Bug#755167: marked as done (cmor: FTBFS - missing build-depends)

Fri, 25 Jul 2014 00:21:41 -0700 

Your message dated Fri, 25 Jul 2014 07:18:33 +0000
with message-id <e1xazlx-0004zq...@franck.debian.org>
and subject line Bug#755167: fixed in cmor 2.9.1-4
has caused the Debian Bug report #755167,
regarding cmor: FTBFS - missing build-depends
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
755167: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=755167
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message --- 
Source: cmor
Version: 2.9.1-3
Severity: serious
Justification: FTBFS on amd64

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256


Hi,

While preparing the hdf5-8 transition I experienced a FTBFS for the
package cmor, which seems missing a few build dependencies:
 libgcrypt-dev, libgnutls-dev, libgpg-error-dev, libtasn1-dev,
 libp11-kit-dev

The FTBFS occurs on an up to date unstable chroot as well (with hdf5-7).

The failure occurs during the configure step while checking for netcdf:
configure:4269: checking for nc_inq_var_deflate in -lnetcdf
configure:4294: gcc -o conftest -lnetcdf -D_FORTIFY_SOURCE=2 -lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt    -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 -lp11-kit
    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 conftest.c -lnetcdf  
-lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  
-lz -lidn -lrtmp -lgcrypt     -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-erro
r -ltasn1 -lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3   
>&5
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit

Full build log attached.

Thanks,

_g.

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dpkg-checkbuilddeps: Unmet build dependencies: dh-buildinfo libossp-uuid-dev 
libudunits2-dev libnetcdf-dev uuid-dev python-all-dev (>= 2.6.6-3~) 
python-setuptools (>= 0.6b3) libcurl4-gnutls-dev libldap2-dev heimdal-multidev 
libsqlite3-dev libsasl2-dev libkeyutils-dev libffi-dev libhdf5-mpi-dev | 
libhdf5-dev librtmp-dev libidn11-dev libkrb5-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package cmor
dpkg-buildpackage: source version 2.9.1-3
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Alastair McKinstry <mckins...@debian.org>
 dpkg-source --before-build cmor-2.9.1
dpkg-source: info: using options from cmor-2.9.1/debian/source/options: 
--compression=xz
dpkg-checkbuilddeps: Unmet build dependencies: dh-buildinfo libossp-uuid-dev 
libudunits2-dev libnetcdf-dev uuid-dev python-all-dev (>= 2.6.6-3~) 
python-setuptools (>= 0.6b3) libcurl4-gnutls-dev libldap2-dev heimdal-multidev 
libsqlite3-dev libsasl2-dev libkeyutils-dev libffi-dev libhdf5-mpi-dev | 
libhdf5-dev librtmp-dev libidn11-dev libkrb5-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 python2
   dh_testdir
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/home/pini/hdf5-transition/cmor-2.9.1'
rm -rf config.sub config.log config.status libcmor.a libcmor.so.2 build 
test_grid configure CMIP5
rm -f ipcc_test_code Makefile setup.py *.mod compile_line.txt 
include/cmor_locale.h cmor.pc
find . -name '*.nc' -delete
find . -name '*.o' -delete
find .  -name '*.pic_o' -delete
find . -name '*.pyc' -delete
make[1]: Leaving directory '/home/pini/hdf5-transition/cmor-2.9.1'
   dh_clean
        rm -f debian/libcmor2.substvars
        rm -f debian/libcmor2.*.debhelper
        rm -rf debian/libcmor2/
        rm -f debian/libcmor-dev.substvars
        rm -f debian/libcmor-dev.*.debhelper
        rm -rf debian/libcmor-dev/
        rm -f debian/python-cmor.substvars
        rm -f debian/python-cmor.*.debhelper
        rm -rf debian/python-cmor/
        rm -f debian/*.debhelper.log
        rm -f debian/files
        find .  \( \( -type f -a \
                \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
                 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
                 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
                 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
                \) -exec rm -f {} + \) -o \
                \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) 
\)
        rm -f *-stamp
 dpkg-source -b cmor-2.9.1
dpkg-source: info: using options from cmor-2.9.1/debian/source/options: 
--compression=xz
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building cmor using existing ./cmor_2.9.1.orig.tar.xz
dpkg-source: warning: ignoring deletion of file config.sub, use 
--include-removal to override
dpkg-source: warning: ignoring deletion of file configure, use 
--include-removal to override
dpkg-source: info: building cmor in cmor_2.9.1-3.debian.tar.xz
dpkg-source: info: building cmor in cmor_2.9.1-3.dsc
 dpkg-genchanges -S >../cmor_2.9.1-3_source.changes
dpkg-genchanges: not including original source code in upload
 dpkg-source --after-build cmor-2.9.1
dpkg-source: info: using options from cmor-2.9.1/debian/source/options: 
--compression=xz
dpkg-buildpackage: binary and diff upload (original source NOT included)
 -> Copying COW directory
  forking: rm -rf /var/cache/pbuilder/build//cow.21320 
  forking: cp -al /home/pbuilder/base-sid.cow 
/var/cache/pbuilder/build//cow.21320 
I: removed stale ilistfile /var/cache/pbuilder/build//cow.21320/.ilist
  forking: chroot /var/cache/pbuilder/build//cow.21320 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.21320 --buildresult /home/pini/hdf5-transition 
--debbuildopts   --no-targz --internal-chrootexec chroot 
/var/cache/pbuilder/build//cow.21320 cow-shell 
/home/pini/hdf5-transition/cmor_2.9.1-3.dsc 
I: Running in no-targz mode
I: using fakeroot in build.
I: Current time: Fri Jul 18 14:32:39 CEST 2014
I: pbuilder-time-stamp: 1405686759
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-ma...@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-buildinfo, libossp-uuid-dev, libudunits2-dev, 
libnetcdf-dev, uuid-dev, python-all-dev (>= 2.6.6-3~), python-setuptools (>= 
0.6b3), python-numpy, libgfortran3, automake, gfortran, pkg-config, 
libcurl4-gnutls-dev, libldap2-dev, heimdal-multidev, libsqlite3-dev, 
libsasl2-dev, libkeyutils-dev, libffi-dev, libhdf5-mpi-dev | libhdf5-dev, 
librtmp-dev, libidn11-dev, libkrb5-dev
Conflicts: libcmor2, python-cmor, python3-cmor
dpkg-deb: building package `pbuilder-satisfydepends-dummy' in 
`/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 12520 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
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-buildinfo; however:
  Package dh-buildinfo is not installed.
 pbuilder-satisfydepends-dummy depends on libossp-uuid-dev; however:
  Package libossp-uuid-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libudunits2-dev; however:
  Package libudunits2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however:
  Package libnetcdf-dev is not installed.
 pbuilder-satisfydepends-dummy depends on uuid-dev; however:
  Package uuid-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python-all-dev (>= 2.6.6-3~); however:
  Package python-all-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python-setuptools (>= 0.6b3); however:
  Package python-setuptools is not installed.
 pbuilder-satisfydepends-dummy dep
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
The following NEW packages will be installed:
  adduser{a} autoconf{a} automake{a} autotools-dev{a} bsdmainutils{a} 
  comerr-dev{a} debhelper{a} dh-buildinfo{a} file{a} gettext{a} 
  gettext-base{a} gfortran{a} gfortran-4.9{a} groff-base{a} hdf5-helpers{a} 
  heimdal-multidev{a} intltool-debian{a} krb5-multidev{a} 
  libasn1-8-heimdal{a} libasprintf0c2{a} libblas3{a} libbsd0{a} libcf0{a} 
  libcr0{a} libcroco3{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} 
  libedit2{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libffi6{a} 
  libgcrypt11{a} libgcrypt20{a} libgfortran-4.9-dev{a} libgfortran3{a} 
  libglib2.0-0{a} libgmp-dev{a} libgnutls-deb0-28{a} libgnutls26{a} 
  libgpg-error0{a} libgssapi-krb5-2{a} libgssapi3-heimdal{a} libgssrpc4{a} 
  libhcrypto4-heimdal{a} libhdb9-heimdal{a} libhdf5-7{a} libhdf5-mpi-dev{a} 
  libhdf5-openmpi-7{ab} libhdf5-openmpi-dev{a} libheimbase1-heimdal{a} 
  libheimntlm0-heimdal{a} libhogweed2{a} libhwloc-dev{a} libhwloc5{a} 
  libhx509-5-heimdal{a} libibverbs-dev{a} libibverbs1{a} libidn11{a} 
  libidn11-dev{a} libjpeg8{a} libjpeg8-dev{a} libk5crypto3{a} 
  libkadm5clnt-mit9{a} libkadm5clnt7-heimdal{a} libkadm5srv-mit9{a} 
  libkadm5srv8-heimdal{a} libkafs0-heimdal{a} libkdb5-7{a} 
  libkdc2-heimdal{a} libkeyutils-dev{a} libkeyutils1{a} 
  libkrb5-26-heimdal{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} 
  liblapack3{a} libldap-2.4-2{a} libldap2-dev{a} libltdl7{a} libmagic1{a} 
  libnetcdf-dev{a} libnetcdfc++4{a} libnetcdfc7{a} libnetcdff5{a} 
  libnettle4{a} libnuma1{a} libopenmpi-dev{a} libopenmpi1.6{a} 
  libossp-uuid-dev{a} libossp-uuid16{a} libotp0-heimdal{a} libp11-kit0{a} 
  libpci-dev{a} libpci3{a} libpipeline1{a} libpython-all-dev{a} 
  libpython-dev{a} libpython-stdlib{a} libpython2.7{a} libpython2.7-dev{a} 
  libpython2.7-minimal{a} libpython2.7-stdlib{a} libroken18-heimdal{a} 
  librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-dev{a} 
  libsasl2-modules-db{a} libsigsegv2{a} libsl0-heimdal{a} libsqlite3-dev{a} 
  libssh2-1{a} libssl1.0.0{a} libtasn1-6{a} libtorque2{a} libudunits2-0{a} 
  libudunits2-dev{a} libunistring0{a} libwind0-heimdal{a} libxml2{a} 
  libxml2-dev{a} m4{a} man-db{a} mime-support{a} mpi-default-dev{a} 
  openmpi-common{a} pkg-config{a} po-debconf{a} python{a} python-all{a} 
  python-all-dev{a} python-dev{a} python-minimal{a} python-numpy{a} 
  python-pkg-resources{a} python-setuptools{a} python2.7{a} 
  python2.7-dev{a} python2.7-minimal{a} uuid-dev{a} zlib1g-dev{a} 
0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded.
Need to get 7333 kB/77.7 MB of archives. After unpacking 210 MB will be used.
The following packages have unmet dependencies:
 libhdf5-openmpi-7 : Conflicts: libhdf5-7 but 1.8.12+docs-1.1+b1 is to be 
installed.
The following actions will resolve these dependencies:

     Keep the following packages at their current version:
1)     libhdf5-7 [Not Installed]                          



The following NEW packages will be installed:
  adduser{a} autoconf{a} automake{a} autotools-dev{a} bsdmainutils{a} 
  comerr-dev{a} debhelper{a} dh-buildinfo{a} file{a} gettext{a} 
  gettext-base{a} gfortran{a} gfortran-4.9{a} groff-base{a} hdf5-helpers{a} 
  heimdal-multidev{a} intltool-debian{a} krb5-multidev{a} 
  libasn1-8-heimdal{a} libasprintf0c2{a} libblas3{a} libbsd0{a} libcf0{a} 
  libcr0{a} libcroco3{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} 
  libedit2{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libffi6{a} 
  libgcrypt11{a} libgcrypt20{a} libgfortran-4.9-dev{a} libgfortran3{a} 
  libglib2.0-0{a} libgmp-dev{a} libgnutls-deb0-28{a} libgnutls26{a} 
  libgpg-error0{a} libgssapi-krb5-2{a} libgssapi3-heimdal{a} libgssrpc4{a} 
  libhcrypto4-heimdal{a} libhdb9-heimdal{a} libhdf5-mpi-dev{a} 
  libhdf5-openmpi-7{a} libhdf5-openmpi-dev{a} libheimbase1-heimdal{a} 
  libheimntlm0-heimdal{a} libhogweed2{a} libhwloc-dev{a} libhwloc5{a} 
  libhx509-5-heimdal{a} libibverbs-dev{a} libibverbs1{a} libidn11{a} 
  libidn11-dev{a} libjpeg8{a} libjpeg8-dev{a} libk5crypto3{a} 
  libkadm5clnt-mit9{a} libkadm5clnt7-heimdal{a} libkadm5srv-mit9{a} 
  libkadm5srv8-heimdal{a} libkafs0-heimdal{a} libkdb5-7{a} 
  libkdc2-heimdal{a} libkeyutils-dev{a} libkeyutils1{a} 
  libkrb5-26-heimdal{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} 
  liblapack3{a} libldap-2.4-2{a} libldap2-dev{a} libltdl7{a} libmagic1{a} 
  libnetcdf-dev{a} libnetcdfc++4{a} libnetcdfc7{a} libnetcdff5{a} 
  libnettle4{a} libnuma1{a} libopenmpi-dev{a} libopenmpi1.6{a} 
  libossp-uuid-dev{a} libossp-uuid16{a} libotp0-heimdal{a} libp11-kit0{a} 
  libpci-dev{a} libpci3{a} libpipeline1{a} libpython-all-dev{a} 
  libpython-dev{a} libpython-stdlib{a} libpython2.7{a} libpython2.7-dev{a} 
  libpython2.7-minimal{a} libpython2.7-stdlib{a} libroken18-heimdal{a} 
  librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-dev{a} 
  libsasl2-modules-db{a} libsigsegv2{a} libsl0-heimdal{a} libsqlite3-dev{a} 
  libssh2-1{a} libssl1.0.0{a} libtasn1-6{a} libtorque2{a} libudunits2-0{a} 
  libudunits2-dev{a} libunistring0{a} libwind0-heimdal{a} libxml2{a} 
  libxml2-dev{a} m4{a} man-db{a} mime-support{a} mpi-default-dev{a} 
  openmpi-common{a} pkg-config{a} po-debconf{a} python{a} python-all{a} 
  python-all-dev{a} python-dev{a} python-minimal{a} python-numpy{a} 
  python-pkg-resources{a} python-setuptools{a} python2.7{a} 
  python2.7-dev{a} python2.7-minimal{a} uuid-dev{a} zlib1g-dev{a} 
0 packages upgraded, 141 newly installed, 0 to remove and 0 not upgraded.
Need to get 7333 kB/76.7 MB of archives. After unpacking 206 MB will be used.
Writing extended state information...
Get: 1 http://ftp.fr.debian.org/debian/ unstable/main libasprintf0c2 amd64 
0.18.3.2-4 [29.6 kB]
Get: 2 http://ftp.fr.debian.org/debian/ unstable/main libgfortran3 amd64 
4.9.1-1 [255 kB]
Get: 3 http://ftp.fr.debian.org/debian/ unstable/main gettext-base amd64 
0.18.3.2-4 [116 kB]
Get: 4 http://ftp.fr.debian.org/debian/ unstable/main gettext amd64 0.18.3.2-4 
[1208 kB]
Get: 5 http://ftp.fr.debian.org/debian/ unstable/main libgfortran-4.9-dev amd64 
4.9.1-1 [282 kB]
Get: 6 http://ftp.fr.debian.org/debian/ unstable/main gfortran-4.9 amd64 
4.9.1-1 [5442 kB]
Get: 7 http://ftp.fr.debian.org/debian/ unstable/main gfortran amd64 4:4.9.1-1 
[1282 B]
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debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libhwloc-dev:amd64.
Preparing to unpack .../libhwloc-dev_1.9-4_amd64.deb ...
Unpacking libhwloc-dev:amd64 (1.9-4) ...
Selecting previously unselected package libopenmpi-dev.
Preparing to unpack .../libopenmpi-dev_1.6.5-8+b1_amd64.deb ...
Unpacking libopenmpi-dev (1.6.5-8+b1) ...
Selecting previously unselected package libhdf5-openmpi-dev.
Preparing to unpack .../libhdf5-openmpi-dev_1.8.12+docs-1.1+b1_amd64.deb ...
Unpacking libhdf5-openmpi-dev (1.8.12+docs-1.1+b1) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../mpi-default-dev_1.0.2+nmu1_amd64.deb ...
Unpacking mpi-default-dev (1.0.2+nmu1) ...
Selecting previously unselected package libhdf5-mpi-dev.
Preparing to unpack .../libhdf5-mpi-dev_1.8.12+docs-1.1+b1_amd64.deb ...
Unpacking libhdf5-mpi-dev (1.8.12+docs-1.1+b1) ...
Selecting previously unselected package libkrb5-dev.
Preparing to unpack .../libkrb5-dev_1.12.1+dfsg-4_amd64.deb ...
Unpacking libkrb5-dev (1.12.1+dfsg-4) ...
Selecting previously unselected package libldap2-dev:amd64.
Preparing to unpack .../libldap2-dev_2.4.39-1_amd64.deb ...
Unpacking libldap2-dev:amd64 (2.4.39-1) ...
Selecting previously unselected package librtmp-dev:amd64.
Preparing to unpack .../librtmp-dev_2.4+20131018.git79459a2-3_amd64.deb ...
Unpacking librtmp-dev:amd64 (2.4+20131018.git79459a2-3) ...
Selecting previously unselected package uuid-dev.
Preparing to unpack .../uuid-dev_2.20.1-5.8_amd64.deb ...
Unpacking uuid-dev (2.20.1-5.8) ...
Setting up libpipeline1:amd64 (1.3.0-1) ...
Setting up libssl1.0.0:amd64 (1.0.1h-3) ...
Setting up groff-base (1.22.2-6) ...
Setting up bsdmainutils (9.0.5) ...
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 man-db (2.6.7.1-1) ...
Building database of manual pages ...
Setting up libasprintf0c2:amd64 (0.18.3.2-4) ...
Setting up libbsd0:amd64 (0.6.0-2) ...
Setting up libedit2:amd64 (3.1-20140620-1) ...
Setting up libgpg-error0:amd64 (1.13-0.1) ...
Setting up libgcrypt11:amd64 (1.5.3-4) ...
Setting up libgcrypt20:amd64 (1.6.1-2) ...
Setting up libnettle4:amd64 (2.7.1-2+b1) ...
Setting up libhogweed2:amd64 (2.7.1-2+b1) ...
Setting up libffi6:amd64 (3.1-2) ...
Setting up libp11-kit0:amd64 (0.20.2-5) ...
Setting up libtasn1-6:amd64 (4.0-2) ...
Setting up libgnutls-deb0-28:amd64 (3.2.15-3) ...
Setting up libgnutls26:amd64 (2.12.23-17) ...
Setting up libkeyutils1:amd64 (1.5.9-4) ...
Setting up libkrb5support0:amd64 (1.12.1+dfsg-4) ...
Setting up libk5crypto3:amd64 (1.12.1+dfsg-4) ...
Setting up libkrb5-3:amd64 (1.12.1+dfsg-4) ...
Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-4) ...
Setting up libgssrpc4:amd64 (1.12.1+dfsg-4) ...
Setting up libidn11:amd64 (1.28-2) ...
Setting up libkadm5clnt-mit9:amd64 (1.12.1+dfsg-4) ...
Setting up libkdb5-7:amd64 (1.12.1+dfsg-4) ...
Setting up libkadm5srv-mit9:amd64 (1.12.1+dfsg-4) ...
Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-11) ...
Setting up libsasl2-2:amd64 (2.1.26.dfsg1-11) ...
Setting up libldap-2.4-2:amd64 (2.4.39-1) ...
Setting up libmagic1:amd64 (1:5.19-1) ...
Setting up libpci3:amd64 (1:3.2.1-2) ...
Setting up libxml2:amd64 (2.9.1+dfsg1-4) ...
Setting up libroken18-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libasn1-8-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libglib2.0-0:amd64 (2.40.0-3) ...
No schema files found: doing nothing.
Setting up libcroco3:amd64 (0.6.8-2) ...
Setting up libssh2-1:amd64 (1.4.3-3) ...
Setting up libcurl3-gnutls:amd64 (7.37.0-1+b1) ...
Setting up libexpat1:amd64 (2.1.0-6) ...
Setting up libgfortran3:amd64 (4.9.1-1) ...
Setting up libhcrypto4-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libheimbase1-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libwind0-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libhx509-5-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libkrb5-26-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libheimntlm0-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libgssapi3-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libhdb9-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libjpeg8:amd64 (8d1-1) ...
Setting up libkadm5clnt7-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libkadm5srv8-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libltdl7:amd64 (2.4.2-1.7) ...
Setting up libnuma1:amd64 (2.0.9-1) ...
Setting up libpython2.7-minimal:amd64 (2.7.8-1) ...
Setting up mime-support (3.56) ...
Setting up libpython2.7-stdlib:amd64 (2.7.8-1) ...
Setting up libpython2.7:amd64 (2.7.8-1) ...
Setting up libexpat1-dev:amd64 (2.1.0-6) ...
Setting up libpython2.7-dev:amd64 (2.7.8-1) ...
Setting up libsigsegv2:amd64 (2.10-4) ...
Setting up libudunits2-0:amd64 (2.2.14-1) ...
Setting up libunistring0:amd64 (0.9.3-5) ...
Setting up python2.7-minimal (2.7.8-1) ...
Setting up libhwloc5:amd64 (1.9-4) ...
Setting up libcr0 (0.8.5-2.1) ...
Setting up adduser (3.113+nmu3) ...
Setting up libibverbs1 (1.1.8-1) ...
Setting up libtorque2 (2.4.16+dfsg-1.4) ...
Setting up libopenmpi1.6 (1.6.5-8+b1) ...
Setting up libhdf5-openmpi-7:amd64 (1.8.12+docs-1.1+b1) ...
Setting up libkafs0-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libkdc2-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up libotp0-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up librtmp1:amd64 (2.4+20131018.git79459a2-3) ...
Setting up libsl0-heimdal:amd64 (1.6~rc2+dfsg-7) ...
Setting up file (1:5.19-1) ...
Setting up gettext-base (0.18.3.2-4) ...
Setting up m4 (1.4.17-4) ...
Setting up python2.7 (2.7.8-1) ...
Setting up python-minimal (2.7.8-1) ...
Setting up libpython-stdlib:amd64 (2.7.8-1) ...
Setting up python (2.7.8-1) ...
Setting up autoconf (2.69-7) ...
Setting up autotools-dev (20140510.1) ...
Setting up automake (1:1.14.1-3) ...
update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake 
(automake) in auto mode
Setting up gettext (0.18.3.2-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20140613) ...
Setting up dh-buildinfo (0.11) ...
Setting up libgfortran-4.9-dev:amd64 (4.9.1-1) ...
Setting up gfortran-4.9 (4.9.1-1) ...
Setting up gfortran (4:4.9.1-1) ...
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 hdf5-helpers (1.8.12+docs-1.1+b1) ...
Setting up comerr-dev (2.1-1.42.11-2) ...
Setting up krb5-multidev (1.12.1+dfsg-4) ...
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide 
/usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libcf0 (1:4.1.3-7+b1) ...
Setting up libcurl4-gnutls-dev:amd64 (7.37.0-1+b1) ...
Setting up libffi-dev:amd64 (3.1-2) ...
Setting up libgmp-dev:amd64 (2:6.0.0+dfsg-4) ...
Setting up pkg-config (0.28-1) ...
Setting up libidn11-dev (1.28-2) ...
Setting up libjpeg8-dev:amd64 (8d1-1) ...
Setting up libkeyutils-dev (1.5.9-4) ...
Setting up liblapack3 (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide 
/usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libnetcdfc7 (1:4.1.3-7+b1) ...
Setting up libnetcdff5 (1:4.1.3-7+b1) ...
Setting up libnetcdfc++4 (1:4.1.3-7+b1) ...
Setting up libnetcdf-dev (1:4.1.3-7+b1) ...
Setting up libossp-uuid16 (1.6.2-1.3+b1) ...
Setting up libossp-uuid-dev (1.6.2-1.3+b1) ...
Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ...
Setting up libpci-dev (1:3.2.1-2) ...
Setting up libpython-dev:amd64 (2.7.8-1) ...
Setting up libpython-all-dev:amd64 (2.7.8-1) ...
Setting up libsasl2-dev (2.1.26.dfsg1-11) ...
Setting up libsqlite3-dev:amd64 (3.8.5-2) ...
Setting up libudunits2-dev (2.2.14-1) ...
Setting up libxml2-dev:amd64 (2.9.1+dfsg1-4) ...
Setting up python-all (2.7.8-1) ...
Setting up python2.7-dev (2.7.8-1) ...
Setting up python-dev (2.7.8-1) ...
Setting up python-all-dev (2.7.8-1) ...
Setting up python-numpy (1:1.8.1-1+b1) ...
Setting up python-pkg-resources (5.4.1-1) ...
Setting up python-setuptools (5.4.1-1) ...
Setting up heimdal-multidev (1.6~rc2+dfsg-7) ...
Setting up openmpi-common (1.6.5-8) ...
Setting up libibverbs-dev (1.1.8-1) ...
Setting up libhwloc-dev:amd64 (1.9-4) ...
Setting up libopenmpi-dev (1.6.5-8+b1) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi 
(mpi) in auto mode
Setting up libhdf5-openmpi-dev (1.8.12+docs-1.1+b1) ...
Setting up mpi-default-dev (1.0.2+nmu1) ...
Setting up libhdf5-mpi-dev (1.8.12+docs-1.1+b1) ...
Setting up libkrb5-dev (1.12.1+dfsg-4) ...
Setting up libldap2-dev:amd64 (2.4.39-1) ...
Setting up librtmp-dev:amd64 (2.4+20131018.git79459a2-3) ...
Setting up uuid-dev (2.20.1-5.8) ...
Processing triggers for libc-bin (2.19-7) ...
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/123 kB of archives.
After this operation, 414 kB of additional disk space will be used.
Selecting previously unselected package libfakeroot:amd64.
(Reading database ... 18495 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.20.1-1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.20.1-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.20.1-1_amd64.deb ...
Unpacking fakeroot (1.20.1-1) ...
Processing triggers for man-db (2.6.7.1-1) ...
Setting up libfakeroot:amd64 (1.20.1-1) ...
Setting up fakeroot (1.20.1-1) ...
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: new cache content gettext_0.18.3.2-4_amd64.deb added
I: new cache content gfortran_4%3a4.9.1-1_amd64.deb added
I: new cache content gfortran-4.9_4.9.1-1_amd64.deb added
I: new cache content libgfortran-4.9-dev_4.9.1-1_amd64.deb added
I: new cache content libasprintf0c2_0.18.3.2-4_amd64.deb added
I: new cache content libgfortran3_4.9.1-1_amd64.deb added
I: new cache content gettext-base_0.18.3.2-4_amd64.deb added
I: Copying source file
I: copying [/home/pini/hdf5-transition/cmor_2.9.1-3.dsc]
I: copying [/home/pini/hdf5-transition/cmor_2.9.1.orig.tar.xz]
I: copying [/home/pini/hdf5-transition/cmor_2.9.1-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (cmor_2.9.1-3.dsc)
dpkg-source: info: extracting cmor in cmor-2.9.1
dpkg-source: info: unpacking cmor_2.9.1.orig.tar.xz
dpkg-source: info: unpacking cmor_2.9.1-3.debian.tar.xz
dpkg-source: info: applying shlib-link.patch
dpkg-source: info: applying pkgconfig.patch
dpkg-source: info: applying makefile-fix.patch
dpkg-source: info: applying destdir.patch
dpkg-source: info: applying cmor_ver.patch
dpkg-source: info: applying silence-warning.patch
dpkg-source: info: applying fix-makefile.patch
dpkg-source: info: applying ncldflags.patch
I: Building the package
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A00-pini-backport-hook 
starting
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A00-pini-backport-hook 
finished
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A00-test-hook starting
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A00-test-hook finished
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A10-pbuilder-shell-hook 
starting
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/A10-pbuilder-shell-hook 
finished
I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" 
dpkg-buildpackage -us -uc      -rfakeroot
dpkg-buildpackage: source package cmor
dpkg-buildpackage: source version 2.9.1-3
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Alastair McKinstry <mckins...@debian.org>
 dpkg-source --before-build cmor-2.9.1
dpkg-buildpackage: host architecture amd64
dpkg-source: info: using options from cmor-2.9.1/debian/source/options: 
--compression=xz
 fakeroot debian/rules clean
dh clean --with python2
   dh_testdir
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/tmp/buildd/cmor-2.9.1'
rm -rf config.sub config.log config.status libcmor.a libcmor.so.2 build 
test_grid configure CMIP5
rm -f ipcc_test_code Makefile setup.py *.mod compile_line.txt 
include/cmor_locale.h cmor.pc
find . -name '*.nc' -delete
find . -name '*.o' -delete
find .  -name '*.pic_o' -delete
find . -name '*.pyc' -delete
make[1]: Leaving directory '/tmp/buildd/cmor-2.9.1'
   dh_clean
        rm -f debian/libcmor2.substvars
        rm -f debian/libcmor2.*.debhelper
        rm -rf debian/libcmor2/
        rm -f debian/libcmor-dev.substvars
        rm -f debian/libcmor-dev.*.debhelper
        rm -rf debian/libcmor-dev/
        rm -f debian/python-cmor.substvars
        rm -f debian/python-cmor.*.debhelper
        rm -rf debian/python-cmor/
        rm -f debian/*.debhelper.log
        rm -f debian/files
        find .  \( \( -type f -a \
                \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
                 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
                 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
                 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
                \) -exec rm -f {} + \) -o \
                \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) 
\)
        rm -f *-stamp
 dpkg-source -b cmor-2.9.1
dpkg-source: info: using options from cmor-2.9.1/debian/source/options: 
--compression=xz
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building cmor using existing ./cmor_2.9.1.orig.tar.xz
dpkg-source: warning: ignoring deletion of file config.sub, use 
--include-removal to override
dpkg-source: warning: ignoring deletion of file configure, use 
--include-removal to override
dpkg-source: info: building cmor in cmor_2.9.1-3.debian.tar.xz
dpkg-source: info: building cmor in cmor_2.9.1-3.dsc
 debian/rules build
dh build --with python2
   dh_testdir
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/tmp/buildd/cmor-2.9.1'
autoreconf -fiv
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force 
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: running: /usr/bin/autoconf --force
autoreconf: configure.ac: not using Autoheader
autoreconf: configure.ac: not using Automake
autoreconf: Leaving directory `.'
ln -sf  /usr/share/misc/config.sub 
dh_auto_configure -- --disable-color --enable-verbose-test  --with-uuid 
--without-python \
        UUIDLDFLAGS="-lossp-uuid" UUIDFLAGS="-I/usr/include/ossp" 
SZLIBFLAGS=nosz \
        EXTRA_NCLDFLAGS="-lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal 
-lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt \
         -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 -lp11-kit \
         -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3" \
        CFLAGS="-I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security  " LDFLAGS="-Wl,-z,relro"
        ./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 --disable-color --enable-verbose-test --with-uuid 
--without-python UUIDLDFLAGS=-lossp-uuid UUIDFLAGS=-I/usr/include/ossp 
SZLIBFLAGS=nosz "EXTRA_NCLDFLAGS=-lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt          -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3" 
"CFLAGS=-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 
-Wformat -Wformat-security -Werror=format-security  -I/usr/include/ossp  
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security 
-Werror=format-security  " LDFLAGS=-Wl,-z,re
 lro
configure: WARNING: unrecognized options: --disable-silent-rules, 
--disable-maintainer-mode, --disable-dependency-tracking
sh: 1: git: not found
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
TARGET: linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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
checking how to run the C preprocessor... gcc -E
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for ranlib... ranlib
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  
-L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgfortran -lm -lquadmath
checking for uuid_create in -luuid... yes
checking for ut_parse in -ludunits2... yes
checking for nc_inq_var_deflate in -lnetcdf... no
checking for nc_open in -lnetcdf... no
../configure: line 4358: test: ==: unary operator expected
checking if you have netcdf 3.6.3)... "no"
configure: error: Could not get a working NetCDF
        "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 cmor configure 2.9.1, 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 --disable-color --enable-verbose-test --with-uuid 
--without-python UUIDLDFLAGS=-lossp-uuid UUIDFLAGS=-I/usr/include/ossp 
SZLIBFLAGS=nosz EXTRA_NCLDFLAGS=-lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt    -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 
CFLAGS=-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 
-Wformat -Wformat-security -Werror=format-security  -I/usr/include/ossp  
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security 
-Werror=format-security   LDFLAGS=-Wl,-z,relro

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

hostname = pinizbox
uname -m = x86_64
uname -r = 3.2.0-4-amd64
uname -s = Linux
uname -v = #1 SMP Debian 3.2.41-2

/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:2022: checking build system type
configure:2036: result: x86_64-pc-linux-gnu
configure:2056: checking host system type
configure:2069: result: x86_64-pc-linux-gnu
configure:2089: checking target system type
configure:2102: result: x86_64-pc-linux-gnu
configure:2352: checking for gcc
configure:2368: found /usr/bin/gcc
configure:2379: result: gcc
configure:2608: checking for C compiler version
configure:2617: gcc --version >&5
gcc (Debian 4.9.1-1) 4.9.1
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2628: $? = 0
configure:2617: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.9.1-1' 
--with-bugurl=file:///usr/share/doc/gcc-4.9/README.Bugs 
--enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr 
--program-suffix=-4.9 --enable-shared --enable-linker-build-id 
--libexecdir=/usr/lib --without-included-gettext --enable-threads=posix 
--with-gxx-include-dir=/usr/include/c++/4.9 --libdir=/usr/lib --enable-nls 
--with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug 
--enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap 
--disable-vtable-verify --enable-plugin --with-system-zlib 
--disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo 
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64/jre --enable-java-home 
--with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64 
--with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.9-amd64 
--with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar 
--enable-objc-gc --enable-multiarch --with-arch-32
 =i586 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib 
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu 
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.9.1 (Debian 4.9.1-1) 
configure:2628: $? = 0
configure:2617: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2628: $? = 4
configure:2617: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:2628: $? = 4
configure:2648: checking whether the C compiler works
configure:2670: gcc -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 -Wl,-z,relro 
conftest.c  >&5
configure:2674: $? = 0
configure:2722: result: yes
configure:2725: checking for C compiler default output file name
configure:2727: result: a.out
configure:2733: checking for suffix of executables
configure:2740: gcc -o conftest -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 -Wl,-z,relro 
conftest.c  >&5
configure:2744: $? = 0
configure:2766: result: 
configure:2788: checking whether we are cross compiling
configure:2796: gcc -o conftest -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 -Wl,-z,relro 
conftest.c  >&5
configure:2800: $? = 0
configure:2807: ./conftest
configure:2811: $? = 0
configure:2826: result: no
configure:2831: checking for suffix of object files
configure:2853: gcc -c -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 conftest.c >&5
configure:2857: $? = 0
configure:2878: result: o
configure:2882: checking whether we are using the GNU C compiler
configure:2901: gcc -c -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 conftest.c >&5
configure:2901: $? = 0
configure:2910: result: yes
configure:2919: checking whether gcc accepts -g
configure:2939: gcc -c -g -D_FORTIFY_SOURCE=2 conftest.c >&5
configure:2939: $? = 0
configure:2980: result: yes
configure:2997: checking for gcc option to accept ISO C89
configure:3060: gcc  -c -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 conftest.c >&5
configure:3060: $? = 0
configure:3073: result: none needed
configure:3098: checking how to run the C preprocessor
configure:3129: gcc -E -D_FORTIFY_SOURCE=2 conftest.c
configure:3129: $? = 0
configure:3143: gcc -E -D_FORTIFY_SOURCE=2 conftest.c
conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3143: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "cmor"
| #define PACKAGE_TARNAME "cmor"
| #define PACKAGE_VERSION "2.9.1"
| #define PACKAGE_STRING "cmor 2.9.1"
| #define PACKAGE_BUGREPORT "doutria...@llnl.gov"
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3168: result: gcc -E
configure:3188: gcc -E -D_FORTIFY_SOURCE=2 conftest.c
configure:3188: $? = 0
configure:3202: gcc -E -D_FORTIFY_SOURCE=2 conftest.c
conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3202: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "cmor"
| #define PACKAGE_TARNAME "cmor"
| #define PACKAGE_VERSION "2.9.1"
| #define PACKAGE_STRING "cmor 2.9.1"
| #define PACKAGE_BUGREPORT "doutria...@llnl.gov"
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3230: checking whether ln -s works
configure:3234: result: yes
configure:3241: checking for a sed that does not truncate output
configure:3305: result: /bin/sed
configure:3310: checking for a thread-safe mkdir -p
configure:3349: result: /bin/mkdir -p
configure:3395: checking for ranlib
configure:3411: found /usr/bin/ranlib
configure:3422: result: ranlib
configure:3498: checking for gfortran
configure:3514: found /usr/bin/gfortran
configure:3525: result: gfortran
configure:3551: checking for Fortran compiler version
configure:3560: gfortran --version >&5
GNU Fortran (Debian 4.9.1-1) 4.9.1
Copyright (C) 2014 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:3571: $? = 0
configure:3560: gfortran -v >&5
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.9.1-1' 
--with-bugurl=file:///usr/share/doc/gcc-4.9/README.Bugs 
--enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr 
--program-suffix=-4.9 --enable-shared --enable-linker-build-id 
--libexecdir=/usr/lib --without-included-gettext --enable-threads=posix 
--with-gxx-include-dir=/usr/include/c++/4.9 --libdir=/usr/lib --enable-nls 
--with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug 
--enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap 
--disable-vtable-verify --enable-plugin --with-system-zlib 
--disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo 
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64/jre --enable-java-home 
--with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64 
--with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.9-amd64 
--with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar 
--enable-objc-gc --enable-multiarch --with-arch-32
 =i586 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib 
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu 
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.9.1 (Debian 4.9.1-1) 
configure:3571: $? = 0
configure:3560: gfortran -V >&5
gfortran: error: unrecognized command line option '-V'
gfortran: fatal error: no input files
compilation terminated.
configure:3571: $? = 4
configure:3560: gfortran -qversion >&5
gfortran: error: unrecognized command line option '-qversion'
gfortran: fatal error: no input files
compilation terminated.
configure:3571: $? = 4
configure:3580: checking whether we are using the GNU Fortran compiler
configure:3593: gfortran -c -g -O2 -fstack-protector --param=ssp-buffer-size=4  
conftest.F >&5
configure:3593: $? = 0
configure:3602: result: yes
configure:3608: checking whether gfortran accepts -g
configure:3619: gfortran -c -g  conftest.f >&5
configure:3619: $? = 0
configure:3627: result: yes
configure:3661: checking how to get verbose linking output from gfortran
configure:3671: gfortran -c -g -O2 -fstack-protector --param=ssp-buffer-size=4  
conftest.f >&5
configure:3671: $? = 0
configure:3689: gfortran -o conftest -g -O2 -fstack-protector 
--param=ssp-buffer-size=4 -v -Wl,-z,relro conftest.f
Using built-in specs.
Target: x86_64-linux-gnu
Thread model: posix
gcc version 4.9.1 (Debian 4.9.1-1) 
 /usr/lib/gcc/x86_64-linux-gnu/4.9/f951 conftest.f -ffixed-form -quiet 
-dumpbase conftest.f -mtune=generic -march=x86-64 -auxbase conftest -g -O2 
-version -fstack-protector --param ssp-buffer-size=4 -fintrinsic-modules-path 
/usr/lib/gcc/x86_64-linux-gnu/4.9/finclude -o /tmp/ccJFDnco.s
GNU Fortran (Debian 4.9.1-1) version 4.9.1 (x86_64-linux-gnu)
        compiled by GNU C version 4.9.1, GMP version 6.0.0, MPFR version 
3.1.2-p3, MPC version 1.0.2
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU Fortran (Debian 4.9.1-1) version 4.9.1 (x86_64-linux-gnu)
        compiled by GNU C version 4.9.1, GMP version 6.0.0, MPFR version 
3.1.2-p3, MPC version 1.0.2
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 as -v --64 -o /tmp/ccSRcAA8.o /tmp/ccJFDnco.s
GNU assembler version 2.24.51 (x86_64-linux-gnu) using BFD version (GNU 
Binutils for Debian) 2.24.51.20140709
Reading specs from /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.spec
rename spec lib to liborig
 /usr/lib/gcc/x86_64-linux-gnu/4.9/collect2 -plugin 
/usr/lib/gcc/x86_64-linux-gnu/4.9/liblto_plugin.so 
-plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper 
-plugin-opt=-fresolution=/tmp/ccodP0nT.res -plugin-opt=-pass-through=-lgcc_s 
-plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lquadmath 
-plugin-opt=-pass-through=-lm -plugin-opt=-pass-through=-lgcc_s 
-plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc 
-plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --sysroot=/ 
--build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu -dynamic-linker 
/lib64/ld-linux-x86-64.so.2 -o conftest 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crt1.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crti.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/crtbegin.o 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/
 lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -z relro /tmp/ccSRcAA8.o 
-lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc 
/usr/lib/gcc/x86_64-linux-gnu/4.9/crtend.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crtn.o
configure:3772: result: -v
configure:3774: checking for Fortran libraries of gfortran
configure:3797: gfortran -o conftest -g -O2 -fstack-protector 
--param=ssp-buffer-size=4 -v -Wl,-z,relro conftest.f
Using built-in specs.
Target: x86_64-linux-gnu
Thread model: posix
gcc version 4.9.1 (Debian 4.9.1-1) 
 /usr/lib/gcc/x86_64-linux-gnu/4.9/f951 conftest.f -ffixed-form -quiet 
-dumpbase conftest.f -mtune=generic -march=x86-64 -auxbase conftest -g -O2 
-version -fstack-protector --param ssp-buffer-size=4 -fintrinsic-modules-path 
/usr/lib/gcc/x86_64-linux-gnu/4.9/finclude -o /tmp/ccJepMaA.s
GNU Fortran (Debian 4.9.1-1) version 4.9.1 (x86_64-linux-gnu)
        compiled by GNU C version 4.9.1, GMP version 6.0.0, MPFR version 
3.1.2-p3, MPC version 1.0.2
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU Fortran (Debian 4.9.1-1) version 4.9.1 (x86_64-linux-gnu)
        compiled by GNU C version 4.9.1, GMP version 6.0.0, MPFR version 
3.1.2-p3, MPC version 1.0.2
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 as -v --64 -o /tmp/cctw4DPk.o /tmp/ccJepMaA.s
GNU assembler version 2.24.51 (x86_64-linux-gnu) using BFD version (GNU 
Binutils for Debian) 2.24.51.20140709
Reading specs from /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.spec
rename spec lib to liborig
 /usr/lib/gcc/x86_64-linux-gnu/4.9/collect2 -plugin 
/usr/lib/gcc/x86_64-linux-gnu/4.9/liblto_plugin.so 
-plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper 
-plugin-opt=-fresolution=/tmp/ccc0NJT5.res -plugin-opt=-pass-through=-lgcc_s 
-plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lquadmath 
-plugin-opt=-pass-through=-lm -plugin-opt=-pass-through=-lgcc_s 
-plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc 
-plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --sysroot=/ 
--build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu -dynamic-linker 
/lib64/ld-linux-x86-64.so.2 -o conftest 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crt1.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crti.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/crtbegin.o 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/
 lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -z relro /tmp/cctw4DPk.o 
-lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc 
/usr/lib/gcc/x86_64-linux-gnu/4.9/crtend.o 
/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/crtn.o
configure:3993: result:  -L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgfortran -lm -lquadmath
configure:4035: checking for uuid_create in -luuid
configure:4060: gcc -o conftest -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 -Wl,-z,relro 
-lm  conftest.c -luuid   -lossp-uuid    >&5
configure:4060: $? = 0
configure:4069: result: yes
configure:4109: checking for ut_parse in -ludunits2
configure:4134: gcc -o conftest -I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security   -D_FORTIFY_SOURCE=2 -Wl,-z,relro 
-lm  conftest.c -ludunits2  -ludunits2  -lm    >&5
configure:4134: $? = 0
configure:4143: result: yes
configure:4269: checking for nc_inq_var_deflate in -lnetcdf
configure:4294: gcc -o conftest -lnetcdf -D_FORTIFY_SOURCE=2 -lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt    -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 conftest.c 
-lnetcdf  -lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi 
-lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt     -lgnutls -lgssapi_krb5 -llber 
-lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto -lkrb5support -lsasl2 
-lkeyutils -lsqlite3   >&5
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
collect2: error: ld returned 1 exit status
configure:4294: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "cmor"
| #define PACKAGE_TARNAME "cmor"
| #define PACKAGE_VERSION "2.9.1"
| #define PACKAGE_STRING "cmor 2.9.1"
| #define PACKAGE_BUGREPORT "doutria...@llnl.gov"
| #define PACKAGE_URL ""
| #define HAVE_LIBUUID 1
| #define HAVE_LIBUDUNITS2 1
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char nc_inq_var_deflate ();
| int
| main ()
| {
| return nc_inq_var_deflate ();
|   ;
|   return 0;
| }
configure:4303: result: no
configure:4316: checking for nc_open in -lnetcdf
configure:4341: gcc -o conftest -lnetcdf -D_FORTIFY_SOURCE=2 -lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt    -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 conftest.c 
-lnetcdf  -lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi 
-lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt     -lgnutls -lgssapi_krb5 -llber 
-lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto -lkrb5support -lsasl2 
-lkeyutils -lsqlite3  -lnetcdf -lnetcdf -lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt       -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 >&5
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
collect2: error: ld returned 1 exit status
configure:4341: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "cmor"
| #define PACKAGE_TARNAME "cmor"
| #define PACKAGE_VERSION "2.9.1"
| #define PACKAGE_STRING "cmor 2.9.1"
| #define PACKAGE_BUGREPORT "doutria...@llnl.gov"
| #define PACKAGE_URL ""
| #define HAVE_LIBUUID 1
| #define HAVE_LIBUDUNITS2 1
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char nc_open ();
| int
| main ()
| {
| return nc_open ();
|   ;
|   return 0;
| }
configure:4350: result: no
configure:4361: checking if you have netcdf 3.6.3)
configure:4393: gcc -o conftest -lnetcdf -D_FORTIFY_SOURCE=2 -lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt    -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 conftest.c 
-lnetcdf -lnetcdf -lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal 
-lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt     -lgnutls -lgssapi_krb5 
-llber -lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto -lkrb5support 
-lsasl2 -lkeyutils -lsqlite3 >&5
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
/usr/bin/ld: cannot find -lgcrypt
/usr/bin/ld: cannot find -lgnutls
/usr/bin/ld: cannot find -lgpg-error
/usr/bin/ld: cannot find -ltasn1
/usr/bin/ld: cannot find -lp11-kit
collect2: error: ld returned 1 exit status
configure:4393: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "cmor"
| #define PACKAGE_TARNAME "cmor"
| #define PACKAGE_VERSION "2.9.1"
| #define PACKAGE_STRING "cmor 2.9.1"
| #define PACKAGE_BUGREPORT "doutria...@llnl.gov"
| #define PACKAGE_URL ""
| #define HAVE_LIBUUID 1
| #define HAVE_LIBUDUNITS2 1
| /* end confdefs.h.  */
| 
|         #include <stdio.h>
|         #include <string.h>
|       #include <stdlib.h>
|         #include <netcdf.h>
| 
| int
| main ()
| {
| 
| 
|      char version[50];
|      int major,minor,patch;
|      strncpy(version,nc_inq_libvers(),50);
|      sscanf(version,"%*c%1d%*c%1d%*c%1d%*s",&major,&minor,&patch);
|      if ((major!=3) && (minor!=6) && (patch!=3)) return 1;
|      return 0;
| 
|   ;
|   return 0;
| }
configure:4403: result: "no"
configure:4405: error: Could not get a working NetCDF

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

ac_cv_build=x86_64-pc-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-I/usr/include/ossp  -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security  
-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -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_FCFLAGS_set=set
ac_cv_env_FCFLAGS_value='-g -O2 -fstack-protector --param=ssp-buffer-size=4'
ac_cv_env_FC_set=
ac_cv_env_FC_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_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_fc_compiler_gnu=yes
ac_cv_fc_libs=' -L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgfortran -lm -lquadmath'
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_lib_netcdf_nc_inq_var_deflate=no
ac_cv_lib_netcdf_nc_open=no
ac_cv_lib_udunits2_ut_parse=yes
ac_cv_lib_uuid_uuid_create=yes
ac_cv_objext=o
ac_cv_path_SED=/bin/sed
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_FC=gfortran
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_fc_g=yes
ac_cv_prog_fc_v=-v
ac_cv_target=x86_64-pc-linux-gnu

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

CC='gcc'
CDATPREFIX=' '
CFLAGS='-lnetcdf'
CPP='gcc -E'
CPPFLAGS='-D_FORTIFY_SOURCE=2'
DEBUG='-g'
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EXEEXT=''
FC='gfortran'
FCFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4'
FCLIBS=' -L/usr/lib/gcc/x86_64-linux-gnu/4.9 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu 
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib 
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgfortran -lm -lquadmath'
FFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4'
FTAG='-Wl,-rpath='
INCFILES='include/cmor.h  include/cmor_func_def.h include/cmor_md5.h 
include/cdTime/cddrs.h     include/cdTime/cddrsint.h  include/cdTime/cdms.h  
include/cdTime/cdmsint.h  include/cdTime/cdmsint_new.h  include/cdTime/cdrra.h  
include/cdTime/cdunif.h  include/cdTime/cdunifint.h  
include/cdTime/cdunifpp/cdunifpp.h  include/cdTime/cdunifpp/cdunifpp_frename.h  
include/cdTime/cdunifpp/crayio.h  include/cdTime/cdunifpp/util.h  
include/cdTime/cdunifpp/vardef.h  include/cdTime/cfortran.h  
include/cdTime/drscdf.h  include/cdTime/drsdef.h  include/cdTime/fcddrs.h  
include/cdTime/gaussLats.h  include/cdTime/grads.h  include/cdTime/gx.h  
include/cdTime/isdb.h'
LDFLAGS='-lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi 
-lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt        -lgnutls -lgssapi_krb5 -llber 
-lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto -lkrb5support -lsasl2 
-lkeyutils -lsqlite3'
LIBFILES='cmor.o cmor_axes.o cmor_variables.o cmor_tables.o cdTimeConv.o 
cdUtil.o timeConv.o timeArith.o cmor_grids.o cmor_md5.o  
cmor_cfortran_interface.o cmor_fortran_interface.o'
LIBFSOURCES=''
LIBOBJS=''
LIBS='-lnetcdf -lnetcdf -lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal 
-lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt         -lgnutls 
-lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto 
-lkrb5support -lsasl2 -lkeyutils -lsqlite3'
LIBSOURCES=''
LN_S='ln -s'
LTLIBOBJS=''
MACROS=''
MAKEDEPPYTHON=' '
MAKETESTPYTHON=' '
MKDIR_P='/bin/mkdir -p'
MODFILES='cmor_users_functions.*'
NCCFLAGS='-lnetcdf'
NCCONFIG=''
NCLDFLAGS='-lhdf5 -lm -lcurl -L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi 
-lnetcdf -lffi  -lz -lidn -lrtmp -lgcrypt      -lgnutls -lgssapi_krb5 -llber 
-lldap_r -lgpg-error -ltasn1 -lp11-kit    -lk5crypto -lkrb5support -lsasl2 
-lkeyutils -lsqlite3'
NO_COLOR=''
OBJEXT='o'
OK_COLOR=''
PACKAGE_BUGREPORT='doutria...@llnl.gov'
PACKAGE_NAME='cmor'
PACKAGE_STRING='cmor 2.9.1'
PACKAGE_TARNAME='cmor'
PACKAGE_URL=''
PACKAGE_VERSION='2.9.1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin'
PATH_SEPARATOR=':'
PYTHONEXEC=' '
RANLIB='ranlib'
RTAG='-Wl,-rpath='
SED='/bin/sed'
SHELL='/bin/bash'
TEST_FORTRAN='test_fortran'
UDUNITS2FLAGS='-ludunits2'
UDUNITS2LDFLAGS=''
USERCFLAGS='-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 
-Wformat -Wformat-security -Werror=format-security  -I/usr/include/ossp  
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security 
-Werror=format-security  '
USERFFLAGS='-g -O2 -fstack-protector --param=ssp-buffer-size=4'
USERLDFLAGS='-Wl,-z,relro -lm '
UUIDFLAGS=''
UUIDLDFLAGS='-lossp-uuid'
VERB=''
ZFLAGS=''
ZLDFLAGS=''
ac_ct_CC='gcc'
ac_ct_FC='gfortran'
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias='x86_64-linux-gnu'
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-pc-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${prefix}/share/info'
libdir='${prefix}/lib/x86_64-linux-gnu'
libexecdir='${prefix}/lib/x86_64-linux-gnu'
localedir='${datarootdir}/locale'
localstatedir='/var'
mandir='${prefix}/share/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target='x86_64-pc-linux-gnu'
target_alias=''
target_cpu='x86_64'
target_os='linux-gnu'
target_vendor='pc'

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

/* confdefs.h */
#define PACKAGE_NAME "cmor"
#define PACKAGE_TARNAME "cmor"
#define PACKAGE_VERSION "2.9.1"
#define PACKAGE_STRING "cmor 2.9.1"
#define PACKAGE_BUGREPORT "doutria...@llnl.gov"
#define PACKAGE_URL ""
#define HAVE_LIBUUID 1
#define HAVE_LIBUDUNITS2 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 --disable-color --enable-verbose-test --with-uuid 
--without-python UUIDLDFLAGS=-lossp-uuid UUIDFLAGS=-I/usr/include/ossp 
SZLIBFLAGS=nosz EXTRA_NCLDFLAGS=-lhdf5 -lm -lcurl 
-L/usr/lib/x86_64-linux-gnu/heimdal -lgssapi -lnetcdf -lffi  -lz -lidn -lrtmp 
-lgcrypt     -lgnutls -lgssapi_krb5 -llber -lldap_r -lgpg-error -ltasn1 
-lp11-kit    -lk5crypto -lkrb5support -lsasl2 -lkeyutils -lsqlite3 
CFLAGS=-I/usr/include/ossp  -fstack-protector --param=ssp-buffer-size=4 
-Wformat -Wformat-security -Werror=format-security  -I/usr/include/ossp  
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security 
-Werror=format-security   LDFLAGS=
 -Wl,-z,relro returned exit code 1
debian/rules:37: recipe for target 'override_dh_auto_configure' failed
make[1]: *** [override_dh_auto_configure] Error 255
make[1]: Leaving directory '/tmp/buildd/cmor-2.9.1'
debian/rules:34: 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
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/C99-failure-shell-hook 
starting

Build failed. Trying to invoke a shell.

Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  vim-common
Suggested packages:
  indent
The following NEW packages will be installed:
  less sudo tree vim-common vim-tiny
0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.
Need to get 1441 kB/1574 kB of archives.
After this operation, 4262 kB of additional disk space will be used.
Get:1 http://ftp.fr.debian.org/debian/ unstable/main vim-common amd64 
2:7.4.335-1 [177 kB]
Get:2 http://ftp.fr.debian.org/debian/ unstable/main vim-tiny amd64 2:7.4.335-1 
[397 kB]
Get:3 http://ftp.fr.debian.org/debian/ unstable/main sudo amd64 1.8.9p5-1 [823 
kB]
Get:4 http://ftp.fr.debian.org/debian/ unstable/main tree amd64 1.7.0-1 [43.9 
kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 1441 kB in 0s (2713 kB/s)
Selecting previously unselected package vim-common.
(Reading database ... 18539 files and directories currently installed.)
Preparing to unpack .../vim-common_2%3a7.4.335-1_amd64.deb ...
Unpacking vim-common (2:7.4.335-1) ...
Selecting previously unselected package vim-tiny.
Preparing to unpack .../vim-tiny_2%3a7.4.335-1_amd64.deb ...
Unpacking vim-tiny (2:7.4.335-1) ...
Selecting previously unselected package less.
Preparing to unpack .../archives/less_458-2_amd64.deb ...
Unpacking less (458-2) ...
Selecting previously unselected package sudo.
Preparing to unpack .../sudo_1.8.9p5-1_amd64.deb ...
Unpacking sudo (1.8.9p5-1) ...
Selecting previously unselected package tree.
Preparing to unpack .../tree_1.7.0-1_amd64.deb ...
Unpacking tree (1.7.0-1) ...
Processing triggers for mime-support (3.56) ...
Processing triggers for man-db (2.6.7.1-1) ...
Setting up vim-common (2:7.4.335-1) ...
Setting up vim-tiny (2:7.4.335-1) ...
update-alternatives: using /usr/bin/vim.tiny to provide /usr/bin/rview (rview) 
in auto mode
update-alternatives: using /usr/bin/vim.tiny to provide /usr/bin/vi (vi) in 
auto mode
update-alternatives: using /usr/bin/vim.tiny to provide /usr/bin/view (view) in 
auto mode
update-alternatives: using /usr/bin/vim.tiny to provide /usr/bin/ex (ex) in 
auto mode
update-alternatives: using /usr/bin/vim.tiny to provide /usr/bin/editor 
(editor) in auto mode
Setting up less (458-2) ...
Setting up sudo (1.8.9p5-1) ...
Setting up tree (1.7.0-1) ...
I: user script /home/pbuilder/build/cow.21320/tmp/hooks/C99-failure-shell-hook 
finished
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.21320

--- End Message ---
--- Begin Message --- 
Source: cmor
Source-Version: 2.9.1-4

We believe that the bug you reported is fixed in the latest version of
cmor, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 755...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (supplier of updated cmor package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Thu, 24 Jul 2014 19:05:11 +0100
Source: cmor
Binary: libcmor2 libcmor-dev python-cmor
Architecture: source amd64
Version: 2.9.1-4
Distribution: unstable
Urgency: medium
Maintainer: Alastair McKinstry <mckins...@debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
Description:
 libcmor-dev - Development files for Climate Model Output Rewriter
 libcmor2   - Climate Model Output Rewriter library
 python-cmor - Python interface to CMOR
Closes: 754640 755167
Changes:
 cmor (2.9.1-4) unstable; urgency=medium
 .
   * Make additional flags  and pkgs a requirement for ppc64el only.
     Closes: #755167, #754640.
Checksums-Sha1:
 7adc8e9a8511a9b0a3d5e2f38a3834f0837a967d 2318 cmor_2.9.1-4.dsc
 6e7e56f5af97788c5766772595914152c6f98863 31880 cmor_2.9.1-4.debian.tar.xz
 0bd7cbb386c451c5a07232f695473446505f6d5f 126126 libcmor2_2.9.1-4_amd64.deb
 59f048d9f3afab2fc421e4a7c3ab5e0f2e4a2c72 4494132 libcmor-dev_2.9.1-4_amd64.deb
 1b0db2488b8584913ffdf3cf6aaadcf44cedcace 128066 python-cmor_2.9.1-4_amd64.deb
Checksums-Sha256:
 a3bbe100e0a7623cf80fa519cc8df1a8f30a32e90e9c255d57409e02b3d8aa3f 2318 
cmor_2.9.1-4.dsc
 6fb713503033c8b23f1567fda0ead4aacea7fa069a020ad2e4a34aee9b285aa3 31880 
cmor_2.9.1-4.debian.tar.xz
 e2b1db2ea5a44809ae1a3d2aec90e67df7f98096b5d38669432fa3b2ec78e8ac 126126 
libcmor2_2.9.1-4_amd64.deb
 3e02c8ff0130e23e3a219c53a445f4c2ede6b055e1c814d5ba0adaca0b88bd32 4494132 
libcmor-dev_2.9.1-4_amd64.deb
 39393a96b2bc4ecf1ed6a44833adc289fb8d06aaed3a1a8f1397b82b2146aba4 128066 
python-cmor_2.9.1-4_amd64.deb
Files:
 d9ee45fb54bd531828ba954eacf21967 126126 libs extra libcmor2_2.9.1-4_amd64.deb
 03b4202888d0a4776d4f090b64cfbba5 4494132 libdevel extra 
libcmor-dev_2.9.1-4_amd64.deb
 de02f4d0818c5a1a2b3ed78f35fe9e1c 128066 python extra 
python-cmor_2.9.1-4_amd64.deb
 7a6d03ba0fde7a2f3fd14c7753f32f02 2318 utils extra cmor_2.9.1-4.dsc
 2235aa8851f273afe703ef0a57851f6a 31880 utils extra cmor_2.9.1-4.debian.tar.xz

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-----END PGP SIGNATURE-----

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