printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioconductor-keggraph-r31 2>&1 WARNING: your info file index has not been updated for 22 days. You should run 'fink selfupdate' to get the latest package descriptions. The package 'bioconductor-keggraph-r31' will be built without being installed. Reading build dependency for bioconductor-keggraph-r31-1.22.1-1... Reading dependency for bioconductor-keggraph-r31-1.22.1-1... Reading build conflict for bioconductor-keggraph-r31-1.22.1-1... The package 'r-base31-dev' will be installed. Reading dependency for r-base31-dev-3.1.1-2... Reading runtime dependency for r-base31-dev-3.1.1-2... The package 'libgettext8-dev' will be installed. Reading dependency for libgettext8-dev-0.18.3.1-2... Reading runtime dependency for libgettext8-dev-0.18.3.1-2... The package 'r-base31' will be installed. Reading dependency for r-base31-3.1.1-2... Reading runtime dependency for r-base31-3.1.1-2... The package 'bioconductor-graph-r31' will be installed. Reading dependency for bioconductor-graph-r31-1.42.0-1... Reading runtime dependency for bioconductor-graph-r31-1.42.0-1... The package 'cran-xml-r31' will be installed. Reading dependency for cran-xml-r31-3.98-1.1-1... Reading runtime dependency for cran-xml-r31-3.98-1.1-1... The package 'r-base31-shlibs' will be installed. Reading dependency for r-base31-shlibs-3.1.1-2... Reading runtime dependency for r-base31-shlibs-3.1.1-2... The package 'gettext-bin' will be installed. Reading dependency for gettext-bin-0.18.3.1-2... Reading runtime dependency for gettext-bin-0.18.3.1-2... The package 'flag-sort' will be installed. Reading dependency for flag-sort-0.5-1... Reading runtime dependency for flag-sort-0.5-1... The package 'bioconductor-biobase-r31' will be installed. Reading dependency for bioconductor-biobase-r31-2.24.0-1... Reading runtime dependency for bioconductor-biobase-r31-2.24.0-1... The package 'bioconductor-biocgenerics-r31' will be installed. Reading dependency for bioconductor-biocgenerics-r31-0.10.0-1... Reading runtime dependency for bioconductor-biocgenerics-r31-0.10.0-1... The package 'libxml2-shlibs' will be installed. Reading dependency for libxml2-shlibs-2.9.1-3... Reading runtime dependency for libxml2-shlibs-2.9.1-3... The package 'cairo-shlibs' will be installed. Reading dependency for cairo-shlibs-1.12.14-1... Reading runtime dependency for cairo-shlibs-1.12.14-1... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'glib2-shlibs' will be installed. Reading dependency for glib2-shlibs-2.22.4-8... Reading runtime dependency for glib2-shlibs-2.22.4-8... The package 'libicu48-shlibs' will be installed. Reading dependency for libicu48-shlibs-4.8.1.1-2... Reading runtime dependency for libicu48-shlibs-4.8.1.1-2... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'liblzma5-shlibs' will be installed. Reading dependency for liblzma5-shlibs-5.0.5-2... Reading runtime dependency for liblzma5-shlibs-5.0.5-2... The package 'libpng16-shlibs' will be installed. Reading dependency for libpng16-shlibs-1.6.12-1... Reading runtime dependency for libpng16-shlibs-1.6.12-1... The package 'libtiff5-shlibs' will be installed. Reading dependency for libtiff5-shlibs-4.0.3-5... Reading runtime dependency for libtiff5-shlibs-4.0.3-5... The package 'pango1-xft2-ft219-shlibs' will be installed. Reading dependency for pango1-xft2-ft219-shlibs-1.24.5-9... Reading runtime dependency for pango1-xft2-ft219-shlibs-1.24.5-9... The package 'libpcre1-shlibs' will be installed. Reading dependency for libpcre1-shlibs-8.35-1... Reading runtime dependency for libpcre1-shlibs-8.35-1... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The package 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-8.6.1-104... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... The package 'pixman-shlibs' will be installed. Reading dependency for pixman-shlibs-0.32.4-1... Reading runtime dependency for pixman-shlibs-0.32.4-1... The package 'xdg-base' will be installed. Reading dependency for xdg-base-0.8-2... Reading runtime dependency for xdg-base-0.8-2... The package 'libjbig-shlibs' will be installed. Reading dependency for libjbig-shlibs-2.0-1... Reading runtime dependency for libjbig-shlibs-2.0-1... The package 'libthai-shlibs' will be installed. Reading dependency for libthai-shlibs-0.1.20-1... Reading runtime dependency for libthai-shlibs-0.1.20-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'tcltk-shlibs' will be installed. Reading dependency for tcltk-shlibs-8.6.1-104... Reading runtime dependency for tcltk-shlibs-8.6.1-104... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The package 'expat1-shlibs' will be installed. Reading dependency for expat1-shlibs-2.1.0-1... Reading runtime dependency for expat1-shlibs-2.1.0-1... The package 'libdatrie1-shlibs' will be installed. Reading dependency for libdatrie1-shlibs-0.2.8-2... Reading runtime dependency for libdatrie1-shlibs-0.2.8-2... The package 'libthai' will be installed. Reading dependency for libthai-0.1.20-1... Reading runtime dependency for libthai-0.1.20-1... The following package will be rebuilt: bioconductor-keggraph-r31 The following 35 additional packages will be installed: bioconductor-biobase-r31 bioconductor-biocgenerics-r31 bioconductor-graph-r31 cairo-shlibs cran-xml-r31 expat1-shlibs flag-sort fontconfig-config fontconfig2-shlibs freetype219-shlibs gcc49-shlibs gettext-bin glib2-shlibs libdatrie1-shlibs libgettext8-dev libicu48-shlibs libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpcre1-shlibs libpng16-shlibs libthai libthai-shlibs libtiff5-shlibs libxml2-shlibs pango1-xft2-ft219-shlibs pixman-shlibs r-base31 r-base31-dev r-base31-shlibs readline6-shlibs tcltk tcltk-shlibs xdg-base xft2-shlibs Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb Selecting previously deselected package expat1-shlibs. (Reading database ... 4405 files and directories currently installed.) Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ... Setting up expat1-shlibs (2.1.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/flag-sort_0.5-1_darwin-x86_64.deb Selecting previously deselected package flag-sort. (Reading database ... 4410 files and directories currently installed.) Unpacking flag-sort (from .../flag-sort_0.5-1_darwin-x86_64.deb) ... Setting up flag-sort (0.5-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/freetype219-shlibs_2.4.12-1_darwin-x86_64.deb Selecting previously deselected package freetype219-shlibs. (Reading database ... 4411 files and directories currently installed.) Unpacking freetype219-shlibs (from .../freetype219-shlibs_2.4.12-1_darwin-x86_64.deb) ... Setting up freetype219-shlibs (2.4.12-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-shlibs. (Reading database ... 4422 files and directories currently installed.) Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... 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/libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb Selecting previously deselected package libdatrie1-shlibs. (Reading database ... 4467 files and directories currently installed.) Unpacking libdatrie1-shlibs (from .../libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb) ... Setting up libdatrie1-shlibs (0.2.8-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libgettext8-dev_0.18.3.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/base/gettext-bin_0.18.3.1-2_darwin-x86_64.deb Selecting previously deselected package libgettext8-dev. (Reading database ... 4474 files and directories currently installed.) Unpacking libgettext8-dev (from .../libgettext8-dev_0.18.3.1-2_darwin-x86_64.deb) ... Selecting previously deselected package gettext-bin. Unpacking gettext-bin (from .../gettext-bin_0.18.3.1-2_darwin-x86_64.deb) ... Setting up gettext-bin (0.18.3.1-2) ... Setting up libgettext8-dev (0.18.3.1-2) ... 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/libicu48-shlibs_4.8.1.1-2_darwin-x86_64.deb Selecting previously deselected package libicu48-shlibs. (Reading database ... 4568 files and directories currently installed.) Unpacking libicu48-shlibs (from .../libicu48-shlibs_4.8.1.1-2_darwin-x86_64.deb) ... Setting up libicu48-shlibs (4.8.1.1-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libjbig-shlibs_2.0-1_darwin-x86_64.deb Selecting previously deselected package libjbig-shlibs. (Reading database ... 4582 files and directories currently installed.) Unpacking libjbig-shlibs (from .../libjbig-shlibs_2.0-1_darwin-x86_64.deb) ... Setting up libjbig-shlibs (2.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libjpeg9-shlibs_9a-1_darwin-x86_64.deb Selecting previously deselected package libjpeg9-shlibs. (Reading database ... 4589 files and directories currently installed.) Unpacking libjpeg9-shlibs (from .../libjpeg9-shlibs_9a-1_darwin-x86_64.deb) ... Setting up libjpeg9-shlibs (9a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/utils/liblzma5-shlibs_5.0.5-2_darwin-x86_64.deb Selecting previously deselected package liblzma5-shlibs. (Reading database ... 4592 files and directories currently installed.) Unpacking liblzma5-shlibs (from .../liblzma5-shlibs_5.0.5-2_darwin-x86_64.deb) ... Setting up liblzma5-shlibs (5.0.5-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libpcre1-shlibs_8.35-1_darwin-x86_64.deb Selecting previously deselected package libpcre1-shlibs. (Reading database ... 4603 files and directories currently installed.) Unpacking libpcre1-shlibs (from .../libpcre1-shlibs_8.35-1_darwin-x86_64.deb) ... Setting up libpcre1-shlibs (8.35-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libpng16-shlibs_1.6.12-1_darwin-x86_64.deb Selecting previously deselected package libpng16-shlibs. (Reading database ... 4616 files and directories currently installed.) Unpacking libpng16-shlibs (from .../libpng16-shlibs_1.6.12-1_darwin-x86_64.deb) ... Setting up libpng16-shlibs (1.6.12-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libthai-shlibs_0.1.20-1_darwin-x86_64.deb /sw/fink/debs/libthai_0.1.20-1_darwin-x86_64.deb Selecting previously deselected package libthai-shlibs. (Reading database ... 4624 files and directories currently installed.) Unpacking libthai-shlibs (from .../libthai-shlibs_0.1.20-1_darwin-x86_64.deb) ... Selecting previously deselected package libthai. Unpacking libthai (from .../libthai_0.1.20-1_darwin-x86_64.deb) ... Setting up libthai (0.1.20-1) ... Setting up libthai-shlibs (0.1.20-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/libtiff5-shlibs_4.0.3-5_darwin-x86_64.deb Selecting previously deselected package libtiff5-shlibs. (Reading database ... 4639 files and directories currently installed.) Unpacking libtiff5-shlibs (from .../libtiff5-shlibs_4.0.3-5_darwin-x86_64.deb) ... Setting up libtiff5-shlibs (4.0.3-5) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libxml2-shlibs_2.9.1-3_darwin-x86_64.deb Selecting previously deselected package libxml2-shlibs. (Reading database ... 4644 files and directories currently installed.) Unpacking libxml2-shlibs (from .../libxml2-shlibs_2.9.1-3_darwin-x86_64.deb) ... Setting up libxml2-shlibs (2.9.1-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/pixman-shlibs_0.32.4-1_darwin-x86_64.deb Selecting previously deselected package pixman-shlibs. (Reading database ... 4648 files and directories currently installed.) Unpacking pixman-shlibs (from .../pixman-shlibs_0.32.4-1_darwin-x86_64.deb) ... Setting up pixman-shlibs (0.32.4-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6-shlibs. (Reading database ... 4652 files and directories currently installed.) Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/xdg-base_0.8-2_darwin-x86_64.deb Selecting previously deselected package xdg-base. (Reading database ... 4663 files and directories currently installed.) Unpacking xdg-base (from .../xdg-base_0.8-2_darwin-x86_64.deb) ... Setting up xdg-base (0.8-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig-config_2.10.2-1_darwin-x86_64.deb Selecting previously deselected package fontconfig2-shlibs. (Reading database ... 4665 files and directories currently installed.) Unpacking fontconfig2-shlibs (from .../fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.10.2-1_darwin-x86_64.deb) ... Setting up fontconfig-config (2.10.2-1) ... Setting up fontconfig2-shlibs (2.10.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/glib2-shlibs_2.22.4-8_darwin-x86_64.deb Selecting previously deselected package glib2-shlibs. (Reading database ... 4750 files and directories currently installed.) Unpacking glib2-shlibs (from .../glib2-shlibs_2.22.4-8_darwin-x86_64.deb) ... Setting up glib2-shlibs (2.22.4-8) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/xft2-shlibs_2.2.0-3_darwin-x86_64.deb Selecting previously deselected package xft2-shlibs. (Reading database ... 4969 files and directories currently installed.) Unpacking xft2-shlibs (from .../xft2-shlibs_2.2.0-3_darwin-x86_64.deb) ... Setting up xft2-shlibs (2.2.0-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/cairo-shlibs_1.12.14-1_darwin-x86_64.deb Selecting previously deselected package cairo-shlibs. (Reading database ... 4978 files and directories currently installed.) Unpacking cairo-shlibs (from .../cairo-shlibs_1.12.14-1_darwin-x86_64.deb) ... Setting up cairo-shlibs (1.12.14-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/gnome/pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb Selecting previously deselected package pango1-xft2-ft219-shlibs. (Reading database ... 4997 files and directories currently installed.) Unpacking pango1-xft2-ft219-shlibs (from .../pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb) ... Setting up pango1-xft2-ft219-shlibs (1.24.5-9) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/tcltk_8.6.1-104_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/tcltk-shlibs_8.6.1-104_darwin-x86_64.deb Selecting previously deselected package tcltk. (Reading database ... 5041 files and directories currently installed.) Unpacking tcltk (from .../tcltk_8.6.1-104_darwin-x86_64.deb) ... Selecting previously deselected package tcltk-shlibs. Unpacking tcltk-shlibs (from .../tcltk-shlibs_8.6.1-104_darwin-x86_64.deb) ... Setting up tcltk-shlibs (8.6.1-104) ... Setting up tcltk (8.6.1-104) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/r-base31_3.1.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base31-shlibs_3.1.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base31-dev_3.1.1-2_darwin-x86_64.deb Selecting previously deselected package r-base31. (Reading database ... 5517 files and directories currently installed.) Unpacking r-base31 (from .../r-base31_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31-shlibs. Unpacking r-base31-shlibs (from .../r-base31-shlibs_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31-dev. Unpacking r-base31-dev (from .../r-base31-dev_3.1.1-2_darwin-x86_64.deb) ... Setting up r-base31-shlibs (3.1.1-2) ... Setting up r-base31-dev (3.1.1-2) ... Setting up r-base31 (3.1.1-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-biocgenerics-r31_0.10.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-biocgenerics-r31. (Reading database ... 7484 files and directories currently installed.) Unpacking bioconductor-biocgenerics-r31 (from .../bioconductor-biocgenerics-r31_0.10.0-1_darwin-x86_64.deb) ... Setting up bioconductor-biocgenerics-r31 (0.10.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cran-xml-r31_3.98-1.1-1_darwin-x86_64.deb Selecting previously deselected package cran-xml-r31. (Reading database ... 7513 files and directories currently installed.) Unpacking cran-xml-r31 (from .../cran-xml-r31_3.98-1.1-1_darwin-x86_64.deb) ... Setting up cran-xml-r31 (3.98-1.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-biobase-r31_2.24.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-biobase-r31. (Reading database ... 7742 files and directories currently installed.) Unpacking bioconductor-biobase-r31 (from .../bioconductor-biobase-r31_2.24.0-1_darwin-x86_64.deb) ... Setting up bioconductor-biobase-r31 (2.24.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-graph-r31_1.42.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-graph-r31. (Reading database ... 7896 files and directories currently installed.) Unpacking bioconductor-graph-r31 (from .../bioconductor-graph-r31_1.42.0-1_darwin-x86_64.deb) ... Setting up bioconductor-graph-r31 (1.42.0-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioconductor-keggraph-r31-1.22.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioconductor-keggraph-r31-1.22.1-1' in `/sw/build.build/fink-buildlock-bioconductor-keggraph-r31-1.22.1-1_2014.08.16-08.32.24_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioconductor-keggraph-r31-1.22.1-1_2014.08.16-08.32.24_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioconductor-keggraph-r31-1.22.1-1. (Reading database ... 8003 files and directories currently installed.) Unpacking fink-buildlock-bioconductor-keggraph-r31-1.22.1-1 (from .../fink-buildlock-bioconductor-keggraph-r31-1.22.1-1_2014.08.16-08.32.24_darwin-x86_64.deb) ... Setting up fink-buildlock-bioconductor-keggraph-r31-1.22.1-1 (2014.08.16-08.32.24) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.N2o9T env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/KEGGgraph_1.22.1.tar.gz KEGGgraph/ChangeLog KEGGgraph/DESCRIPTION KEGGgraph/Makefile KEGGgraph/NAMESPACE KEGGgraph/NEWS KEGGgraph/R/ KEGGgraph/R/annotation.R KEGGgraph/R/graph.R KEGGgraph/R/kegg2graph-functions.R KEGGgraph/R/kgmlfile.R KEGGgraph/R/misc.R KEGGgraph/R/parse.R KEGGgraph/R/vis.R KEGGgraph/build/ KEGGgraph/build/vignette.rds KEGGgraph/data/ KEGGgraph/data/KEGGEdgeSubtype.csv KEGGgraph/data/KEGGEdgeType.csv KEGGgraph/data/KEGGNodeType.csv KEGGgraph/data/colorectalcancerSPIA.RData KEGGgraph/inst/ KEGGgraph/inst/CITATION KEGGgraph/inst/doc/ KEGGgraph/inst/doc/KEGGgraph.R KEGGgraph/inst/doc/KEGGgraph.Rnw KEGGgraph/inst/doc/KEGGgraph.pdf KEGGgraph/inst/doc/KEGGgraphApp.R KEGGgraph/inst/doc/KEGGgraphApp.Rnw KEGGgraph/inst/doc/KEGGgraphApp.pdf KEGGgraph/inst/extdata/ KEGGgraph/inst/extdata/hsa00020.xml KEGGgraph/inst/extdata/hsa04010.xml KEGGgraph/inst/extdata/hsa04012.xml KEGGgraph/inst/extdata/hsa04110.xml KEGGgraph/inst/extdata/hsa04115.xml KEGGgraph/inst/extdata/hsa04210.xml KEGGgraph/inst/extdata/hsa04310.xml KEGGgraph/inst/extdata/hsa04350.xml KEGGgraph/inst/extdata/hsa04370.xml KEGGgraph/inst/extdata/hsa04630.xml KEGGgraph/inst/extdata/hsa05210.xml KEGGgraph/inst/extdata/hsa05212.xml KEGGgraph/inst/extdata/kgml-ed-toy.xml KEGGgraph/inst/extdata/ko00051.xml KEGGgraph/inst/extdata/map00260.xml KEGGgraph/inst/unitTests/ KEGGgraph/inst/unitTests/test_KEGGgraph.R KEGGgraph/man/ KEGGgraph/man/KEGGEdge-class.Rd KEGGgraph/man/KEGGEdgeSubType-class.Rd KEGGgraph/man/KEGGEdgeSubtype.Rd KEGGgraph/man/KEGGGraphics-class.Rd KEGGgraph/man/KEGGGroup-class.Rd KEGGgraph/man/KEGGNode-class.Rd KEGGgraph/man/KEGGPathway-class.Rd KEGGgraph/man/KEGGPathwayInfo-class.Rd KEGGgraph/man/KEGGReaction-class.Rd KEGGgraph/man/KEGGpathway2Graph.Rd KEGGgraph/man/KEGGpathway2reactionGraph.Rd KEGGgraph/man/expandKEGGNode.Rd KEGGgraph/man/expandKEGGPathway.Rd KEGGgraph/man/getDisplayName-methods.Rd KEGGgraph/man/getEntryID-methods.Rd KEGGgraph/man/getKEGGID-methods.Rd KEGGgraph/man/getKEGGgeneLink-methods.Rd KEGGgraph/man/getKEGGnodeData.Rd KEGGgraph/man/getKGMLurl.Rd KEGGgraph/man/getName-methods.Rd KEGGgraph/man/getNamedElement.Rd KEGGgraph/man/getPathwayInfo-methods.Rd KEGGgraph/man/getReactions-methods.Rd KEGGgraph/man/getRgraphvizEdgeNames.Rd KEGGgraph/man/getSubtype-methods.Rd KEGGgraph/man/getTitle-methods.Rd KEGGgraph/man/getType-methods.Rd KEGGgraph/man/getValue-methods.Rd KEGGgraph/man/graphDensity.Rd KEGGgraph/man/isHomoList.Rd KEGGgraph/man/kgmlFileName2PathwayName.Rd KEGGgraph/man/mergeGraphs.Rd KEGGgraph/man/mergeKEGGgraphs.Rd KEGGgraph/man/neighborhood.Rd KEGGgraph/man/parseEntry.Rd KEGGgraph/man/parseGraphics.Rd KEGGgraph/man/parseKGML.Rd KEGGgraph/man/parseKGML2DataFrame.Rd KEGGgraph/man/parseKGML2Graph.Rd KEGGgraph/man/parseKGMLexpandMaps.Rd KEGGgraph/man/parsePathwayInfo.Rd KEGGgraph/man/parseReaction.Rd KEGGgraph/man/parseRelation.Rd KEGGgraph/man/parseSubType.Rd KEGGgraph/man/plotKEGGgraph.Rd KEGGgraph/man/pvalue2asterisk.Rd KEGGgraph/man/queryKEGGsubgraph.Rd KEGGgraph/man/randomSubGraph.Rd KEGGgraph/man/splitKEGGgroup.Rd KEGGgraph/man/subGraphByNodeType.Rd KEGGgraph/man/subKEGGgraph.Rd KEGGgraph/man/subtypeDisplay-methods.Rd KEGGgraph/man/top.Rd KEGGgraph/man/translateKEGGID2GeneID.Rd KEGGgraph/man/translateKEGGgraph.Rd KEGGgraph/tests/ KEGGgraph/tests/kegg2graph.R KEGGgraph/tests/testGraph.R KEGGgraph/vignettes/ KEGGgraph/vignettes/KEGGgraph.Rnw KEGGgraph/vignettes/KEGGgraphApp.Rnw sudo -u fink-bld [ENV] sh -c /tmp/fink.Iu9qX /tmp/fink.r4HZy #!/bin/bash -ev export TMPDIR=/sw/build.build/bioconductor-keggraph-r31-1.22.1-1/KEGGgraph/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R pushd .. /sw/build.build/bioconductor-keggraph-r31-1.22.1-1 /sw/build.build/bioconductor-keggraph-r31-1.22.1-1/KEGGgraph $BIN_R --verbose CMD build --no-build-vignettes KEGGgraph * checking for file 'KEGGgraph/DESCRIPTION' ... OK * preparing 'KEGGgraph': * checking DESCRIPTION meta-information ... OK * checking vignette meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a 'data/datalist' file should be added * re-saving tabular files * building 'KEGGgraph_1.22.1.tar.gz' /bin/rm -rf /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1 /bin/mkdir -p /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw /bin/mkdir -p /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.8IQve /tmp/fink.p5kf6 #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw/lib/R/3.1/site-library pushd /sw/build.build/bioconductor-keggraph-r31-1.22.1-1/KEGGgraph/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw/lib/R/3.1/site-library KEGGgraph /sw/build.build/bioconductor-keggraph-r31-1.22.1-1 /sw/build.build/bioconductor-keggraph-r31-1.22.1-1/KEGGgraph * installing *source* package 'KEGGgraph' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (KEGGgraph) sudo -u fink-bld [ENV] sh -c /tmp/fink.rnJm1 /bin/rm -f /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw/info/dir /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw/info/dir.old /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/sw/share/info/dir /sw/build.build/root-bioconductor-keggraph-r31-1.22.1-1/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-bioconductor-keggraph-r31-1.22.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `bioconductor-keggraph-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-keggraph-r31_1.22.1-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-keggraph-r31-1.22.1-1 (Reading database ... 8004 files and directories currently installed.) Removing fink-buildlock-bioconductor-keggraph-r31-1.22.1-1 ...