printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioconductor-graph-r30 2>&1 The package 'bioconductor-graph-r30' will be built without being installed. Reading build dependency for bioconductor-graph-r30-1.42.0-1... Reading dependency for bioconductor-graph-r30-1.42.0-1... Reading build conflict for bioconductor-graph-r30-1.42.0-1... The package 'r-base30-dev' will be installed. Reading dependency for r-base30-dev-3.0.3-8... Reading runtime dependency for r-base30-dev-3.0.3-8... The package 'r-base30' will be installed. Reading dependency for r-base30-3.0.3-8... Reading runtime dependency for r-base30-3.0.3-8... The package 'bioconductor-biobase-r30' will be installed. Reading dependency for bioconductor-biobase-r30-2.22.0-1... Reading runtime dependency for bioconductor-biobase-r30-2.22.0-1... The package 'bioconductor-biocgenerics-r30' will be installed. Reading dependency for bioconductor-biocgenerics-r30-0.10.0-1... Reading runtime dependency for bioconductor-biocgenerics-r30-0.10.0-1... The package 'r-base30-shlibs' will be installed. Reading dependency for r-base30-shlibs-3.0.3-8... Reading runtime dependency for r-base30-shlibs-3.0.3-8... The following package will be rebuilt: bioconductor-graph-r30 The following 5 additional packages will be installed: bioconductor-biobase-r30 bioconductor-biocgenerics-r30 r-base30 r-base30-dev r-base30-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/graph_1.42.0.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 19 936k 19 182k 0 0 261k 0 0:00:03 --:--:-- 0:00:03 261k 100 936k 100 936k 0 0 611k 0 0:00:01 0:00:01 --:--:-- 611k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/r-base30_3.0.3-8_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base30-shlibs_3.0.3-8_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base30-dev_3.0.3-8_darwin-x86_64.deb Selecting previously deselected package r-base30. (Reading database ... 7371 files and directories currently installed.) Unpacking r-base30 (from .../r-base30_3.0.3-8_darwin-x86_64.deb) ... Selecting previously deselected package r-base30-shlibs. Unpacking r-base30-shlibs (from .../r-base30-shlibs_3.0.3-8_darwin-x86_64.deb) ... Selecting previously deselected package r-base30-dev. dpkg: considering removing r-base31-dev in favour of r-base30-dev ... dpkg: yes, will remove r-base31-dev in favour of r-base30-dev. Unpacking r-base30-dev (from .../r-base30-dev_3.0.3-8_darwin-x86_64.deb) ... Setting up r-base30-shlibs (3.0.3-8) ... Setting up r-base30-dev (3.0.3-8) ... Setting up r-base30 (3.0.3-8) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-biocgenerics-r30_0.10.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-biocgenerics-r30. (Reading database ... 9300 files and directories currently installed.) Unpacking bioconductor-biocgenerics-r30 (from .../bioconductor-biocgenerics-r30_0.10.0-1_darwin-x86_64.deb) ... Setting up bioconductor-biocgenerics-r30 (0.10.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-biobase-r30_2.22.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-biobase-r30. (Reading database ... 9329 files and directories currently installed.) Unpacking bioconductor-biobase-r30 (from .../bioconductor-biobase-r30_2.22.0-1_darwin-x86_64.deb) ... Setting up bioconductor-biobase-r30 (2.22.0-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioconductor-graph-r30-1.42.0-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioconductor-graph-r30-1.42.0-1' in `/sw/build.build/fink-buildlock-bioconductor-graph-r30-1.42.0-1_2014.07.28-02.24.33_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioconductor-graph-r30-1.42.0-1_2014.07.28-02.24.33_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioconductor-graph-r30-1.42.0-1. (Reading database ... 9485 files and directories currently installed.) Unpacking fink-buildlock-bioconductor-graph-r30-1.42.0-1 (from .../fink-buildlock-bioconductor-graph-r30-1.42.0-1_2014.07.28-02.24.33_darwin-x86_64.deb) ... Setting up fink-buildlock-bioconductor-graph-r30-1.42.0-1 (2014.07.28-02.24.33) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.0Rx8W env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/graph_1.42.0.tar.gz graph/DESCRIPTION graph/NAMESPACE graph/R/ graph/R/AllClasses.R graph/R/AllGenerics.R graph/R/GXLformals.R graph/R/MultiGraph.R graph/R/NELhandler.R graph/R/TODOT.R graph/R/attrData.R graph/R/bitarray.R graph/R/buildDepGraph.R graph/R/clustergraph.R graph/R/edgefunctions.R graph/R/graph-constructors.R graph/R/graphNEL.R graph/R/graphfunctions.R graph/R/gxlReader.R graph/R/mat2graph.R graph/R/methods-graph.R graph/R/methods-graphAM.R graph/R/methods-graphBAM.R graph/R/methods-multiGraph.R graph/R/nodes-methods.R graph/R/random.R graph/R/reverseEdgeDirections.R graph/R/settings.R graph/R/standardLabeling.R graph/R/test_graph_package.R graph/R/write.tlp.R graph/R/zzz.R graph/TODO graph/build/ graph/build/vignette.rds graph/data/ graph/data/MAPKsig.rda graph/data/apopGraph.rda graph/data/biocRepos.rda graph/data/defunctGraph.rda graph/data/esetsFemale.rda graph/data/esetsMale.rda graph/data/graphExamples.rda graph/data/integrinMediatedCellAdhesion.rda graph/data/pancrCaIni.rda graph/inst/ graph/inst/GXL/ graph/inst/GXL/attributesExample.gxl graph/inst/GXL/c2.gxl graph/inst/GXL/complexExample.gxl graph/inst/GXL/createGraphExamples.R graph/inst/GXL/graphExample-01.gxl.gz graph/inst/GXL/graphExample-02.gxl.gz graph/inst/GXL/graphExample-03.gxl.gz graph/inst/GXL/graphExample-04.gxl.gz graph/inst/GXL/graphExample-05.gxl.gz graph/inst/GXL/graphExample-06.gxl.gz graph/inst/GXL/graphExample-07.gxl.gz graph/inst/GXL/graphExample-08.gxl.gz graph/inst/GXL/graphExample-09.gxl.gz graph/inst/GXL/graphExample-10.gxl.gz graph/inst/GXL/graphExample-11.gxl.gz graph/inst/GXL/graphExample-12.gxl.gz graph/inst/GXL/graphExample-13.gxl.gz graph/inst/GXL/graphExample-14.gxl.gz graph/inst/GXL/graphExample-15.gxl.gz graph/inst/GXL/graphExample-16.gxl.gz graph/inst/GXL/graphExample-17.gxl.gz graph/inst/GXL/graphExample-18.gxl.gz graph/inst/GXL/gxl-1.0.1.dtd graph/inst/GXL/kmstEx.gxl graph/inst/GXL/outOfOrderExample.gxl graph/inst/GXL/simplExample.gxl.www graph/inst/GXL/simpleExample.gxl graph/inst/Scripts/ graph/inst/Scripts/Graph.R graph/inst/Scripts/distGraph.R graph/inst/Scripts/multigraph.R graph/inst/Scripts/pTreetest.R graph/inst/Scripts/testintersection.R graph/inst/doc/ graph/inst/doc/GraphClass.R graph/inst/doc/GraphClass.Rnw graph/inst/doc/GraphClass.pdf graph/inst/doc/MultiGraphClass.R graph/inst/doc/MultiGraphClass.Rnw graph/inst/doc/MultiGraphClass.pdf graph/inst/doc/clusterGraph.R graph/inst/doc/clusterGraph.Rnw graph/inst/doc/clusterGraph.pdf graph/inst/doc/graph.R graph/inst/doc/graph.Rnw graph/inst/doc/graph.pdf graph/inst/doc/graphAttributes.R graph/inst/doc/graphAttributes.Rnw graph/inst/doc/graphAttributes.pdf graph/inst/perf/ graph/inst/perf/Makefile graph/inst/perf/bgt.R graph/inst/perf/graphperf.Rnw graph/inst/perf/multigraphs.Rnw graph/inst/unitTests/ graph/inst/unitTests/MultiGraph_test.R graph/inst/unitTests/attrData_test.R graph/inst/unitTests/clusterGraph_test.R graph/inst/unitTests/degree_test.R graph/inst/unitTests/edgeWeights_test.R graph/inst/unitTests/graphAM_test.R graph/inst/unitTests/graphBAM_test.R graph/inst/unitTests/graphNEL_test.R graph/inst/unitTests/gxl_test.R graph/inst/unitTests/leaves_test.R graph/inst/unitTests/nodeAndEdgeData_test.R graph/inst/unitTests/setbit_test.R graph/inst/unitTests/simple_sparse_test.R graph/man/ graph/man/DFS.Rd graph/man/IMCA.Rd graph/man/MAPKsig.Rd graph/man/MultiGraph-class.Rd graph/man/acc-methods.Rd graph/man/addEdge.Rd graph/man/addNode.Rd graph/man/adj-methods.Rd graph/man/apoptosisGraph.Rd graph/man/attrData-class.Rd graph/man/attrDataItem-methods.Rd graph/man/attrDefaults-methods.Rd graph/man/aveNumEdges.Rd graph/man/biocRepos.Rd graph/man/boundary.Rd graph/man/calcProb.Rd graph/man/calcSumProb.Rd graph/man/clearNode.Rd graph/man/clusterGraph-class.Rd graph/man/clusteringCoefficient-methods.Rd graph/man/combineNodes.Rd graph/man/defunct.Rd graph/man/distGraph-class.Rd graph/man/duplicatedEdges.Rd graph/man/edgeData-methods.Rd graph/man/edgeDataDefaults-methods.Rd graph/man/edgeMatrix.Rd graph/man/edgeSets.Rd graph/man/edgeWeights.Rd graph/man/fromGXL-methods.Rd graph/man/graph-class.Rd graph/man/graph2SparseM.Rd graph/man/graphAM-class.Rd graph/man/graphBAM-class.Rd graph/man/graphExamples.Rd graph/man/graphNEL-class.Rd graph/man/inEdges.Rd graph/man/internal.Rd graph/man/isAdjacent-methods.Rd graph/man/isDirected-methods.Rd graph/man/leaves.Rd graph/man/listEdges.Rd graph/man/matrix2Graph.Rd graph/man/mostEdges.Rd graph/man/multigraph.Rd graph/man/nodeData-methods.Rd graph/man/nodeDataDefaults-methods.Rd graph/man/numNoEdges.Rd graph/man/pancrCaIni.Rd graph/man/randomEGraph.Rd graph/man/randomGraph.Rd graph/man/randomNodeGraph.Rd graph/man/removeEdge.Rd graph/man/removeNode.Rd graph/man/renderInfo-class.Rd graph/man/reverseEdgeDirections.Rd graph/man/settings.Rd graph/man/simpleEdge-class.Rd graph/man/standardLabeling.Rd graph/man/subGraph.Rd graph/man/toDotR-methods.Rd graph/man/ugraph.Rd graph/man/validGraph.Rd graph/man/write.tlp.Rd graph/src/ graph/src/Makevars graph/src/graph.c graph/tests/ graph/tests/graph_unit_tests.R graph/vignettes/ graph/vignettes/GraphClass.Rnw graph/vignettes/MultiGraphClass.Rnw graph/vignettes/clusterGraph.Rnw graph/vignettes/graph.Rnw graph/vignettes/graphAttributes.Rnw sudo -u fink-bld [ENV] sh -c /tmp/fink.Km3j6 /tmp/fink.UsqT_ #!/bin/bash -ev export TMPDIR=/sw/build.build/bioconductor-graph-r30-1.42.0-1/graph/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/bioconductor-graph-r30-1.42.0-1 /sw/build.build/bioconductor-graph-r30-1.42.0-1/graph $BIN_R --verbose CMD build --no-build-vignettes graph WARNING: ignoring environment value of R_HOME * checking for file 'graph/DESCRIPTION' ... OK * preparing 'graph': * checking DESCRIPTION meta-information ... OK * cleaning src * 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 * building 'graph_1.42.0.tar.gz' /bin/rm -rf /sw/build.build/root-bioconductor-graph-r30-1.42.0-1 /bin/mkdir -p /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw /bin/mkdir -p /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-graph-r30-1.42.0-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.qrs6J /tmp/fink.QlWuI #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/lib/R/3.0/site-library pushd /sw/build.build/bioconductor-graph-r30-1.42.0-1/graph/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/lib/R/3.0/site-library graph /sw/build.build/bioconductor-graph-r30-1.42.0-1 /sw/build.build/bioconductor-graph-r30-1.42.0-1/graph WARNING: ignoring environment value of R_HOME * installing *source* package 'graph' ... ** libs flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c graph.c -o graph.o flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o graph.dylib graph.o -L/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation mv graph.dylib BioC_graph.dylib installing to /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/lib/R/3.0/site-library/graph/libs ** 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 (graph) install_name_tool -id /sw/lib/R/3.0/site-library/graph/libs/BioC_graph.dylib /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/lib/R/3.0/site-library/graph/libs/BioC_graph.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.de4Di /bin/rm -f /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/info/dir /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/info/dir.old /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/share/info/dir /sw/build.build/root-bioconductor-graph-r30-1.42.0-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Creating shlibs files... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bioconductor-graph-r30-1.42.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `bioconductor-graph-r30' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-graph-r30_1.42.0-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-graph-r30-1.42.0-1 (Reading database ... 9486 files and directories currently installed.) Removing fink-buildlock-bioconductor-graph-r30-1.42.0-1 ...