceptable C compiler found in $PATH

The full build log is attached.

Kind Regards,

Bas
-------------- next part --------------
Building with cowbuilder for distribution sid+rebuild
I: using cowbuilder as pbuilder
dpkg-checkbuilddeps: Unmet build dependencies: netcdf-bin libnetpbm10-dev libudunits2-dev libxaw7-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package ncview
dpkg-buildpackage: source version 2.1.5+ds1-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Bas Couwenberg <sebastic at debian.org>
 dpkg-source --before-build ncview
dpkg-source: info: applying auxiliary-typo.patch
dpkg-source: info: applying manpage.patch
dpkg-source: info: applying autoreconf.patch
dpkg-checkbuilddeps: Unmet build dependencies: netcdf-bin libnetpbm10-dev libudunits2-dev libxaw7-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 \
  --parallel
   dh_testdir -O--parallel
   dh_auto_clean -O--parallel
   dh_autoreconf_clean -O--parallel
   debian/rules override_dh_clean
make[1]: Entering directory '/home/bas/git/pkg-grass/ncview'
dh_clean ncview.1
make[1]: Leaving directory '/home/bas/git/pkg-grass/ncview'
 dpkg-source -b ncview
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building ncview using existing ./ncview_2.1.5+ds1.orig.tar.gz
dpkg-source: info: building ncview in ncview_2.1.5+ds1-1.debian.tar.xz
dpkg-source: info: building ncview in ncview_2.1.5+ds1-1.dsc
 dpkg-genchanges -S >../ncview_2.1.5+ds1-1_source.changes
dpkg-genchanges: not including original source code in upload
 dpkg-source --after-build ncview
dpkg-source: info: unapplying autoreconf.patch
dpkg-source: info: unapplying manpage.patch
dpkg-source: info: unapplying auxiliary-typo.patch
dpkg-buildpackage: binary and diff upload (original source NOT included)
 -> Copying COW directory
  forking: rm -rf /var/cache/pbuilder/build//cow.17339 
  forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow /var/cache/pbuilder/build//cow.17339 
I: removed stale ilistfile /var/cache/pbuilder/build//cow.17339/.ilist
  forking: chroot /var/cache/pbuilder/build//cow.17339 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.17339 --buildresult /home/bas/git/pkg-grass --debbuildopts  --no-targz --internal-chrootexec chroot /var/cache/pbuilder/build//cow.17339 cow-shell /home/bas/git/pkg-grass/ncview_2.1.5+ds1-1.dsc 
I: Running in no-targz mode
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jul 28 20:51:55 CEST 2015
I: pbuilder-time-stamp: 1438109515
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), dh-autoreconf, autotools-dev, chrpath, libexpat1-dev, libpng-dev, libnetcdf-dev, netcdf-bin, libnetpbm10-dev, libudunits2-dev, libxaw7-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
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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 autotools-dev; however:
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 pbuilder-satisfydepends-dummy depends on libpng-dev; however:
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 pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however:
  Package libnetcdf-dev is not installed.
 pbuilder-satisfydepends-dummy depends on netcdf-bin; however:
  Package netcdf-bin is not installed.
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  Package libnetpbm10-d
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  gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} 
  libasprintf0c2{a} libcr0{a} libcroco3{a} libcurl3-gnutls{a} 
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  libltdl-dev{a} libltdl7{a} libmagic1{a} libnetcdf-dev{a} libnetcdf7{a} 
  libnetpbm10{a} libnetpbm10-dev{a} libnettle6{a} libnuma-dev{a} 
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  libpipeline1{a} libpng12-0{a} libpng12-dev{a} libpthread-stubs0-dev{a} 
  librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} 
  libsm-dev{a} libsm6{a} libssh2-1{a} libtasn1-6{a} libtool{a} 
  libudunits2-0{a} libudunits2-dev{a} libunistring0{a} libx11-6{a} 
  libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} 
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  x11proto-kb-dev{a} x11proto-xext-dev{a} xorg-sgml-doctools{a} 
  xtrans-dev{a} zlib1g-dev{a} 
0 packages upgraded, 110 newly installed, 0 to remove and 0 not upgraded.
Need to get 612 kB/37.5 MB of archives. After unpacking 137 MB will be used.
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Get: 1 http://debian.linuxminded.nl/ sid-rebuild/main libnetcdf7 amd64 1:4.4.0~rc2-1~exp3 [314 kB]
Get: 2 http://debian.linuxminded.nl/ sid-rebuild/main libnetcdf-dev amd64 1:4.4.0~rc2-1~exp3 [71.9 kB]
Get: 3 http://debian.linuxminded.nl/ sid-rebuild/main netcdf-bin amd64 1:4.4.0~rc2-1~exp3 [227 kB]
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Reading package lists...
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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.
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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/git/pkg-grass/ncview_2.1.5+ds1-1.dsc]
I: copying [/home/bas/git/pkg-grass/ncview_2.1.5+ds1.orig.tar.gz]
I: copying [/home/bas/git/pkg-grass/ncview_2.1.5+ds1-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (ncview_2.1.5+ds1-1.dsc)
dpkg-source: info: extracting ncview in ncview-2.1.5+ds1
dpkg-source: info: unpacking ncview_2.1.5+ds1.orig.tar.gz
dpkg-source: info: unpacking ncview_2.1.5+ds1-1.debian.tar.xz
dpkg-source: info: applying auxiliary-typo.patch
dpkg-source: info: applying manpage.patch
dpkg-source: info: applying autoreconf.patch
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 ncview
dpkg-buildpackage: source version 2.1.5+ds1-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Bas Couwenberg <sebastic at debian.org>
 dpkg-source --before-build ncview-2.1.5+ds1
dpkg-buildpackage: host architecture amd64
 fakeroot debian/rules clean
dh clean \
  --with autoreconf \
  --parallel
   dh_testdir -O--parallel
   dh_auto_clean -O--parallel
   dh_autoreconf_clean -O--parallel
   debian/rules override_dh_clean
make[1]: Entering directory '/tmp/buildd/ncview-2.1.5+ds1'
dh_clean ncview.1
make[1]: Leaving directory '/tmp/buildd/ncview-2.1.5+ds1'
 dpkg-source -b ncview-2.1.5+ds1
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building ncview using existing ./ncview_2.1.5+ds1.orig.tar.gz
dpkg-source: info: building ncview in ncview_2.1.5+ds1-1.debian.tar.xz
dpkg-source: info: building ncview in ncview_2.1.5+ds1-1.dsc
 debian/rules build
dh build \
  --with autoreconf \
  --parallel
   dh_testdir -O--parallel
   dh_autoreconf -O--parallel
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:33: installing './compile'
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/tmp/buildd/ncview-2.1.5+ds1'
ls -l /usr/bin/mpicc* /etc/alternatives/mpicc* /usr/bin/opal_wrapper
lrwxrwxrwx 1 root root    22 Jul 28 18:53 /etc/alternatives/mpicc -> /usr/bin/mpicc.openmpi
lrwxrwxrwx 1 root root    38 Jul 28 18:53 /etc/alternatives/mpicc.1.gz -> /usr/share/man/man1/mpicc.openmpi.1.gz
lrwxrwxrwx 1 root root    23 Jul 28 18:53 /usr/bin/mpicc -> /etc/alternatives/mpicc
lrwxrwxrwx 1 root root    12 Jun 25 09:47 /usr/bin/mpicc.openmpi -> opal_wrapper
-rwxr-xr-x 1 root root 18856 Jun 25 09:47 /usr/bin/opal_wrapper
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 nc-config... yes
Netcdf library version: netCDF 4.4.0-rc2
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: /usr/bin/mpicc
checking for /usr/bin/mpicc... no
configure: error: in `/tmp/buildd/ncview-2.1.5+ds1':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details
	"tail -v -n +0 config.log"
==> config.log <==
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by ncview configure 2.0.0, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./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

## --------- ##
## Platform. ##
## --------- ##

hostname = anubis
uname -m = x86_64
uname -r = 3.16.0-4-amd64
uname -s = Linux
uname -v = #1 SMP Debian 3.16.7-ckt11-1+deb8u2 (2015-07-17)

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2216: checking for nc-config
configure:2232: found /usr/bin/nc-config
configure:2244: result: yes
configure:2371: checking for /usr/bin/mpicc
configure:2401: result: no
configure:2423: error: in `/tmp/buildd/ncview-2.1.5+ds1':
configure:2425: error: no acceptable C compiler found in $PATH
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-g -O2 -fstack-protector-strong -Wformat -Werror=format-security'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-D_FORTIFY_SOURCE=2
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=-Wl,-z,relro
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_XMKMF_set=
ac_cv_env_XMKMF_value=
ac_cv_env_build_alias_set=set
ac_cv_env_build_alias_value=x86_64-linux-gnu
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_prog_HAS_NC_CONFIG=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='debian/aclocal'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR=''
AM_BACKSLASH=''
AM_DEFAULT_V=''
AM_DEFAULT_VERBOSITY=''
AM_V=''
AUTOCONF=''
AUTOHEADER=''
AUTOMAKE=''
AWK=''
CC=''
CCDEPMODE=''
CFLAGS='-g -O2 -fstack-protector-strong -Wformat -Werror=format-security'
CPP=''
CPPFLAGS='-D_FORTIFY_SOURCE=2'
CYGPATH_W=''
DEFS=''
DEPDIR=''
DO_PNG_INCDIR=''
DO_PNG_LIBDIR=''
DO_PNG_LIBNAME=''
DO_PNG_LINE=''
DO_UDUNITS2_INCDIR=''
DO_UDUNITS2_LIBDIR=''
DO_UDUNITS2_LIBNAME=''
DO_UDUNITS2_LINE=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
GREP=''
HAS_NC_CONFIG='yes'
INSTALL_DATA=''
INSTALL_PROGRAM=''
INSTALL_SCRIPT=''
INSTALL_STRIP_PROGRAM=''
LDFLAGS='-Wl,-z,relro'
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MAKEINFO=''
MKDIR_P=''
NETCDF_CC='/usr/bin/mpicc'
NETCDF_CPPFLAGS='-I/usr/include'
NETCDF_LDFLAGS='-L/usr/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl -lm -lcurl'
NETCDF_LIBS=''
NETCDF_VERSION='netCDF 4.4.0-rc2'
OBJEXT=''
PACKAGE=''
PACKAGE_BUGREPORT='dpierce at ucsd.edu'
PACKAGE_NAME='ncview'
PACKAGE_STRING='ncview 2.0.0'
PACKAGE_TARNAME='ncview'
PACKAGE_URL=''
PACKAGE_VERSION='2.0.0'
PATH_SEPARATOR=':'
PNG_CPPFLAGS=''
PNG_LDFLAGS=''
PNG_LIBS=''
PREFIX=''
RPATH_FLAGS=''
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
UDUNITS2_CPPFLAGS=''
UDUNITS2_LDFLAGS=''
UDUNITS2_LIBS=''
VERSION=''
X11_LIBS=''
XAW_LIBS=''
XMKMF=''
X_CFLAGS=''
X_EXTRA_LIBS=''
X_INCLUDES=''
X_LIBS=''
X_PRE_LIBS=''
ac_ct_CC=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__include=''
am__isrc=''
am__leading_dot=''
am__nodep=''
am__quote=''
am__tar=''
am__untar=''
bindir='${exec_prefix}/bin'
build_alias='x86_64-linux-gnu'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${prefix}/share/info'
install_sh=''
libdir='${prefix}/lib/x86_64-linux-gnu'
libexecdir='${prefix}/lib/x86_64-linux-gnu'
localedir='${datarootdir}/locale'
localstatedir='/var'
mandir='${prefix}/share/man'
mkdir_p=''
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "ncview"
#define PACKAGE_TARNAME "ncview"
#define PACKAGE_VERSION "2.0.0"
#define PACKAGE_STRING "ncview 2.0.0"
#define PACKAGE_BUGREPORT "dpierce at ucsd.edu"
#define PACKAGE_URL ""
#define HAVE_NETCDF 1
#define HAVE_NETCDF4 1

configure: exit 1
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 returned exit code 1
debian/rules:13: recipe for target 'override_dh_auto_configure' failed
make[1]: *** [override_dh_auto_configure] Error 255
make[1]: Leaving directory '/tmp/buildd/ncview-2.1.5+ds1'
debian/rules:8: 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.17339 
gbp:error: 'git-pbuilder' failed: it exited with 1


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