[MacPorts] #38885: cufflinks @ 0.9.3: build fails (was: failed install of cufflinks 0.9.3)

MacPorts noreply at macports.org
Mon Apr 22 06:15:06 PDT 2013


#38885: cufflinks @ 0.9.3: build fails
-------------------------+------------------------------
  Reporter:  malabady@…  |      Owner:  haroldpimentel@…
      Type:  defect      |     Status:  new
  Priority:  Normal      |  Milestone:
 Component:  ports       |    Version:  2.1.3
Resolution:              |   Keywords:
      Port:  cufflinks   |
-------------------------+------------------------------
Changes (by ciserlohn@…):

 * port:  cufflinks 0.9.3 => cufflinks
 * owner:  macports-tickets@… => haroldpimentel@…
 * priority:  High => Normal


Old description:

> installing cufflinks 0.9.3 failed. Here is the main.log file
>
> ------
> version:1
> :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/12.3.0 (Mac OS X 10.8) 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 samtools 0.1.18_0 exists in the ports tree
> :debug:main samtools 0.1.18_0  is the latest installed
> :debug:main samtools 0.1.18_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/samtools
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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! samtools 0.1.18_0 >= samtools 0.1.18_0
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main ncurses 5.9_2 exists in the ports tree
> :debug:main ncurses 5.9_2  is the latest installed
> :debug:main ncurses 5.9_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/ncurses
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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_2 >= ncurses 5.9_2
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main boost 1.53.0_1 exists in the ports tree
> :debug:main boost 1.53.0_1 +no_single+no_static+python27 is the latest
> installed
> :debug:main boost 1.53.0_1 +no_single+no_static+python27 is active
> :debug:main Merging existing variants '+no_single+no_static+python27'
> into variants
> :debug:main new fully merged portvariants: no_static + no_single +
> python27 +
> :debug:main Changing to port directory:
> /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/boost
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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 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 Executing variant python27 provides python27
> :debug:main Executing variant no_static provides no_static
> :debug:main Executing variant no_single provides no_single
> :debug:main No need to upgrade! boost 1.53.0_1 >= boost 1.53.0_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/12.3.0 (Mac OS X 10.8) 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: 0 installed: 0
> :debug:main bzip2 1.0.6_0 exists in the ports tree
> :debug:main bzip2 1.0.6_0  is the latest installed
> :debug:main bzip2 1.0.6_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/bzip2
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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 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! bzip2 1.0.6_0 >= bzip2 1.0.6_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/12.3.0 (Mac OS X 10.8) 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 icu 49.1.2_1 exists in the ports tree
> :debug:main icu 49.1.2_1  is the latest installed
> :debug:main icu 49.1.2_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/icu
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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! icu 49.1.2_1 >= icu 49.1.2_1
> :debug:main epoch: in tree: 2 installed: 2
> :debug:main python27 2.7.3_1 exists in the ports tree
> :debug:main python27 2.7.3_1  is the latest installed
> :debug:main python27 2.7.3_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/lang/python27
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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/select-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! python27 2.7.3_1 >= python27 2.7.3_1
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main gettext 0.18.2.1_0 exists in the ports tree
> :debug:main gettext 0.18.2.1_0  is the latest installed
> :debug:main gettext 0.18.2.1_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/gettext
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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/compiler_blacklist_versions-1.0.tcl
> :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 compiler clang 425.0.24 not blacklisted because does not
> match {clang < 211.10.1}
> :debug:main universal variant already exists, so not adding the default
> one
> :debug:main No need to upgrade! gettext 0.18.2.1_0 >= gettext 0.18.2.1_0
> :debug:main epoch: in tree: 1 installed: 1
> :debug:main openssl 1.0.1e_1 exists in the ports tree
> :debug:main openssl 1.0.1e_1  is the latest installed
> :debug:main openssl 1.0.1e_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/openssl
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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 1.0.1e_1 >= openssl 1.0.1e_1
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main sqlite3 3.7.16_0 exists in the ports tree
> :debug:main sqlite3 3.7.16_0  is the latest installed
> :debug:main sqlite3 3.7.16_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/databases/sqlite3
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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! sqlite3 3.7.16_0 >= sqlite3 3.7.16_0
> :debug:main epoch: in tree: 20090923 installed: 20090923
> :debug:main libedit 20121213-3.0_0 exists in the ports tree
> :debug:main libedit 20121213-3.0_0  is the latest installed
> :debug:main libedit 20121213-3.0_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/devel/libedit
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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! libedit 20121213-3.0_0 >= libedit
> 20121213-3.0_0
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main db46 4.6.21_7 exists in the ports tree
> :debug:main db46 4.6.21_7  is the latest installed
> :debug:main db46 4.6.21_7  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/databases/db46
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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! db46 4.6.21_7 >= db46 4.6.21_7
> :debug:main epoch: in tree: 0 installed: 0
> :debug:main python_select 0.3_2 exists in the ports tree
> :debug:main python_select 0.3_2  is the latest installed
> :debug:main python_select 0.3_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/sysutils/python_select
> :debug:main OS darwin/12.3.0 (Mac OS X 10.8) 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/select-1.0.tcl
> :debug:main universal_variant is false, so not adding the default
> universal variant
> :debug:main No need to upgrade! python_select 0.3_2 >= python_select
> 0.3_2
> :msg:main --->  Computing dependencies for cufflinks:info:main
> .:debug:main cufflinks has no conflicts
> :debug:main Searching for dependency: zlib
> :debug:main Found Dependency: receipt exists for zlib
> :debug:main Searching for dependency: samtools
> :debug:main Found Dependency: receipt exists for samtools
> :debug:main Searching for dependency: boost
> :debug:main Found Dependency: receipt exists for boost
> :msg:main
> :debug:main Executing org.macports.main (cufflinks)
> :debug:main changing euid/egid - current euid: 0 - current egid: 0
> :debug:main egid changed to: 501
> :debug:main euid changed to: 503
> :debug:main Skipping completed org.macports.archivefetch (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:main Skipping completed org.macports.fetch (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:main Skipping completed org.macports.checksum (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:main Skipping completed org.macports.extract (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:main Skipping completed org.macports.patch (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:main Skipping completed org.macports.configure (cufflinks)
> :debug:main Privilege de-escalation not attempted as not running as root.
> :debug:build build phase started at Mon Apr 22 08:16:49 EDT 2013
> :notice:build --->  Building cufflinks
> :debug:build Executing org.macports.build (cufflinks)
> :debug:build 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_cufflinks/cufflinks/work/.CC_PRINT_OPTIONS'
> LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES'
> MACOSX_DEPLOYMENT_TARGET='10.8'
> :debug:build Assembled command: 'cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3"
> && /usr/bin/make -j24 -w all'
> :debug:build Executing command line:  cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3"
> && /usr/bin/make -j24 -w all
> :info:build make: Entering directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
> :info:build /usr/bin/make  all-recursive
> :info:build make[1]: Entering directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
> :info:build Making all in src
> :info:build make[2]: Entering directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3/src'
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o
> clustering.cpp; \
> :info:build     then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po";
> else rm -f ".deps/clustering.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o
> differential.cpp; \
> :info:build     then mv -f ".deps/differential.Tpo"
> ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT common.o
> -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
> :info:build     then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm
> -f ".deps/common.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> assemble.o -MD -MP -MF ".deps/assemble.Tpo" -c -o assemble.o
> assemble.cpp; \
> :info:build     then mv -f ".deps/assemble.Tpo" ".deps/assemble.Po"; else
> rm -f ".deps/assemble.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> abundances.o -MD -MP -MF ".deps/abundances.Tpo" -c -o abundances.o
> abundances.cpp; \
> :info:build     then mv -f ".deps/abundances.Tpo" ".deps/abundances.Po";
> else rm -f ".deps/abundances.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> scaffolds.o -MD -MP -MF ".deps/scaffolds.Tpo" -c -o scaffolds.o
> scaffolds.cpp; \
> :info:build     then mv -f ".deps/scaffolds.Tpo" ".deps/scaffolds.Po";
> else rm -f ".deps/scaffolds.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT hits.o
> -MD -MP -MF ".deps/hits.Tpo" -c -o hits.o hits.cpp; \
> :info:build     then mv -f ".deps/hits.Tpo" ".deps/hits.Po"; else rm -f
> ".deps/hits.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT genes.o
> -MD -MP -MF ".deps/genes.Tpo" -c -o genes.o genes.cpp; \
> :info:build     then mv -f ".deps/genes.Tpo" ".deps/genes.Po"; else rm -f
> ".deps/genes.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> bundles.o -MD -MP -MF ".deps/bundles.Tpo" -c -o bundles.o bundles.cpp; \
> :info:build     then mv -f ".deps/bundles.Tpo" ".deps/bundles.Po"; else
> rm -f ".deps/bundles.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> filters.o -MD -MP -MF ".deps/filters.Tpo" -c -o filters.o filters.cpp; \
> :info:build     then mv -f ".deps/filters.Tpo" ".deps/filters.Po"; else
> rm -f ".deps/filters.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> scaffold_graph.o -MD -MP -MF ".deps/scaffold_graph.Tpo" -c -o
> scaffold_graph.o scaffold_graph.cpp; \
> :info:build     then mv -f ".deps/scaffold_graph.Tpo"
> ".deps/scaffold_graph.Po"; else rm -f ".deps/scaffold_graph.Tpo"; exit 1;
> fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> matching_merge.o -MD -MP -MF ".deps/matching_merge.Tpo" -c -o
> matching_merge.o matching_merge.cpp; \
> :info:build     then mv -f ".deps/matching_merge.Tpo"
> ".deps/matching_merge.Po"; else rm -f ".deps/matching_merge.Tpo"; exit 1;
> fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> graph_optimize.o -MD -MP -MF ".deps/graph_optimize.Tpo" -c -o
> graph_optimize.o graph_optimize.cpp; \
> :info:build     then mv -f ".deps/graph_optimize.Tpo"
> ".deps/graph_optimize.Po"; else rm -f ".deps/graph_optimize.Tpo"; exit 1;
> fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> biascorrection.o -MD -MP -MF ".deps/biascorrection.Tpo" -c -o
> biascorrection.o biascorrection.cpp; \
> :info:build     then mv -f ".deps/biascorrection.Tpo"
> ".deps/biascorrection.Po"; else rm -f ".deps/biascorrection.Tpo"; exit 1;
> fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> jensen_shannon.o -MD -MP -MF ".deps/jensen_shannon.Tpo" -c -o
> jensen_shannon.o jensen_shannon.cpp; \
> :info:build     then mv -f ".deps/jensen_shannon.Tpo"
> ".deps/jensen_shannon.Po"; else rm -f ".deps/jensen_shannon.Tpo"; exit 1;
> fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o
> GFaSeqGet.cpp; \
> :info:build     then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po";
> else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT gff.o
> -MD -MP -MF ".deps/gff.Tpo" -c -o gff.o gff.cpp; \
> :info:build     then mv -f ".deps/gff.Tpo" ".deps/gff.Po"; else rm -f
> ".deps/gff.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> gtf_tracking.o -MD -MP -MF ".deps/gtf_tracking.Tpo" -c -o gtf_tracking.o
> gtf_tracking.cpp; \
> :info:build     then mv -f ".deps/gtf_tracking.Tpo"
> ".deps/gtf_tracking.Po"; else rm -f ".deps/gtf_tracking.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> cufflinks.o -MD -MP -MF ".deps/cufflinks.Tpo" -c -o cufflinks.o
> cufflinks.cpp; \
> :info:build     then mv -f ".deps/cufflinks.Tpo" ".deps/cufflinks.Po";
> else rm -f ".deps/cufflinks.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> cuffcompare.o -MD -MP -MF ".deps/cuffcompare.Tpo" -c -o cuffcompare.o
> cuffcompare.cpp; \
> :info:build     then mv -f ".deps/cuffcompare.Tpo"
> ".deps/cuffcompare.Po"; else rm -f ".deps/cuffcompare.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> cuffdiff.o -MD -MP -MF ".deps/cuffdiff.Tpo" -c -o cuffdiff.o
> cuffdiff.cpp; \
> :info:build     then mv -f ".deps/cuffdiff.Tpo" ".deps/cuffdiff.Po"; else
> rm -f ".deps/cuffdiff.Tpo"; exit 1; fi
> :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src
> -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g
> -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64
> -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT
> gtf_to_sam.o -MD -MP -MF ".deps/gtf_to_sam.Tpo" -c -o gtf_to_sam.o
> gtf_to_sam.cpp; \
> :info:build     then mv -f ".deps/gtf_to_sam.Tpo" ".deps/gtf_to_sam.Po";
> else rm -f ".deps/gtf_to_sam.Tpo"; exit 1; fi
> :info:build In file included from GFaSeqGet.cpp:1:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from gtf_tracking.cpp:11:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from gff.cpp:1:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from cuffcompare.cpp:10:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GffCDSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build gff.cpp:1386:13: note: in instantiation of member function
> 'GArray<GffCDSeg>::Add' requested here
> :info:build         cds.Add(cdseg);
> :info:build             ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build GFaSeqGet.cpp:62:17: error: use of undeclared identifier
> 'fseeko'; did you mean 'fseek'?
> :info:build  if (fofs!=0) { fseeko(fh,fofs,SEEK_SET); } //e.g. for
> offsets provided by cdbyank
> :info:build                 ^~~~~~
> :info:build                 fseek
> :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
> :info:build int      fseek(FILE *, long, int);
> :info:build          ^
> :info:build GFaSeqGet.cpp:128:2: error: use of undeclared identifier
> 'fseeko'; did you mean 'fseek'?
> :info:build  fseeko(fh,fseqstart,SEEK_SET);
> :info:build  ^~~~~~
> :info:build  fseek
> :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
> :info:build int      fseek(FILE *, long, int);
> :info:build          ^
> :info:build GFaSeqGet.cpp:261:3: error: use of undeclared identifier
> 'fseeko'; did you mean 'fseek'?
> :info:build   fseeko(fh, fstart, SEEK_SET);
> :info:build   ^~~~~~
> :info:build   fseek
> :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
> :info:build int      fseek(FILE *, long, int);
> :info:build          ^
> :info:build GFaSeqGet.cpp:280:5: error: use of undeclared identifier
> 'fseeko'; did you mean 'fseek'?
> :info:build     fseeko(fh, lendlen, SEEK_CUR);
> :info:build     ^~~~~~
> :info:build     fseek
> :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
> :info:build int      fseek(FILE *, long, int);
> :info:build          ^
> :info:build GFaSeqGet.cpp:300:5: error: use of undeclared identifier
> 'fseeko'; did you mean 'fseek'?
> :info:build     fseeko(fh, lendlen, SEEK_CUR);
> :info:build     ^~~~~~
> :info:build     fseek
> :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
> :info:build int      fseek(FILE *, long, int);
> :info:build          ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 1 warning and 1 error generated.
> :info:build ./GList.hh:537:5: error: use of undeclared identifie1r
> warning and 5 errors  generated.
> :info:build 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 1 warning and 3 errors generated.
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 1 warning and 3 errors generated.
> :info:build make[2]: *** [gff.o] Error 1
> :info:build make[2]: *** Waiting for unfinished jobs....
> :info:build make[2]: *** [gtf_tracking.o] Error 1
> :info:build make[2]: *** [GFaSeqGet.o] Error 1
> :info:build make[2]: *** [cuffcompare.o] Error 1
> :info:build In file included from jensen_shannon.cpp:12:
> :info:build In file included from ./jensen_shannon.h:10:
> :info:build In file included from
> /opt/local/include/boost/numeric/ublas/matrix.hpp:16:
> :info:build In file included from
> /opt/local/include/boost/numeric/ublas/vector.hpp:19:
> :info:build In file included from
> /opt/local/include/boost/numeric/ublas/storage.hpp:26:
> :info:build /opt/local/include/boost/numeric/ublas/traits.hpp:45:27:
> warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function]
> :info:build   template<> unsigned int boost_numeric_ublas_abs (const
> unsigned int& t) {
> :info:build                           ^
> :info:build /opt/local/include/boost/numeric/ublas/traits.hpp:49:28:
> warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function]
> :info:build   template<> unsigned long boost_numeric_ublas_abs (const
> unsigned long& t) {
> :info:build                            ^
> :info:build 2 warnings generated.
> :info:build In file included from genes.cpp:10:
> :info:build In file included from ./genes.h:17:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from genes.cpp:10:
> :info:build In file included from ./genes.h:18:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from scaffold_graph.cpp:12:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from differential.cpp:14:
> :info:build In file included from ./abundances.h:21:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from biascorrection.cpp:10:
> :info:build In file included from ./biascorrection.h:14:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from differential.cpp:14:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from abundances.cpp:11:
> :info:build In file included from ./abundances.h:21:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from biascorrection.cpp:10:
> :info:build In file included from ./biascorrection.h:14:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from matching_merge.cpp:10:
> :info:build In file included from ./matching_merge.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from abundances.cpp:11:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from scaffolds.cpp:13:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build scaffolds.cpp:1144:47: warning: '&&' within '||' [-Wlogical-
> op-parentheses]
> :info:build                 if (hit.left_alignment()->antisense_align()
> && strand() != CUFF_REV
> :info:build
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
> :info:build scaffolds.cpp:1144:47: note: place parentheses around the
> '&&' expression to silence this warning
> :info:build                 if (hit.left_alignment()->antisense_align()
> && strand() != CUFF_REV
> :info:build                                                             ^
> :info:build                     (
> )
> :info:build scaffolds.cpp:1145:50: warning: '&&' within '||' [-Wlogical-
> op-parentheses]
> :info:build                         ||
> !(hit.left_alignment()->antisense_align()) && strand() == CUFF_REV)
> :info:build                         ~~
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
> :info:build scaffolds.cpp:1145:50: note: place parentheses around the
> '&&' expression to silence this warning
> :info:build                         ||
> !(hit.left_alignment()->antisense_align()) && strand() == CUFF_REV)
> :info:build
> ^
> :info:build                            (
> )
> :info:build In file included from cuffdiff.cpp:27:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from filters.cpp:10:
> :info:build In file included from ./filters.h:17:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from cuffdiff.cpp:27:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from gtf_to_sam.cpp:24:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from bundles.cpp:16:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from gtf_to_sam.cpp:24:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from bundles.cpp:16:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from filters.cpp:10:
> :info:build In file included from ./filters.h:18:
> :info:build In file included from ./genes.h:18:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from graph_optimize.cpp:13:
> :info:build In file included from ./graph_optimize.h:17:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build bundles.cpp:1172:33: warning: expression result unused
> [-Wunused-value]
> :info:build                     itr->second.fwd_strand_frags;
> :info:build                     ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~
> :info:build In file included from graph_optimize.cpp:13:
> :info:build In file included from ./graph_optimize.h:17:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build In file included from assemble.cpp:48:
> :info:build In file included from ./assemble.h:26:
> :info:build In file included from ./bundles.h:20:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from clustering.cpp:10:
> :info:build In file included from ./clustering.h:38:
> :info:build In file included from ./abundances.h:21:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build In file included from assemble.cpp:48:
> :info:build In file included from ./assemble.h:26:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build In file included from clustering.cpp:10:
> :info:build In file included from ./clustering.h:38:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build 2 warnings and 3 errors generated.
> :info:build make[2]: *** [genes.o] Error 1
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build In file included from differential.cpp:15:
> :info:build In file included from ./differential.h:23:
> :info:build In file included from
> /opt/local/include/boost/graph/adjacency_list.hpp:45:
> :info:build In file included from
> /opt/local/include/boost/graph/named_graph.hpp:17:
> :info:build
> /opt/local/include/boost/multi_index/hashed_index.hpp:1254:10: error: no
> member named 'BOOST_FOREACH' in namespace 'boost'
> :info:build   boost::foreach::tag)
> :info:build   ~~~~~~~^
> :info:build ./common.h:26:25: note: expanded from macro 'foreach'
> :info:build #define foreach         BOOST_FOREACH
> :info:build                         ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_weight_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:63:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(weight_map, edge_weight) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:174:1: note: expanded from macro '_'
> :info:build _weight_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_weight_map2' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:64:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(weight_map2, edge_weight2) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:178:1: note: expanded from macro '_'
> :info:build _weight_map2
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_distance_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:65:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(distance_map, vertex_distance) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:182:1: note: expanded from macro '_'
> :info:build _distance_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_predecessor_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:66:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(predecessor_map,
> vertex_predecessor) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:186:1: note: expanded from macro '_'
> :info:build _predecessor_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_rank_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:67:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(rank_map, vertex_rank) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:190:1: note: expanded from macro '_'
> :info:build _rank_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_root_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:68:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(root_map, vertex_root) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:194:1: note: expanded from macro '_'
> :info:build _root_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_edge_centrality_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:70:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(edge_centrality_map,
> edge_centrality) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:202:1: note: expanded from macro '_'
> :info:build _edge_centrality_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_centrality_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:71:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(centrality_map,
> vertex_centrality) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:206:1: note: expanded from macro '_'
> :info:build _centrality_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_parity_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:72:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(parity_map, parity_map) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build In file included from cufflinks.cpp#define
> BOOST_BGL_ONE_PARAM_CREF(name, key) BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9:25:
> :info:build In file included from ./clustering.h:19:
> :info:build In file included from
> /opt/local/include/boost/graph/adjacency_list.hpp: note: exp:45:
> :info:build In file included from
> /opt/local/include/boost/graph/named_graph.hpp:17:
> :info:build
> /opt/local/include/boost/multi_index/hashed_index.hpp:1254a:nde10: error:
> nod fr membomer na macrmed 'o 'BOOBOOSTST__PAFORRAMEACH' ETER_in
> namespacNAMe 'Eb'
> :info:build oost'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:210:1: note: expanded from macro '_'
> :info:build _parity_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build   boost::foreach::tag)
> :info:build   ~~~~~~~^
> :info:build In file included from scaffold_graph.cpp./common.h:26::14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:257:
> warning: unus:ed var note: iabexple anded'_col for_rommap macro ''
> [foreach'-W
> :info:build unused-variable]
> :info:build #define foreach         BOOST_FOREACH
> :info:build                         ^
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:73:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(color_map, vertex_color) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:4:1: note: expanded from macro '_'
> :info:build _color_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_edge_color_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:74:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(edge_color_map, edge_color) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:8:1: note: expanded from macro '_'
> :info:build _edge_color_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_capacity_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:75:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(capacity_map, edge_capacity) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:12:1: note: expanded from macro '_'
> :info:build _capacity_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_residual_capacity_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:76:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(residual_capacity_map,
> edge_residual_capacity) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:16:1: note: expanded from macro '_'
> :info:build _residual_capacity_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_reverse_edge_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:77:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(reverse_edge_map, edge_reverse)
> \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:20:1: note: expanded from macro '_'
> :info:build _reverse_edge_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_discover_time_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:78:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(discover_time_map,
> vertex_discover_time) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:24:1: note: expanded from macro '_'
> :info:build _discover_time_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_lowpoint_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:79:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(lowpoint_map, vertex_lowpoint) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:28:1: note: expanded from macro '_'
> :info:build _lowpoint_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_index1_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:81:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_index1_map,
> vertex_index1) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:36:1: note: expanded from macro '_'
> :info:build _vertex_index1_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_index2_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:82:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_index2_map,
> vertex_index2) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:40:1: note: expanded from macro '_'
> :info:build _vertex_index2_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_assignment_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:83:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_assignment_map,
> vertex_assignment_map) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:44:1: note: expanded from macro '_'
> :info:build _vertex_assignment_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_distance_compare' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:85:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(distance_compare,
> distance_compare) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:52:1: note: expanded from macro '_'
> :info:build _distance_compare
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_distance_combine' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:86:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(distance_combine,
> distance_combine) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:56:1: note: expanded from macro '_'
> :info:build _distance_combine
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_distance_inf' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:87:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(distance_inf, distance_inf) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:60:1: note: expanded from macro '_'
> :info:build _distance_inf
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_distance_zero' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:88:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(distance_zero, distance_zero) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:64:1: note: expanded from macro '_'
> :info:build _distance_zero
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_edge_copy' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:89:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(edge_copy, edge_copy) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:68:1: note: expanded from macro '_'
> :info:build _edge_copy
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_copy' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:90:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_copy, vertex_copy) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:72:1: note: expanded from macro '_'
> :info:build _vertex_copy
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_buffer' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:91:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_REF(buffer, buffer_param) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:333:44: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_REF'
> :info:build #define BOOST_BGL_ONE_PARAM_REF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                            ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:76:1: note: expanded from macro '_'
> :info:build _buffer
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_orig_to_copy' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:92:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(orig_to_copy, orig_to_copy) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:80:1: note: expanded from macro '_'
> :info:build _orig_to_copy
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_isomorphism_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:93:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(isomorphism_map,
> vertex_isomorphism) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:84:1: note: expanded from macro '_'
> :info:build _isomorphism_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_invariant' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:94:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_invariant,
> vertex_invariant) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:88:1: note: expanded from macro '_'
> :info:build _vertex_invariant
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_invariant1' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:95:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_invariant1,
> vertex_invariant1) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:92:1: note: expanded from macro '_'
> :info:build _vertex_invariant1
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_invariant2' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:96:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_invariant2,
> vertex_invariant2) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:96:1: note: expanded from macro '_'
> :info:build _vertex_invariant2
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertex_max_invariant' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:97:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertex_max_invariant,
> vertex_max_invariant) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:100:1: note: expanded from macro '_'
> :info:build _vertex_max_invariant
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_polling' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:98:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(polling, polling) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:104:1: note: expanded from macro '_'
> :info:build _polling
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_lookahead' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:99:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(lookahead, lookahead) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:108:1: note: expanded from macro '_'
> :info:build _lookahead
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_in_parallel' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:100:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(in_parallel, in_parallel) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:112:1: note: expanded from macro '_'
> :info:build _in_parallel
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_displacement_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:101:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(displacement_map,
> vertex_displacement) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:116:1: note: expanded from macro '_'
> :info:build _displacement_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_attractive_force' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:102:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(attractive_force,
> attractive_force) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:120:1: note: expanded from macro '_'
> :info:build _attractive_force
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_repulsive_force' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:103:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(repulsive_force,
> repulsive_force) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:124:1: note: expanded from macro '_'
> :info:build _repulsive_force
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_force_pairs' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:104:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(force_pairs, force_pairs) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:128:1: note: expanded from macro '_'
> :info:build _force_pairs
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_cooling' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:105:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(cooling, cooling) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:132:1: note: expanded from macro '_'
> :info:build _cooling
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_iterations' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:106:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(iterations, iterations) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:136:1: note: expanded from macro '_'
> :info:build _iterations
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_diameter_range' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:107:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(diameter_range, diameter_range)
> \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:140:1: note: expanded from macro '_'
> :info:build _diameter_range
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_learning_constant_range' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:108:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(learning_constant_range,
> learning_constant_range) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:144:1: note: expanded from macro '_'
> :info:build _learning_constant_range
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_vertices_equivalent' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:109:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(vertices_equivalent,
> vertices_equivalent) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:148:1: note: expanded from macro '_'
> :info:build _vertices_equivalent
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_edges_equivalent' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:110:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(edges_equivalent,
> edges_equivalent) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:152:1: note: expanded from macro '_'
> :info:build _edges_equivalent
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_index_in_heap_map' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:111:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_CREF(index_in_heap_map,
> index_in_heap_map) \
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:334:45: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_CREF'
> :info:build #define BOOST_BGL_ONE_PARAM_CREF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                             ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:156:1: note: expanded from macro '_'
> :info:build _index_in_heap_map
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build In file included from scaffold_graph.cpp:14:
> :info:build In file included from
> /opt/local/include/boost/graph/depth_first_search.hpp:21:
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:335:7: warning:
> unused variable '_max_priority_queue' [-Wunused-variable]
> :info:build       BOOST_BGL_DECLARE_NAMED_PARAMS
> :info:build       ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:112:5: note:
> expanded from macro 'BOOST_BGL_DECLARE_NAMED_PARAMS'
> :info:build     BOOST_BGL_ONE_PARAM_REF(max_priority_queue,
> max_priority_queue)
> :info:build     ^
> :info:build
> /opt/local/include/boost/graph/named_function_params.hpp:333:44: note:
> expanded from macro 'BOOST_BGL_ONE_PARAM_REF'
> :info:build #define BOOST_BGL_ONE_PARAM_REF(name, key)
> BOOST_PARAMETER_NAME(name)
> :info:build                                            ^
> :info:build /opt/local/include/boost/parameter/name.hpp:139:9: note:
> expanded from macro 'BOOST_PARAMETER_NAME'
> :info:build       , BOOST_PARAMETER_SIMPLE_NAME
> \
> :info:build         ^
> :info:build note: (skipping 6 expansions in backtrace; use -fmacro-
> backtrace-limit=0 to see all)
> :info:build <scratch space>:160:1: note: expanded from macro '_'
> :info:build _max_priority_queue
> :info:build ^
> :info:build /opt/local/include/boost/parameter/name.hpp:110:53: note:
> expanded from macro 'BOOST_PARAMETER_BASIC_NAME'
> :info:build     BOOST_PARAMETER_NAME_OBJECT(tag_namespace::tag, name)
> :info:build                                                     ^
> :info:build /opt/local/include/boost/parameter/name.hpp:86:48: note:
> expanded from macro 'BOOST_PARAMETER_NAME_OBJECT'
> :info:build        ::boost::parameter::keyword<tag> const& name
> \
> :info:build                                                ^
> :info:build 2 warnings and 3 errors generated.
> :info:build make[2]: *** [gtf_to_sam.o] Error 1
> :info:build In file included from bundles.cpp:16:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build In file included from differential.cpp:15:
> :info:build ./differential.h:176:50: warning: unused variable 's2'
> [-Wunused-variable]
> :info:build             const vector<shared_ptr<Scaffold> >& s2 =
> bundles[i-1]->ref_scaffolds();
> :info:build                                                  ^
> :info:build assemble.cpp:188:21: warning: unused variable 'a_for_b'
> [-Wunused-variable]
> :info:build                 ReachGraph::ANode a_for_b = b_to_a[b_id];
> :info:build                                   ^
> :info:build assemble.cpp:123:17: warning: unused variable 'hits_for_node'
> [-Wunused-variable]
> :info:build         HitsForNodeMap hits_for_node = get(vertex_name, dag);
> :info:build                        ^
> :info:build assemble.cpp:262:21: warning: unused variable 'a_for_b'
> [-Wunused-variable]
> :info:build                 ReachGraph::ANode a_for_b =
> bp.nodeFromANodeId(a_id_for_b);
> :info:build                                   ^
> :info:build In file included from graph_optimize.cpp:13:
> :info:build In file included from ./graph_optimize.h:18:
> :info:build In file included from ./scaffold_graph.h:14:
> :info:build In file included from
> /opt/local/include/boost/graph/adjacency_list.hpp:45:
> :info:build In file included from
> /opt/local/include/boost/graph/named_graph.hpp:17:
> :info:build
> /opt/local/include/boost/multi_index/hashed_index.hpp:1254:10: error: no
> member named 'BOOST_FOREACH' in namespace 'boost'
> :info:build   boost::foreach::tag)
> :info:build   ~~~~~~~^
> :info:build ./common.h:26:25: note: expanded from macro 'foreach'
> :info:build #define foreach         BOOST_FOREACH
> :info:build                         ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 3 warnings and 3 errors generated.
> :info:build In file included from cuffdiff.cpp:33:
> :info:build In file included from
> /opt/local/include/boost/graph/adjacency_list.hpp:45:
> :info:build In file included from
> /opt/local/include/boost/graph/named_graph.hpp:17:
> :info:build
> /opt/local/include/boost/multi_index/hashed_index.hpp:1254:10: error: no
> member named 'BOOST_FOREACH' in namespace 'boost'
> :info:build   boost::foreach::tag)
> :info:build   ~~~~~~~^
> :info:build ./common.h:26:25: note: expanded from macro 'foreach'
> :info:build #define foreach         BOOST_FOREACH
> :info:build                         ^
> :info:build make[2]: *** [bundles.o] Error 1
> :info:build 2 warnings and 3 errors generated.
> :info:build make[2]: *** [filters.o] Error 1
> :info:build 2 warnings and 3 errors generated.
> :info:build 2 warnings and 3 errors generated.
> :info:build 2 warnings and 3 errors generated.
> :info:build make[2]: *** [biascorrection.o] Error 1
> :info:build make[2]: *** [clustering.o] Error 1
> :info:build make[2]: *** [abundances.o] Error 1
> :info:build In file included from cufflinks.cpp:25:
> :info:build In file included from ./clustering.h:38:
> :info:build In file included from ./abundances.h:21:
> :info:build ./scaffolds.h:247:34: warning: unused variable 'op'
> [-Wunused-variable]
> :info:build         foreach(AugmentedCuffOp& op, aug_ops)
> :info:build                                  ^
> :info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded
> from macro 'BOOST_FOREACH'
> :info:build         for (VAR = BOOST_FOREACH_DEREF(COL);
> !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue)
> = true)
> :info:build              ^
> :info:build differential.cpp:632:8: warning: unused variable
> 'multi_transcript_locus' [-Wunused-variable]
> :info:build                 bool multi_transcript_locus =
> samples[i]->transcripts.abundances().size() > 1;
> :info:build                      ^
> :info:build In file included from cufflinks.cpp:25:
> :info:build In file included from ./clustering.h:38:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:972:6: warning: unused variable 'result'
> [-Wunused-variable]
> :info:build  int result=-1;
> :info:build      ^
> :info:build 1 warning generated.
> :info:build In file included from cuffdiff.cpp:42:
> :info:build ./differential.h:176:50: warning: unused variable 's2'
> [-Wunused-variable]
> :info:build             const vector<shared_ptr<Scaffold> >& s2 =
> bundles[i-1]->ref_scaffolds();
> :info:build                                                  ^
> :info:build cuffdiff.cpp:805:35: warning: unused variable 's2' [-Wunused-
> variable]
> :info:build             const AbundanceGroup& s2 =  prev.transcripts;
> :info:build                                   ^
> :info:build In file included from assemble.cpp:48:
> :info:build In file included from ./assemble.h:26:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build In file included from differential.cpp:14:
> :info:build In file included from ./abundances.h:22:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build In file included from assemble.cpp:19:
> :info:build In file included from ./lemon/topology.h:22:
> :info:build In file included from ./lemon/dfs.h:26:
> :info:build In file included from ./lemon/list_graph.h:26:
> :info:build ./lemon/bits/base_extender.h:362:11: error: use of undeclared
> identifier 'aNode'
> :info:build                         return aNode(edge);
> :info:build                                ^
> :info:build                                this->
> :info:build assemble.cpp:258:28: note: in instantiation of member
> function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::source'
> requested here
> :info:build                 ReachGraph::ANode a = bp.source(i);
> :info:build                                          ^
> :info:build ./lemon/smart_graph.h:912:8: note: must qualify identifier to
> find this declaration in dependent base class
> :info:build                 Node aNode(const UEdge& edge) const {
> :info:build                      ^
> :info:build ./lemon/smart_graph.h:919:15: note: must qualify identifier
> to find this declaration in dependent base class
> :info:build                 static bool aNode(const Node& node) {
> :info:build                             ^
> :info:build In file included from assemble.cpp:19:
> :info:build In file included from ./lemon/topology.h:22:
> :info:build In file included from ./lemon/dfs.h:26:
> :info:build In file included from ./lemon/list_graph.h:26:
> :info:build ./lemon/bits/base_extender.h:365:11: error: use of undeclared
> identifier 'bNode'
> :info:build                         return bNode(edge);
> :info:build                                ^
> :info:build                                this->
> :info:build assemble.cpp:259:28: note: in instantiation of member
> function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::target'
> requested here
> :info:build                 ReachGraph::BNode b = bp.target(i);
> :info:build                                          ^
> :info:build ./lemon/smart_graph.h:915:8: note: must qualify identifier to
> find this declaration in dependent base class
> :info:build                 Node bNode(const UEdge& edge) const {
> :info:build                      ^
> :info:build ./lemon/smart_graph.h:923:15: note: must qualify identifier
> to find this declaration in dependent base class
> :info:build                 static bool bNode(const Node& node) {
> :info:build                             ^
> :info:build In file included from cuffdiff.cpp:27:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 3 warnings generated.
> :info:build graph_optimize.cpp:281:30: warning: unused variable 'e'
> [-Wunused-variable]
> :info:build
> ContainmentGraph::UEdge e = containment.addEdge(nj.first,
> :info:build
> ^
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 4 warnings and 4 errors generated.
> :info:build make[2]: *** [differential.o] Error 1
> :info:build 5 warnings and 5 errors generated.
> :info:build 4 warnings and 4 errors generated.
> :info:build make[2]: *** [assemble.o] Error 1
> :info:build In file included from graph_optimize.cpp:13:
> :info:build In file included from ./graph_optimize.h:17:
> :info:build In file included from ./bundles.h:21:
> :info:build In file included from ./gtf_tracking.h:12:
> :info:build In file included from ./gff.h:7:
> :info:build In file included from ./GFaSeqGet.h:4:
> :info:build ./GList.hh:507:4: error: use of undeclared identifier
> 'idxInsert'
> :info:build    idxInsert(result, *item);
> :info:build    ^
> :info:build    this->
> :info:build ./GList.hh:107:33: note: in instantiation of member function
> 'GArray<GSeg>::Add' requested here
> :info:build     int Add(OBJ& item) { return Add(&item); } //both will
> CREATE a new OBJ and COPY to it
> :info:build                                 ^
> :info:build ./gtf_tracking.h:314:12: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                                 uexons.Add(seg);
> :info:build                                        ^
> :info:build ./GList.hh:52:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void idxInsert(int idx, OBJ& item);
> :info:build          ^
> :info:build make[2]: *** [cuffdiff.o] Error 1
> :info:build ./GList.hh:772:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:650:10: note: in instantiation of member
> function 'GList<GffObj>::Add' requested here
> :info:build                 qmrnas.Add(loc.mrnas);
> :info:build                        ^
> :info:build ./GList.hh:171:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build ./GList.hh:537:5: error: use of undeclared identifier
> 'setCapacity'
> :info:build     setCapacity(this->fCapacity+list.fCount);
> :info:build     ^
> :info:build     this->
> :info:build ./gtf_tracking.h:653:11: note: in instantiation of member
> function 'GArray<GSeg>::Add' requested here
> :info:build                 qmexons.Add(loc.mexons);
> :info:build                         ^
> :info:build ./GList.hh:76:10: note: must qualify identifier to find this
> declaration in dependent base class
> :info:build     void setCapacity(int NewCapacity);
> :info:build          ^
> :info:build 48 warnings generated.
> :info:build 2 warnings and 4 errors generated.
> :info:build make[2]: *** [cufflinks.o] Error 1
> :info:build In file included from graph_optimize.cpp:16:
> :info:build In file included from ./lemon/topology.h:22:
> :info:build In file included from ./lemon/dfs.h:26:
> :info:build In file included from ./lemon/list_graph.h:26:
> :info:build ./lemon/bits/base_extender.h:362:11: error: use of undeclared
> identifier 'aNode'
> :info:build                         return aNode(edge);
> :info:build                                ^
> :info:build                                this->
> :info:build ./matching_merge.h:68:41: note: in instantiation of member
> function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::source'
> requested here
> :info:build                                 ReachGraph::ANode
> a_match_to_b = bp.source(matched_b_nodes[b]);
> :info:build
> ^
> :info:build ./matching_merge.h:87:5: note: in instantiation of function
> template specialization
> 'make_chains_from_matching<lemon::MaxBipartiteMatching<lemon::SmartBpUGraph>
> >' requested here
> :info:build     make_chains_from_matching(bp_graph, matcher, chains);
> :info:build     ^
> :info:build graph_optimize.cpp:304:9: note: in instantiation of function
> template specialization
> 'merge_from_matching<lemon::MaxBipartiteMatching<lemon::SmartBpUGraph> >'
> requested here
> :info:build         merge_from_matching(containment, matcher, scaffolds);
> :info:build         ^
> :info:build ./lemon/smart_graph.h:912:8: note: must qualify identifier to
> find this declaration in dependent base class
> :info:build                 Node aNode(const UEdge& edge) const {
> :info:build                      ^
> :info:build ./lemon/smart_graph.h:919:15: note: must qualify identifier
> to find this declaration in dependent base class
> :info:build                 static bool aNode(const Node& node) {
> :info:build                             ^
> :info:build 3 warnings and 5 errors generated.
> :info:build make[2]: *** [graph_optimize.o] Error 1
> :info:build make[2]: Leaving directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3/src'
> :info:build make[1]: *** [all-recursive] Error 1
> :info:build make[1]: Leaving directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
> :info:build make: *** [all] Error 2
> :info:build make: Leaving directory
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
> :info:build Command failed:  cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3"
> && /usr/bin/make -j24 -w all
> :info:build Exit code: 2
> :error:build org.macports.build for port cufflinks returned: command
> execution failed
> :debug:build Error code: CHILDSTATUS 13164 2
> :debug:build Backtrace: command execution failed
>     while executing
> "system -nice 0 $fullcmdstring"
>     ("eval" body line 1)
>     invoked from within
> "eval system $notty $nice \$fullcmdstring"
>     invoked from within
> "command_exec build"
>     (procedure "portbuild::build_main" line 8)
>     invoked from within
> "$procedure $targetname"
> :info:build Warning: targets not executed for cufflinks:
> org.macports.activate org.macports.build org.macports.destroot
> org.macports.install
> :notice:build Please see the log file for port cufflinks for details:
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log
>  -----

New description:

 installing cufflinks 0.9.3 failed. Here is the main.log file

--

Comment:

 This was not a clean attempt. Please try again
 {{{
 $ sudo port clean cufflinks
 $ sudo port selfupdate
 $ sudo port install cufflinks
 }}}
 and attach the log file if it fails.

 In the future please remember to Cc the maintainer, don't paste the log
 file in the description field and note that priority 'high' is reserved
 for MacPorts team members.

-- 
Ticket URL: <https://trac.macports.org/ticket/38885#comment:1>
MacPorts <http://www.macports.org/>
Ports system for OS X


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