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#38885 closed defect

failed install of cufflinks 0.9.3 — at Initial Version

Reported by:	malabady@…	Owned by:	macports-tickets@…
Priority:	Normal	Milestone:
Component:	ports	Version:	2.1.3
Keywords:		Cc:
Port:	cufflinks

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 ':info:build

' [-Wlogical-op-parentheses]

!(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 'BOOBOOSTSTPAFORRAMEACH' 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

-----

Change History (1)

Changed 11 years ago by malabady@…

Attachment:	cufflinks.main.log added

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