cdo: Could not link to szlib

[bbaker@…]

Hello, I am having problems trying to install CDO on a MacbookPro running Mac OS X 10.7.4. This is the error I received;

Error: org.macports.configure for port cdo returned: configure failure: command execution failed

I checked the log file below but cannot figure out how to fix the problem. Any help would be appreciated. Thanks, Barry

version:1
:debug:main epoch: in tree: 2 installed: 2
:debug:main netcdf 4.2.0_4 exists in the ports tree
:debug:main netcdf 4.2.0_4 +dap+netcdf4 is the latest installed
:debug:main netcdf 4.2.0_4 +dap+netcdf4 is active
:debug:main Merging existing variants '+dap+netcdf4' into variants
:debug:main new fully merged portvariants: netcdf4 + dap +
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/netcdf
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Executing variant netcdf4 provides netcdf4
:debug:main Executing variant dap provides dap
:debug:main No need to upgrade! netcdf 4.2.0_4 >= netcdf 4.2.0_4
:debug:main epoch: in tree: 0 installed: 0
:debug:main hdf5-18 1.8.9_0 exists in the ports tree
:debug:main hdf5-18 1.8.9_0  is the latest installed
:debug:main hdf5-18 1.8.9_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/hdf5-18
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! hdf5-18 1.8.9_0 >= hdf5-18 1.8.9_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main zlib 1.2.7_0 exists in the ports tree
:debug:main zlib 1.2.7_0  is the latest installed
:debug:main zlib 1.2.7_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/zlib
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main curl 7.26.0_0 exists in the ports tree
:debug:main curl 7.26.0_0 +ssl is the latest installed
:debug:main curl 7.26.0_0 +ssl is active
:debug:main Merging existing variants '+ssl' into variants
:debug:main new fully merged portvariants: ssl +
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/net/curl
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/archcheck-1.0.tcl
:debug:main universal variant already exists, so not adding the default one
:debug:main Executing variant ssl provides ssl
:debug:main No need to upgrade! curl 7.26.0_0 >= curl 7.26.0_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main libidn 1.25_0 exists in the ports tree
:debug:main libidn 1.25_0  is the latest installed
:debug:main libidn 1.25_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/mail/libidn
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! libidn 1.25_0 >= libidn 1.25_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main libiconv 1.14_0 exists in the ports tree
:debug:main libiconv 1.14_0  is the latest installed
:debug:main libiconv 1.14_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/libiconv
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! libiconv 1.14_0 >= libiconv 1.14_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main gettext 0.18.1.1_2 exists in the ports tree
:debug:main gettext 0.18.1.1_2  is the latest installed
:debug:main gettext 0.18.1.1_2  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/gettext
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/archcheck-1.0.tcl
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! gettext 0.18.1.1_2 >= gettext 0.18.1.1_2
:debug:main epoch: in tree: 0 installed: 0
:debug:main ncurses 5.9_1 exists in the ports tree
:debug:main ncurses 5.9_1  is the latest installed
:debug:main ncurses 5.9_1  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/ncurses
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! ncurses 5.9_1 >= ncurses 5.9_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main expat 2.1.0_0 exists in the ports tree
:debug:main expat 2.1.0_0  is the latest installed
:debug:main expat 2.1.0_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/expat
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! expat 2.1.0_0 >= expat 2.1.0_0
:debug:main epoch: in tree: 1 installed: 1
:debug:main openssl 1.0.1c_0 exists in the ports tree
:debug:main openssl 1.0.1c_0  is the latest installed
:debug:main openssl 1.0.1c_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/openssl
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! openssl 1.0.1c_0 >= openssl 1.0.1c_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main curl-ca-bundle 7.26.0_1 exists in the ports tree
:debug:main curl-ca-bundle 7.26.0_1  is the latest installed
:debug:main curl-ca-bundle 7.26.0_1  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/net/curl-ca-bundle
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main universal_variant is false, so not adding the default universal variant
:debug:main No need to upgrade! curl-ca-bundle 7.26.0_1 >= curl-ca-bundle 7.26.0_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main proj47 4.7.0_0 exists in the ports tree
:debug:main proj47 4.7.0_0  is the latest installed
:debug:main proj47 4.7.0_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/gis/proj47
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! proj47 4.7.0_0 >= proj47 4.7.0_0
:msg:main --->  Computing dependencies for cdo:info:main .:debug:main cdo has no conflicts
:debug:main Searching for dependency: netcdf
:debug:main Found Dependency: receipt exists for netcdf
:debug:main Searching for dependency: proj47
:debug:main Found Dependency: receipt exists for proj47
:msg:main 
:debug:main Executing org.macports.main (cdo)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 503
:debug:archivefetch archivefetch phase started at Fri Jul 27 06:14:30 MDT 2012
:msg:archivefetch --->  Fetching archive for cdo
:debug:archivefetch Executing org.macports.archivefetch (cdo)
:debug:archivefetch euid/egid changed to: 0/0
:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
:debug:archivefetch euid/egid changed to: 503/501
:info:archivefetch --->  cdo-1.5.5_0.darwin_11.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
:msg:archivefetch --->  Attempting to fetch cdo-1.5.5_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/cdo
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
:debug:archivefetch Privilege de-escalation not attempted as not running as root.
:debug:fetch fetch phase started at Fri Jul 27 06:14:30 MDT 2012
:notice:fetch --->  Fetching distfiles for cdo
:debug:fetch Can't run fetch on this port without elevated privileges. Escalating privileges back to root.
:debug:fetch euid changed to: 0. egid changed to: 0.
:debug:fetch changing euid/egid - current euid: 0 - current egid: 0
:debug:fetch egid changed to: 501
:debug:fetch euid changed to: 503
:debug:fetch Executing org.macports.fetch (cdo)
:info:fetch --->  cdo-1.5.5.tar.gz doesn't seem to exist in /opt/local/var/macports/distfiles/cdo
:notice:fetch --->  Attempting to fetch cdo-1.5.5.tar.gz from http://distfiles.macports.org/cdo
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Fri Jul 27 06:14:35 MDT 2012
:notice:checksum --->  Verifying checksum(s) for cdo
:debug:checksum Executing org.macports.checksum (cdo)
:info:checksum --->  Checksumming cdo-1.5.5.tar.gz
:debug:checksum Correct (md5) checksum for cdo-1.5.5.tar.gz
:debug:checksum Correct (sha1) checksum for cdo-1.5.5.tar.gz
:debug:checksum Correct (rmd160) checksum for cdo-1.5.5.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Fri Jul 27 06:14:35 MDT 2012
:notice:extract --->  Extracting cdo
:debug:extract Executing org.macports.extract (cdo)
:info:extract --->  Extracting cdo-1.5.5.tar.gz
:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz'
:debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7'
:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz' | /usr/bin/gnutar --no-same-owner -xf -'
:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
:debug:extract euid/egid changed to: 0/0
:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work to macports
:debug:extract euid/egid changed to: 503/501
:debug:extract Privilege de-escalation not attempted as not running as root.
:debug:patch patch phase started at Fri Jul 27 06:14:37 MDT 2012
:debug:patch Executing org.macports.patch (cdo)
:debug:patch Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Fri Jul 27 06:14:37 MDT 2012
:notice:configure --->  Configuring cdo
:debug:configure Using compiler 'Mac OS X clang'
:debug:configure Executing org.macports.configure (cdo)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.7' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib -arch x86_64' OBJC='/usr/bin/clang' FCFLAGS='-pipe -O2 -m64' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -O2 -arch x86_64' FFLAGS='-pipe -O2 -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local'
:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local 
:info:configure checking build system type... x86_64-apple-darwin11.4.0
:info:configure checking host system type... x86_64-apple-darwin11.4.0
:info:configure checking for a BSD-compatible install... /usr/bin/install -c
:info:configure checking whether build environment is sane... yes
:info:configure checking for a thread-safe mkdir -p... config/install-sh -c -d
:info:configure checking for gawk... no
:info:configure checking for mawk... no
:info:configure checking for nawk... no
:info:configure checking for awk... awk
:info:configure checking whether make sets $(MAKE)... yes
:info:configure checking whether to enable maintainer-specific portions of Makefiles... no
:info:configure configure: setting up libtool
:info:configure checking how to print strings... printf
:info:configure checking for style of include used by make... GNU
:info:configure checking for gcc... /usr/bin/clang
:info:configure checking whether the C compiler works... yes
:info:configure checking for C compiler default output file name... a.out
:info:configure checking for suffix of executables... 
:info:configure checking whether we are cross compiling... no
:info:configure checking for suffix of object files... o
:info:configure checking whether we are using the GNU C compiler... yes
:info:configure checking whether /usr/bin/clang accepts -g... yes
:info:configure checking for /usr/bin/clang option to accept ISO C89... none needed
:info:configure checking dependency style of /usr/bin/clang... none
:info:configure checking for a sed that does not truncate output... /usr/bin/sed
:info:configure checking for grep that handles long lines and -e... /usr/bin/grep
:info:configure checking for egrep... /usr/bin/grep -E
:info:configure checking for fgrep... /usr/bin/grep -F
:info:configure checking for ld used by /usr/bin/clang... /usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm
:info:configure checking the name lister (/opt/local/bin/nm) interface... BSD nm
:info:configure checking whether ln -s works... yes
:info:configure checking the maximum length of command line arguments... 196608
:info:configure checking whether the shell understands some XSI constructs... yes
:info:configure checking whether the shell understands "+="... yes
:info:configure checking for /usr/bin/ld option to reload object files... -r
:info:configure checking for objdump... no
:info:configure checking how to recognize dependent libraries... pass_all
:info:configure checking for ar... ar
:info:configure checking for strip... strip
:info:configure checking for ranlib... ranlib
:info:configure checking command to parse /opt/local/bin/nm output from /usr/bin/clang object... ok
:info:configure checking for dsymutil... dsymutil
:info:configure checking for nmedit... nmedit
:info:configure checking for lipo... lipo
:info:configure checking for otool... otool
:info:configure checking for otool64... no
:info:configure checking for -single_module linker flag... yes
:info:configure checking for -exported_symbols_list linker flag... yes
:info:configure checking for -force_load linker flag... yes
:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
:info:configure checking for ANSI C header files... yes
:info:configure checking for sys/types.h... yes
:info:configure checking for sys/stat.h... yes
:info:configure checking for stdlib.h... yes
:info:configure checking for string.h... yes
:info:configure checking for memory.h... yes
:info:configure checking for strings.h... yes
:info:configure checking for inttypes.h... yes
:info:configure checking for stdint.h... yes
:info:configure checking for unistd.h... yes
:info:configure checking for dlfcn.h... yes
:info:configure checking for objdir... .libs
:info:configure checking if /usr/bin/clang supports -fno-rtti -fno-exceptions... yes
:info:configure checking for /usr/bin/clang option to produce PIC... -fno-common -DPIC
:info:configure checking if /usr/bin/clang PIC flag -fno-common -DPIC works... yes
:info:configure checking if /usr/bin/clang static flag -static works... no
:info:configure checking if /usr/bin/clang supports -c -o file.o... yes
:info:configure checking if /usr/bin/clang supports -c -o file.o... (cached) yes
:info:configure checking whether the /usr/bin/clang linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin11.4.0 dyld
:info:configure checking how to hardcode library paths into programs... immediate
:info:configure checking whether stripping libraries is possible... yes
:info:configure checking if libtool supports shared libraries... yes
:info:configure checking whether to build shared libraries... yes
:info:configure checking whether to build static libraries... yes
:info:configure checking for gcc... (cached) /usr/bin/clang
:info:configure checking for /usr/bin/clang option to accept ISO C99... none needed
:info:configure checking whether /usr/bin/clang and cc understand -c and -o together... yes
:info:configure checking for ar... (cached) ar
:info:configure checking for ld... /usr/bin/ld
:info:configure checking for nm... /opt/local/bin/nm
:info:configure checking for ar... (cached) ar
:info:configure checking for as... as
:info:configure checking for dlltool... no
:info:configure checking for objdump... false
:info:configure checking for strip... (cached) strip
:info:configure checking for ranlib... (cached) ranlib
:info:configure checking whether we are using the GNU C++ compiler... yes
:info:configure checking whether /usr/bin/clang++ accepts -g... yes
:info:configure checking dependency style of /usr/bin/clang++... none
:info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E
:info:configure checking for ld used by /usr/bin/clang++... /usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking whether the /usr/bin/clang++ linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking for /usr/bin/clang++ option to produce PIC... -fno-common -DPIC
:info:configure checking if /usr/bin/clang++ PIC flag -fno-common -DPIC works... yes
:info:configure checking if /usr/bin/clang++ static flag -static works... no
:info:configure checking if /usr/bin/clang++ supports -c -o file.o... yes
:info:configure checking if /usr/bin/clang++ supports -c -o file.o... (cached) yes
:info:configure checking whether the /usr/bin/clang++ linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin11.4.0 dyld
:info:configure checking how to hardcode library paths into programs... immediate
:info:configure checking for special C compiler options needed for large files... no
:info:configure checking for _FILE_OFFSET_BITS value needed for large files... no
:info:configure checking for stdlib.h... (cached) yes
:info:configure checking for unistd.h... (cached) yes
:info:configure checking for sys/param.h... yes
:info:configure checking for getpagesize... yes
:info:configure checking for working mmap... yes
:info:configure checking for malloc in -lmalloc... no
:info:configure checking for struct stat.st_blksize... yes
:info:configure checking sys/resource.h usability... yes
:info:configure checking sys/resource.h presence... yes
:info:configure checking for sys/resource.h... yes
:info:configure checking sys/times.h usability... yes
:info:configure checking sys/times.h presence... yes
:info:configure checking for sys/times.h... yes
:info:configure checking malloc.h usability... no
:info:configure checking malloc.h presence... no
:info:configure checking for malloc.h... no
:info:configure checking for mallinfo... no
:info:configure checking for isnan... yes
:info:configure checking for getrlimit... yes
:info:configure checking for gethostname... yes
:info:configure checking for floor in -lm... yes
:info:configure checking whether pthreads work with -pthread... yes
:info:configure checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
:info:configure checking if more special flags are required for pthreads... -D_THREAD_SAFE
:info:configure CC:/usr/bin/clang CFLAGS:-pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread LIBS: -lm 
:info:configure checking zlib.h usability... yes
:info:configure checking zlib.h presence... yes
:info:configure checking for zlib.h... yes
:info:configure checking for library containing deflate... -lz
:info:configure checking szlib.h usability... no
:info:configure checking szlib.h presence... no
:info:configure checking for szlib.h... no
:info:configure checking for library containing SZ_BufftoBuffCompress... no
:info:configure configure: error: Could not link to szlib
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local 
:info:configure Exit code: 1
:error:configure org.macports.configure for port cdo returned: configure failure: command execution failed
:debug:configure Error code: NONE
:debug:configure Backtrace: configure failure: command execution failed
    while executing
"$procedure $targetname"
:info:configure Warning: targets not executed for cdo: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
:notice:configure Please see the log file for port cdo for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/main.log

[ryandesign (Ryan Carsten Schmidt)]

Please remember to use WikiFormatting, and that attaching voluminous output is preferred over pasting it.

[bbaker@…]

Thank you for catching that CDO cannot connect to szlib. It looks like HDF5 no longer has szlib as a dependency. I cannot find szlib on MacPorts anymore. Do you have a suggestion on how best to proceed? Thank you, Barry

Replying to bbaker@…:

Hello, I am having problems trying to install CDO on a MacbookPro running Mac OS X 10.7.4. This is the error I received;

Error: org.macports.configure for port cdo returned: configure failure: command execution failed

I checked the log file below but cannot figure out how to fix the problem. Any help would be appreciated. Thanks, Barry

version:1
:debug:main epoch: in tree: 2 installed: 2
:debug:main netcdf 4.2.0_4 exists in the ports tree
:debug:main netcdf 4.2.0_4 +dap+netcdf4 is the latest installed
:debug:main netcdf 4.2.0_4 +dap+netcdf4 is active
:debug:main Merging existing variants '+dap+netcdf4' into variants
:debug:main new fully merged portvariants: netcdf4 + dap +
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/netcdf
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Executing variant netcdf4 provides netcdf4
:debug:main Executing variant dap provides dap
:debug:main No need to upgrade! netcdf 4.2.0_4 >= netcdf 4.2.0_4
:debug:main epoch: in tree: 0 installed: 0
:debug:main hdf5-18 1.8.9_0 exists in the ports tree
:debug:main hdf5-18 1.8.9_0  is the latest installed
:debug:main hdf5-18 1.8.9_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/hdf5-18
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! hdf5-18 1.8.9_0 >= hdf5-18 1.8.9_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main zlib 1.2.7_0 exists in the ports tree
:debug:main zlib 1.2.7_0  is the latest installed
:debug:main zlib 1.2.7_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/zlib
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main curl 7.26.0_0 exists in the ports tree
:debug:main curl 7.26.0_0 +ssl is the latest installed
:debug:main curl 7.26.0_0 +ssl is active
:debug:main Merging existing variants '+ssl' into variants
:debug:main new fully merged portvariants: ssl +
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/net/curl
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/archcheck-1.0.tcl
:debug:main universal variant already exists, so not adding the default one
:debug:main Executing variant ssl provides ssl
:debug:main No need to upgrade! curl 7.26.0_0 >= curl 7.26.0_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main libidn 1.25_0 exists in the ports tree
:debug:main libidn 1.25_0  is the latest installed
:debug:main libidn 1.25_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/mail/libidn
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! libidn 1.25_0 >= libidn 1.25_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main libiconv 1.14_0 exists in the ports tree
:debug:main libiconv 1.14_0  is the latest installed
:debug:main libiconv 1.14_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/libiconv
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! libiconv 1.14_0 >= libiconv 1.14_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main gettext 0.18.1.1_2 exists in the ports tree
:debug:main gettext 0.18.1.1_2  is the latest installed
:debug:main gettext 0.18.1.1_2  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/gettext
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/archcheck-1.0.tcl
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! gettext 0.18.1.1_2 >= gettext 0.18.1.1_2
:debug:main epoch: in tree: 0 installed: 0
:debug:main ncurses 5.9_1 exists in the ports tree
:debug:main ncurses 5.9_1  is the latest installed
:debug:main ncurses 5.9_1  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/ncurses
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! ncurses 5.9_1 >= ncurses 5.9_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main expat 2.1.0_0 exists in the ports tree
:debug:main expat 2.1.0_0  is the latest installed
:debug:main expat 2.1.0_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/expat
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! expat 2.1.0_0 >= expat 2.1.0_0
:debug:main epoch: in tree: 1 installed: 1
:debug:main openssl 1.0.1c_0 exists in the ports tree
:debug:main openssl 1.0.1c_0  is the latest installed
:debug:main openssl 1.0.1c_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/openssl
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default one
:debug:main No need to upgrade! openssl 1.0.1c_0 >= openssl 1.0.1c_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main curl-ca-bundle 7.26.0_1 exists in the ports tree
:debug:main curl-ca-bundle 7.26.0_1  is the latest installed
:debug:main curl-ca-bundle 7.26.0_1  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/net/curl-ca-bundle
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main universal_variant is false, so not adding the default universal variant
:debug:main No need to upgrade! curl-ca-bundle 7.26.0_1 >= curl-ca-bundle 7.26.0_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main proj47 4.7.0_0 exists in the ports tree
:debug:main proj47 4.7.0_0  is the latest installed
:debug:main proj47 4.7.0_0  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/gis/proj47
:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! proj47 4.7.0_0 >= proj47 4.7.0_0
:msg:main --->  Computing dependencies for cdo:info:main .:debug:main cdo has no conflicts
:debug:main Searching for dependency: netcdf
:debug:main Found Dependency: receipt exists for netcdf
:debug:main Searching for dependency: proj47
:debug:main Found Dependency: receipt exists for proj47
:msg:main 
:debug:main Executing org.macports.main (cdo)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 503
:debug:archivefetch archivefetch phase started at Fri Jul 27 06:14:30 MDT 2012
:msg:archivefetch --->  Fetching archive for cdo
:debug:archivefetch Executing org.macports.archivefetch (cdo)
:debug:archivefetch euid/egid changed to: 0/0
:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
:debug:archivefetch euid/egid changed to: 503/501
:info:archivefetch --->  cdo-1.5.5_0.darwin_11.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
:msg:archivefetch --->  Attempting to fetch cdo-1.5.5_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/cdo
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
:debug:archivefetch Privilege de-escalation not attempted as not running as root.
:debug:fetch fetch phase started at Fri Jul 27 06:14:30 MDT 2012
:notice:fetch --->  Fetching distfiles for cdo
:debug:fetch Can't run fetch on this port without elevated privileges. Escalating privileges back to root.
:debug:fetch euid changed to: 0. egid changed to: 0.
:debug:fetch changing euid/egid - current euid: 0 - current egid: 0
:debug:fetch egid changed to: 501
:debug:fetch euid changed to: 503
:debug:fetch Executing org.macports.fetch (cdo)
:info:fetch --->  cdo-1.5.5.tar.gz doesn't seem to exist in /opt/local/var/macports/distfiles/cdo
:notice:fetch --->  Attempting to fetch cdo-1.5.5.tar.gz from http://distfiles.macports.org/cdo
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Fri Jul 27 06:14:35 MDT 2012
:notice:checksum --->  Verifying checksum(s) for cdo
:debug:checksum Executing org.macports.checksum (cdo)
:info:checksum --->  Checksumming cdo-1.5.5.tar.gz
:debug:checksum Correct (md5) checksum for cdo-1.5.5.tar.gz
:debug:checksum Correct (sha1) checksum for cdo-1.5.5.tar.gz
:debug:checksum Correct (rmd160) checksum for cdo-1.5.5.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Fri Jul 27 06:14:35 MDT 2012
:notice:extract --->  Extracting cdo
:debug:extract Executing org.macports.extract (cdo)
:info:extract --->  Extracting cdo-1.5.5.tar.gz
:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz'
:debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7'
:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz' | /usr/bin/gnutar --no-same-owner -xf -'
:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cdo/cdo-1.5.5.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
:debug:extract euid/egid changed to: 0/0
:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work to macports
:debug:extract euid/egid changed to: 503/501
:debug:extract Privilege de-escalation not attempted as not running as root.
:debug:patch patch phase started at Fri Jul 27 06:14:37 MDT 2012
:debug:patch Executing org.macports.patch (cdo)
:debug:patch Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Fri Jul 27 06:14:37 MDT 2012
:notice:configure --->  Configuring cdo
:debug:configure Using compiler 'Mac OS X clang'
:debug:configure Executing org.macports.configure (cdo)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.7' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib -arch x86_64' OBJC='/usr/bin/clang' FCFLAGS='-pipe -O2 -m64' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -O2 -arch x86_64' FFLAGS='-pipe -O2 -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local'
:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local 
:info:configure checking build system type... x86_64-apple-darwin11.4.0
:info:configure checking host system type... x86_64-apple-darwin11.4.0
:info:configure checking for a BSD-compatible install... /usr/bin/install -c
:info:configure checking whether build environment is sane... yes
:info:configure checking for a thread-safe mkdir -p... config/install-sh -c -d
:info:configure checking for gawk... no
:info:configure checking for mawk... no
:info:configure checking for nawk... no
:info:configure checking for awk... awk
:info:configure checking whether make sets $(MAKE)... yes
:info:configure checking whether to enable maintainer-specific portions of Makefiles... no
:info:configure configure: setting up libtool
:info:configure checking how to print strings... printf
:info:configure checking for style of include used by make... GNU
:info:configure checking for gcc... /usr/bin/clang
:info:configure checking whether the C compiler works... yes
:info:configure checking for C compiler default output file name... a.out
:info:configure checking for suffix of executables... 
:info:configure checking whether we are cross compiling... no
:info:configure checking for suffix of object files... o
:info:configure checking whether we are using the GNU C compiler... yes
:info:configure checking whether /usr/bin/clang accepts -g... yes
:info:configure checking for /usr/bin/clang option to accept ISO C89... none needed
:info:configure checking dependency style of /usr/bin/clang... none
:info:configure checking for a sed that does not truncate output... /usr/bin/sed
:info:configure checking for grep that handles long lines and -e... /usr/bin/grep
:info:configure checking for egrep... /usr/bin/grep -E
:info:configure checking for fgrep... /usr/bin/grep -F
:info:configure checking for ld used by /usr/bin/clang... /usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm
:info:configure checking the name lister (/opt/local/bin/nm) interface... BSD nm
:info:configure checking whether ln -s works... yes
:info:configure checking the maximum length of command line arguments... 196608
:info:configure checking whether the shell understands some XSI constructs... yes
:info:configure checking whether the shell understands "+="... yes
:info:configure checking for /usr/bin/ld option to reload object files... -r
:info:configure checking for objdump... no
:info:configure checking how to recognize dependent libraries... pass_all
:info:configure checking for ar... ar
:info:configure checking for strip... strip
:info:configure checking for ranlib... ranlib
:info:configure checking command to parse /opt/local/bin/nm output from /usr/bin/clang object... ok
:info:configure checking for dsymutil... dsymutil
:info:configure checking for nmedit... nmedit
:info:configure checking for lipo... lipo
:info:configure checking for otool... otool
:info:configure checking for otool64... no
:info:configure checking for -single_module linker flag... yes
:info:configure checking for -exported_symbols_list linker flag... yes
:info:configure checking for -force_load linker flag... yes
:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
:info:configure checking for ANSI C header files... yes
:info:configure checking for sys/types.h... yes
:info:configure checking for sys/stat.h... yes
:info:configure checking for stdlib.h... yes
:info:configure checking for string.h... yes
:info:configure checking for memory.h... yes
:info:configure checking for strings.h... yes
:info:configure checking for inttypes.h... yes
:info:configure checking for stdint.h... yes
:info:configure checking for unistd.h... yes
:info:configure checking for dlfcn.h... yes
:info:configure checking for objdir... .libs
:info:configure checking if /usr/bin/clang supports -fno-rtti -fno-exceptions... yes
:info:configure checking for /usr/bin/clang option to produce PIC... -fno-common -DPIC
:info:configure checking if /usr/bin/clang PIC flag -fno-common -DPIC works... yes
:info:configure checking if /usr/bin/clang static flag -static works... no
:info:configure checking if /usr/bin/clang supports -c -o file.o... yes
:info:configure checking if /usr/bin/clang supports -c -o file.o... (cached) yes
:info:configure checking whether the /usr/bin/clang linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin11.4.0 dyld
:info:configure checking how to hardcode library paths into programs... immediate
:info:configure checking whether stripping libraries is possible... yes
:info:configure checking if libtool supports shared libraries... yes
:info:configure checking whether to build shared libraries... yes
:info:configure checking whether to build static libraries... yes
:info:configure checking for gcc... (cached) /usr/bin/clang
:info:configure checking for /usr/bin/clang option to accept ISO C99... none needed
:info:configure checking whether /usr/bin/clang and cc understand -c and -o together... yes
:info:configure checking for ar... (cached) ar
:info:configure checking for ld... /usr/bin/ld
:info:configure checking for nm... /opt/local/bin/nm
:info:configure checking for ar... (cached) ar
:info:configure checking for as... as
:info:configure checking for dlltool... no
:info:configure checking for objdump... false
:info:configure checking for strip... (cached) strip
:info:configure checking for ranlib... (cached) ranlib
:info:configure checking whether we are using the GNU C++ compiler... yes
:info:configure checking whether /usr/bin/clang++ accepts -g... yes
:info:configure checking dependency style of /usr/bin/clang++... none
:info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E
:info:configure checking for ld used by /usr/bin/clang++... /usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking whether the /usr/bin/clang++ linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking for /usr/bin/clang++ option to produce PIC... -fno-common -DPIC
:info:configure checking if /usr/bin/clang++ PIC flag -fno-common -DPIC works... yes
:info:configure checking if /usr/bin/clang++ static flag -static works... no
:info:configure checking if /usr/bin/clang++ supports -c -o file.o... yes
:info:configure checking if /usr/bin/clang++ supports -c -o file.o... (cached) yes
:info:configure checking whether the /usr/bin/clang++ linker (/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin11.4.0 dyld
:info:configure checking how to hardcode library paths into programs... immediate
:info:configure checking for special C compiler options needed for large files... no
:info:configure checking for _FILE_OFFSET_BITS value needed for large files... no
:info:configure checking for stdlib.h... (cached) yes
:info:configure checking for unistd.h... (cached) yes
:info:configure checking for sys/param.h... yes
:info:configure checking for getpagesize... yes
:info:configure checking for working mmap... yes
:info:configure checking for malloc in -lmalloc... no
:info:configure checking for struct stat.st_blksize... yes
:info:configure checking sys/resource.h usability... yes
:info:configure checking sys/resource.h presence... yes
:info:configure checking for sys/resource.h... yes
:info:configure checking sys/times.h usability... yes
:info:configure checking sys/times.h presence... yes
:info:configure checking for sys/times.h... yes
:info:configure checking malloc.h usability... no
:info:configure checking malloc.h presence... no
:info:configure checking for malloc.h... no
:info:configure checking for mallinfo... no
:info:configure checking for isnan... yes
:info:configure checking for getrlimit... yes
:info:configure checking for gethostname... yes
:info:configure checking for floor in -lm... yes
:info:configure checking whether pthreads work with -pthread... yes
:info:configure checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
:info:configure checking if more special flags are required for pthreads... -D_THREAD_SAFE
:info:configure CC:/usr/bin/clang CFLAGS:-pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread LIBS: -lm 
:info:configure checking zlib.h usability... yes
:info:configure checking zlib.h presence... yes
:info:configure checking for zlib.h... yes
:info:configure checking for library containing deflate... -lz
:info:configure checking szlib.h usability... no
:info:configure checking szlib.h presence... no
:info:configure checking for szlib.h... no
:info:configure checking for library containing SZ_BufftoBuffCompress... no
:info:configure configure: error: Could not link to szlib
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/work/cdo-1.5.5" && ./configure --prefix=/opt/local --with-netcdf=/opt/local --disable-dependency-tracking --with-proj=/opt/local/lib/proj47 --with-hdf5=/opt/local --with-zlib=/opt/local --with-szlib=/opt/local 
:info:configure Exit code: 1
:error:configure org.macports.configure for port cdo returned: configure failure: command execution failed
:debug:configure Error code: NONE
:debug:configure Backtrace: configure failure: command execution failed
    while executing
"$procedure $targetname"
:info:configure Warning: targets not executed for cdo: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
:notice:configure Please see the log file for port cdo for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/main.log

[tenomoto (Takeshi Enomoto)]

Committed in r96017.

[bbaker@…]

Replying to takeshi@…:

Committed in r96017.

CDO is working now. Thank you!