printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild pygr-py27 2>&1 The package 'pygr-py27' will be built without being installed. Reading build dependency for pygr-py27-0.8.2-1... Reading dependency for pygr-py27-0.8.2-1... Reading build conflict for pygr-py27-0.8.2-1... The package 'python27' will be installed. Reading dependency for python27-2.7.8-1... Reading runtime dependency for python27-2.7.8-1... The package 'python27-shlibs' will be installed. Reading dependency for python27-shlibs-2.7.8-1... Reading runtime dependency for python27-shlibs-2.7.8-1... The package 'blt-shlibs' will be installed. Reading dependency for blt-shlibs-2.4z-160... Reading runtime dependency for blt-shlibs-2.4z-160... The package 'db53-aes-shlibs' will be installed. Reading dependency for db53-aes-shlibs-5.3.21-2... Reading runtime dependency for db53-aes-shlibs-5.3.21-2... The package 'gdbm3-shlibs' will be installed. Reading dependency for gdbm3-shlibs-1.8.3-4... Reading runtime dependency for gdbm3-shlibs-1.8.3-4... The package 'libffi6-shlibs' will be installed. Reading dependency for libffi6-shlibs-3.1-1... Reading runtime dependency for libffi6-shlibs-3.1-1... The package 'libncursesw5-shlibs' will be installed. Reading dependency for libncursesw5-shlibs-5.9-20110507-1... Reading runtime dependency for libncursesw5-shlibs-5.9-20110507-1... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'sqlite3-shlibs' will be installed. Reading dependency for sqlite3-shlibs-3.8.3.1-1... Reading runtime dependency for sqlite3-shlibs-3.8.3.1-1... The following package will be rebuilt: pygr-py27 The following 9 additional packages will be installed: blt-shlibs db53-aes-shlibs gdbm3-shlibs libffi6-shlibs libncursesw5-shlibs openssl100-shlibs python27 python27-shlibs sqlite3-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/pygr-0.8.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 6 1519k 6 100k 0 0 84767 0 0:00:18 0:00:01 0:00:17 84833 23 1519k 23 364k 0 0 190k 0 0:00:07 0:00:01 0:00:06 189k 71 1519k 71 1092k 0 0 374k 0 0:00:04 0:00:02 0:00:02 374k 100 1519k 100 1519k 0 0 442k 0 0:00:03 0:00:03 --:--:-- 442k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/blt-shlibs_2.4z-160_darwin-x86_64.deb Selecting previously deselected package blt-shlibs. (Reading database ... 10808 files and directories currently installed.) Unpacking blt-shlibs (from .../blt-shlibs_2.4z-160_darwin-x86_64.deb) ... Setting up blt-shlibs (2.4z-160) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/crypto/db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb Selecting previously deselected package db53-aes-shlibs. (Reading database ... 10814 files and directories currently installed.) Unpacking db53-aes-shlibs (from .../db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb) ... Setting up db53-aes-shlibs (5.3.21-2) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb Selecting previously deselected package gdbm3-shlibs. (Reading database ... 10824 files and directories currently installed.) Unpacking gdbm3-shlibs (from .../gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb) ... Setting up gdbm3-shlibs (1.8.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libffi6-shlibs_3.1-1_darwin-x86_64.deb Selecting previously deselected package libffi6-shlibs. (Reading database ... 10832 files and directories currently installed.) Unpacking libffi6-shlibs (from .../libffi6-shlibs_3.1-1_darwin-x86_64.deb) ... Setting up libffi6-shlibs (3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncursesw5-shlibs. (Reading database ... 10833 files and directories currently installed.) Unpacking libncursesw5-shlibs (from .../libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncursesw5-shlibs (5.9-20110507-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb Selecting previously deselected package openssl100-shlibs. (Reading database ... 10844 files and directories currently installed.) Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ... Setting up openssl100-shlibs (1.0.1h-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/database/sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb Selecting previously deselected package sqlite3-shlibs. (Reading database ... 10865 files and directories currently installed.) Unpacking sqlite3-shlibs (from .../sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb) ... Setting up sqlite3-shlibs (3.8.3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/python27_2.7.8-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python27-shlibs_2.7.8-1_darwin-x86_64.deb Selecting previously deselected package python27. (Reading database ... 10869 files and directories currently installed.) Unpacking python27 (from .../python27_2.7.8-1_darwin-x86_64.deb) ... Selecting previously deselected package python27-shlibs. Unpacking python27-shlibs (from .../python27-shlibs_2.7.8-1_darwin-x86_64.deb) ... Setting up python27-shlibs (2.7.8-1) ... Setting up python27 (2.7.8-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-pygr-py27-0.8.2-1 /sw/build.build dpkg-deb: building package `fink-buildlock-pygr-py27-0.8.2-1' in `/sw/build.build/fink-buildlock-pygr-py27-0.8.2-1_2014.07.26-19.59.52_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-pygr-py27-0.8.2-1_2014.07.26-19.59.52_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-pygr-py27-0.8.2-1. (Reading database ... 18080 files and directories currently installed.) Unpacking fink-buildlock-pygr-py27-0.8.2-1 (from .../fink-buildlock-pygr-py27-0.8.2-1_2014.07.26-19.59.52_darwin-x86_64.deb) ... Setting up fink-buildlock-pygr-py27-0.8.2-1 (2014.07.26-19.59.52) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.7Y9bT env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/pygr-0.8.2.tar.gz pygr-0.8.2/ pygr-0.8.2/doc/ pygr-0.8.2/doc/rest/ pygr-0.8.2/doc/rest/guides/ pygr-0.8.2/doc/rest/guides/devguide.rst pygr-0.8.2/doc/rest/guides/libnclist.rst pygr-0.8.2/doc/rest/guides/testing.rst pygr-0.8.2/doc/rest/recipes/ pygr-0.8.2/doc/rest/recipes/alignment_recipes.rst pygr-0.8.2/doc/rest/reference/ pygr-0.8.2/doc/rest/reference/annotation.rst pygr-0.8.2/doc/rest/reference/blast.rst pygr-0.8.2/doc/rest/reference/classutil.rst pygr-0.8.2/doc/rest/reference/cnestedlist.rst pygr-0.8.2/doc/rest/reference/coordinator.rst pygr-0.8.2/doc/rest/reference/downloader.rst pygr-0.8.2/doc/rest/reference/mapping.rst pygr-0.8.2/doc/rest/reference/metabase.rst pygr-0.8.2/doc/rest/reference/seqdb.rst pygr-0.8.2/doc/rest/reference/sequence.rst pygr-0.8.2/doc/rest/reference/sequtil.rst pygr-0.8.2/doc/rest/reference/sqlgraph.rst pygr-0.8.2/doc/rest/reference/worldbase.rst pygr-0.8.2/doc/rest/static/ pygr-0.8.2/doc/rest/static/contents.png pygr-0.8.2/doc/rest/static/data-browser.png pygr-0.8.2/doc/rest/static/pygr-doc.css pygr-0.8.2/doc/rest/static/pygr-epydoc.css pygr-0.8.2/doc/rest/static/pygr-logo.gif pygr-0.8.2/doc/rest/templates/ pygr-0.8.2/doc/rest/templates/index.html pygr-0.8.2/doc/rest/templates/indexsidebar.html pygr-0.8.2/doc/rest/templates/layout.html pygr-0.8.2/doc/rest/templates/media.html pygr-0.8.2/doc/rest/tutorials/ pygr-0.8.2/doc/rest/tutorials/alignment.rst pygr-0.8.2/doc/rest/tutorials/annotating-yeast.rst pygr-0.8.2/doc/rest/tutorials/annotation.rst pygr-0.8.2/doc/rest/tutorials/annotation2.rst pygr-0.8.2/doc/rest/tutorials/compgenomics.rst pygr-0.8.2/doc/rest/tutorials/db.rst pygr-0.8.2/doc/rest/tutorials/db_basic.rst pygr-0.8.2/doc/rest/tutorials/develop.rst pygr-0.8.2/doc/rest/tutorials/gene.rst pygr-0.8.2/doc/rest/tutorials/graphquery.rst pygr-0.8.2/doc/rest/tutorials/sequence.rst pygr-0.8.2/doc/rest/tutorials/slice_pickle_obj.py pygr-0.8.2/doc/rest/tutorials/ucsc_ensembl.rst pygr-0.8.2/doc/rest/tutorials/worldbase.rst pygr-0.8.2/doc/rest/tutorials/worldbase2.rst pygr-0.8.2/doc/rest/tutorials/xmlrpc.rst pygr-0.8.2/doc/rest/conf.py pygr-0.8.2/doc/rest/contents.rst pygr-0.8.2/doc/rest/guidelist.rst pygr-0.8.2/doc/rest/sequences.rst pygr-0.8.2/doc/rest/team.rst pygr-0.8.2/doc/rest/whatsnew.rst pygr-0.8.2/doc/Makefile pygr-0.8.2/misc/ pygr-0.8.2/misc/debian/ pygr-0.8.2/misc/debian/changelog pygr-0.8.2/misc/debian/compat pygr-0.8.2/misc/debian/control pygr-0.8.2/misc/debian/copyright pygr-0.8.2/misc/debian/pycompat pygr-0.8.2/misc/debian/rules pygr-0.8.2/misc/debian/watch pygr-0.8.2/misc/fink/ pygr-0.8.2/misc/fink/pygr-doc.info pygr-0.8.2/misc/fink/pygr-py.info pygr-0.8.2/misc/portage/ pygr-0.8.2/misc/portage/pygr-9999.ebuild pygr-0.8.2/misc/portage/pygr-VER.ebuild pygr-0.8.2/misc/pygrrc.example pygr-0.8.2/pygr/ pygr-0.8.2/pygr/apps/ pygr-0.8.2/pygr/apps/__init__.py pygr-0.8.2/pygr/apps/catalog_downloads.py pygr-0.8.2/pygr/apps/leelabdb.py pygr-0.8.2/pygr/apps/maf2VSgraph.py pygr-0.8.2/pygr/apps/maf2nclist.c pygr-0.8.2/pygr/apps/maf2nclist.h pygr-0.8.2/pygr/apps/maf2nclist.py pygr-0.8.2/pygr/apps/seqref.py pygr-0.8.2/pygr/apps/splicegraph.py pygr-0.8.2/pygr/apps/ucsc_ensembl_annot.py pygr-0.8.2/pygr/Data.py pygr-0.8.2/pygr/Makefile pygr-0.8.2/pygr/__init__.py pygr-0.8.2/pygr/annotation.py pygr-0.8.2/pygr/blast.py pygr-0.8.2/pygr/cdict.c pygr-0.8.2/pygr/cdict.pxd pygr-0.8.2/pygr/cdict.pyx pygr-0.8.2/pygr/cgraph.c pygr-0.8.2/pygr/cgraph.h pygr-0.8.2/pygr/classutil.py pygr-0.8.2/pygr/cnestedlist.c pygr-0.8.2/pygr/cnestedlist.pxd pygr-0.8.2/pygr/cnestedlist.pyx pygr-0.8.2/pygr/coordinator.py pygr-0.8.2/pygr/dbfile.py pygr-0.8.2/pygr/default.h pygr-0.8.2/pygr/downloader.py pygr-0.8.2/pygr/graphquery.py pygr-0.8.2/pygr/intervaldb.c pygr-0.8.2/pygr/intervaldb.h pygr-0.8.2/pygr/logger.py pygr-0.8.2/pygr/mapping.py pygr-0.8.2/pygr/metabase.py pygr-0.8.2/pygr/nlmsa_utils.py pygr-0.8.2/pygr/parse_blast.py pygr-0.8.2/pygr/schema.py pygr-0.8.2/pygr/seqdb.py pygr-0.8.2/pygr/seqfmt.c pygr-0.8.2/pygr/seqfmt.pyx pygr-0.8.2/pygr/sequence.py pygr-0.8.2/pygr/sequtil.py pygr-0.8.2/pygr/sqlgraph.py pygr-0.8.2/pygr/translationDB.py pygr-0.8.2/pygr/xnestedlist.py pygr-0.8.2/pygr.egg-info/ pygr-0.8.2/pygr.egg-info/PKG-INFO pygr-0.8.2/pygr.egg-info/SOURCES.txt pygr-0.8.2/pygr.egg-info/dependency_links.txt pygr-0.8.2/pygr.egg-info/top_level.txt pygr-0.8.2/tests/ pygr-0.8.2/tests/data/ pygr-0.8.2/tests/data/alignments.fa pygr-0.8.2/tests/data/alignments.fa.pureseq pygr-0.8.2/tests/data/alignments.fa.seqlen pygr-0.8.2/tests/data/bad_tblastn.txt pygr-0.8.2/tests/data/blastp_output.txt pygr-0.8.2/tests/data/blastx_output.txt pygr-0.8.2/tests/data/dnaseq.fasta pygr-0.8.2/tests/data/dnaseq.fasta.pureseq pygr-0.8.2/tests/data/dnaseq.fasta.seqlen pygr-0.8.2/tests/data/exontuples.txt pygr-0.8.2/tests/data/funnyseq.fasta pygr-0.8.2/tests/data/funnyseq.fasta.pureseq pygr-0.8.2/tests/data/funnyseq.fasta.seqlen pygr-0.8.2/tests/data/gapping.fa pygr-0.8.2/tests/data/gapping.fa.nhr pygr-0.8.2/tests/data/gapping.fa.nin pygr-0.8.2/tests/data/gapping.fa.nsd pygr-0.8.2/tests/data/gapping.fa.nsi pygr-0.8.2/tests/data/gapping.fa.nsq pygr-0.8.2/tests/data/gapping.fa.pureseq pygr-0.8.2/tests/data/gapping.fa.seqlen pygr-0.8.2/tests/data/hbb1_mouse.fa pygr-0.8.2/tests/data/hbb1_mouse.fa.nhr pygr-0.8.2/tests/data/hbb1_mouse.fa.nin pygr-0.8.2/tests/data/hbb1_mouse.fa.nnd pygr-0.8.2/tests/data/hbb1_mouse.fa.nni pygr-0.8.2/tests/data/hbb1_mouse.fa.nsd pygr-0.8.2/tests/data/hbb1_mouse.fa.nsi pygr-0.8.2/tests/data/hbb1_mouse.fa.nsq pygr-0.8.2/tests/data/hbb1_mouse.fa.pureseq pygr-0.8.2/tests/data/hbb1_mouse.fa.seqlen pygr-0.8.2/tests/data/hbb1_mouse_rc.fa pygr-0.8.2/tests/data/hbb1_mouse_rc.fa.pureseq pygr-0.8.2/tests/data/hbb1_mouse_rc.fa.seqlen pygr-0.8.2/tests/data/multiblast_long_correct.txt pygr-0.8.2/tests/data/multiblast_long_output.txt pygr-0.8.2/tests/data/multiblast_output.txt pygr-0.8.2/tests/data/partial-yeast.fasta pygr-0.8.2/tests/data/prefixUnionDict-1.txt pygr-0.8.2/tests/data/prefixUnionDict-2.txt pygr-0.8.2/tests/data/prefixUnionDict-3.txt pygr-0.8.2/tests/data/sp_all_hbb pygr-0.8.2/tests/data/sp_all_hbb.phr pygr-0.8.2/tests/data/sp_all_hbb.pureseq pygr-0.8.2/tests/data/sp_all_hbb.seqlen pygr-0.8.2/tests/data/sp_hbb1 pygr-0.8.2/tests/data/sp_hbb1.phr pygr-0.8.2/tests/data/sp_hbb1.pin pygr-0.8.2/tests/data/sp_hbb1.psd pygr-0.8.2/tests/data/sp_hbb1.psi pygr-0.8.2/tests/data/sp_hbb1.psq pygr-0.8.2/tests/data/sp_hbb1.pureseq pygr-0.8.2/tests/data/sp_hbb1.seqlen pygr-0.8.2/tests/data/tblastn_output.txt pygr-0.8.2/tests/data/test.gz pygr-0.8.2/tests/data/test.zip pygr-0.8.2/tests/testlib/ pygr-0.8.2/tests/testlib/__init__.py pygr-0.8.2/tests/testlib/megatest_utils.py pygr-0.8.2/tests/testlib/pathfix.py pygr-0.8.2/tests/testlib/pygrdata_server.py pygr-0.8.2/tests/testlib/testoptions.py pygr-0.8.2/tests/testlib/testutil.py pygr-0.8.2/tests/testlib/unittest_extensions.py pygr-0.8.2/tests/tools/ pygr-0.8.2/tests/tools/run_megatests pygr-0.8.2/tests/tools/send_megatest_email.py pygr-0.8.2/tests/COMMENTS pygr-0.8.2/tests/README.txt pygr-0.8.2/tests/annotation_dm2_megatest.py pygr-0.8.2/tests/annotation_hg18_megatest.py pygr-0.8.2/tests/annotation_test.py pygr-0.8.2/tests/apps_ucscensembl_test.py pygr-0.8.2/tests/blast_test.py pygr-0.8.2/tests/doctests_test.py pygr-0.8.2/tests/downloadNLMSA_megatest.py pygr-0.8.2/tests/graph_test.py pygr-0.8.2/tests/metabase_test.py pygr-0.8.2/tests/nlmsa_dm2_megatest.py pygr-0.8.2/tests/nlmsa_hg18_megatest.py pygr-0.8.2/tests/nlmsa_test.py pygr-0.8.2/tests/pairwise_hg18_megatest.py pygr-0.8.2/tests/pygrdata_test.py pygr-0.8.2/tests/restartIterator_megatest.py pygr-0.8.2/tests/runtest.py pygr-0.8.2/tests/seqdb_test.py pygr-0.8.2/tests/sequence_test.py pygr-0.8.2/tests/someseqs.csv pygr-0.8.2/tests/sqlsequence_test.py pygr-0.8.2/tests/sqltable_test.py pygr-0.8.2/tests/translationDB_test.py pygr-0.8.2/tests/worldbase_test.py pygr-0.8.2/LICENSE.txt pygr-0.8.2/MANIFEST.in pygr-0.8.2/README.txt pygr-0.8.2/setup.py pygr-0.8.2/PKG-INFO pygr-0.8.2/setup.cfg sudo -u fink-bld [ENV] sh -c /tmp/fink.dUxir /sw/bin/python2.7 setup.py build Setuptools not imported, falling back to distutils running build running build_py creating build creating build/lib.macosx-10.9-x86_64-2.7 creating build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/annotation.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/blast.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/classutil.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/coordinator.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/Data.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/dbfile.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/downloader.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/graphquery.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/logger.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/mapping.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/metabase.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/nlmsa_utils.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/parse_blast.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/schema.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/seqdb.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/sequence.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/sequtil.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/sqlgraph.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/translationDB.py -> build/lib.macosx-10.9-x86_64-2.7/pygr copying pygr/xnestedlist.py -> build/lib.macosx-10.9-x86_64-2.7/pygr creating build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/catalog_downloads.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/leelabdb.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/maf2nclist.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/maf2VSgraph.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/seqref.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/splicegraph.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps copying pygr/apps/ucsc_ensembl_annot.py -> build/lib.macosx-10.9-x86_64-2.7/pygr/apps running build_ext building 'pygr.seqfmt' extension creating build/temp.macosx-10.9-x86_64-2.7 creating build/temp.macosx-10.9-x86_64-2.7/pygr gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/seqfmt.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/seqfmt.o gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pygr/seqfmt.o -L/sw/lib -o build/lib.macosx-10.9-x86_64-2.7/pygr/seqfmt.so building 'pygr.cdict' extension gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/cgraph.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/cgraph.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/cdict.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/cdict.o gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pygr/cgraph.o build/temp.macosx-10.9-x86_64-2.7/pygr/cdict.o -L/sw/lib -o build/lib.macosx-10.9-x86_64-2.7/pygr/cdict.so building 'pygr.cnestedlist' extension creating build/temp.macosx-10.9-x86_64-2.7/pygr/apps gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/intervaldb.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/intervaldb.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/cnestedlist.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/cnestedlist.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pygr/apps/maf2nclist.c -o build/temp.macosx-10.9-x86_64-2.7/pygr/apps/maf2nclist.o pygr/apps/maf2nclist.c:56:19: warning: passing 'unsigned char [32768]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] while ((p=fgets(tmp,32767,ifile))) { ^~~ /usr/include/stdio.h:236:30: note: passing argument to parameter here char *fgets(char * __restrict, int, FILE *); ^ pygr/apps/maf2nclist.c:57:14: warning: passing 'unsigned char [32768]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] l=strlen(tmp); ^~~ /usr/include/string.h:82:28: note: passing argument to parameter here size_t strlen(const char *); ^ pygr/apps/maf2nclist.c:60:16: warning: passing 'unsigned char [32768]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] if (7==sscanf(tmp,"%2s %63s %d %d %2s %d %s",prefix,seqName,&seqStart,&junk, ^~~ /usr/include/stdio.h:268:36: note: passing argument to parameter here int sscanf(const char * __restrict, const char * __restrict, ...) __scanflike(2, 3); ^ pygr/apps/maf2nclist.c:85:23: warning: passing 'unsigned char [32768]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] if (1 != sscanf(tmp, "%s", seq)) ^~~ /usr/include/stdio.h:268:36: note: passing argument to parameter here int sscanf(const char * __restrict, const char * __restrict, ...) __scanflike(2, 3); ^ pygr/apps/maf2nclist.c:135:19: warning: passing 'unsigned char [32768]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] while ((p=fgets(tmp,32767,ifile))) { ^~~ /usr/include/stdio.h:236:30: note: passing argument to parameter here char *fgets(char * __restrict, int, FILE *); ^ pygr/apps/maf2nclist.c:137:21: warning: passing 'unsigned char [32768]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] if (9==sscanf(tmp,"%d %63s %d %d %63s %d %d %2s %d",&junk,srcChr,&srcStart,&srcEnd, ^~~ /usr/include/stdio.h:268:36: note: passing argument to parameter here int sscanf(const char * __restrict, const char * __restrict, ...) __scanflike(2, 3); ^ pygr/apps/maf2nclist.c:132:7: warning: unused variable 'srcLength' [-Wunused-variable] int srcLength, destLength; ^ 7 warnings generated. gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pygr/intervaldb.o build/temp.macosx-10.9-x86_64-2.7/pygr/cnestedlist.o build/temp.macosx-10.9-x86_64-2.7/pygr/apps/maf2nclist.o -L/sw/lib -o build/lib.macosx-10.9-x86_64-2.7/pygr/cnestedlist.so /bin/rm -rf /sw/build.build/root-pygr-py27-0.8.2-1 /bin/mkdir -p /sw/build.build/root-pygr-py27-0.8.2-1/sw /bin/mkdir -p /sw/build.build/root-pygr-py27-0.8.2-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-pygr-py27-0.8.2-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.elnAT /sw/bin/python2.7 setup.py install -O1 --root /sw/build.build/root-pygr-py27-0.8.2-1 Setuptools not imported, falling back to distutils running install running build running build_py running build_ext running install_lib creating /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib creating /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7 creating /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages creating /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/__init__.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/annotation.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr creating /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/__init__.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/catalog_downloads.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/leelabdb.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/maf2nclist.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/maf2VSgraph.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/seqref.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/splicegraph.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/apps/ucsc_ensembl_annot.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps copying build/lib.macosx-10.9-x86_64-2.7/pygr/blast.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/cdict.so -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/classutil.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/cnestedlist.so -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/coordinator.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/Data.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/dbfile.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/downloader.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/graphquery.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/logger.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/mapping.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/metabase.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/nlmsa_utils.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/parse_blast.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/schema.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/seqdb.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/seqfmt.so -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/sequence.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/sequtil.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/sqlgraph.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/translationDB.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr copying build/lib.macosx-10.9-x86_64-2.7/pygr/xnestedlist.py -> /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/annotation.py to annotation.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/catalog_downloads.py to catalog_downloads.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/leelabdb.py to leelabdb.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/maf2nclist.py to maf2nclist.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/maf2VSgraph.py to maf2VSgraph.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/seqref.py to seqref.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/splicegraph.py to splicegraph.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/apps/ucsc_ensembl_annot.py to ucsc_ensembl_annot.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/blast.py to blast.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/classutil.py to classutil.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/coordinator.py to coordinator.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/Data.py to Data.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/dbfile.py to dbfile.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/downloader.py to downloader.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/graphquery.py to graphquery.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/logger.py to logger.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/mapping.py to mapping.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/metabase.py to metabase.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/nlmsa_utils.py to nlmsa_utils.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/parse_blast.py to parse_blast.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/schema.py to schema.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/seqdb.py to seqdb.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/sequence.py to sequence.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/sequtil.py to sequtil.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/sqlgraph.py to sqlgraph.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/translationDB.py to translationDB.pyc byte-compiling /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr/xnestedlist.py to xnestedlist.pyc writing byte-compilation script '/private/tmp/tmpplixla.py' /sw/bin/python2.7 -O /private/tmp/tmpplixla.py removing /private/tmp/tmpplixla.py running install_egg_info Writing /sw/build.build/root-pygr-py27-0.8.2-1/sw/lib/python2.7/site-packages/pygr-0.8.2-py2.7.egg-info sudo -u fink-bld [ENV] sh -c /tmp/fink.9D7kb /usr/bin/install -d -m 700 /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/doc/pygr-py27 /bin/cp -r README.txt /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/doc/pygr-py27/ /bin/cp -r LICENSE.txt /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/doc/pygr-py27/ /bin/cp -r misc/pygrrc.example /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/doc/pygr-py27/ /bin/chmod -R go=u-w /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/doc/pygr-py27 /bin/rm -f /sw/build.build/root-pygr-py27-0.8.2-1/sw/info/dir /sw/build.build/root-pygr-py27-0.8.2-1/sw/info/dir.old /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/info/dir /sw/build.build/root-pygr-py27-0.8.2-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-pygr-py27-0.8.2-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `pygr-py27' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/pygr-py27_0.8.2-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-pygr-py27-0.8.2-1 (Reading database ... 18081 files and directories currently installed.) Removing fink-buildlock-pygr-py27-0.8.2-1 ...