printf '

' | fink --no-use-binary-dist --yes  --build-as-nobody rebuild bioconductor-graph-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-graph-r31' will be built without being installed.
Reading build dependency for bioconductor-graph-r31-1.42.0-1...
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The following package will be rebuilt:
 bioconductor-graph-r31
The following 32 additional packages will be installed:
 bioconductor-biobase-r31 bioconductor-biocgenerics-r31 cairo-shlibs
 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 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)
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sudo -u fink-bld [ENV] sh -c /tmp/fink.TZpZV
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.RXGTC
/tmp/fink.Dq9Kg
#!/bin/bash -ev
  export TMPDIR=/sw/build.build/bioconductor-graph-r31-1.42.0-1/graph/tmp
  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
  
  pushd ..
/sw/build.build/bioconductor-graph-r31-1.42.0-1 /sw/build.build/bioconductor-graph-r31-1.42.0-1/graph
  $BIN_R --verbose CMD build --no-build-vignettes graph
* 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-r31-1.42.0-1
/bin/mkdir -p /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw
/bin/mkdir -p /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-graph-r31-1.42.0-1
sudo -u fink-bld [ENV] sh -c /tmp/fink.tsZZv
/tmp/fink.SMS9U
#!/bin/sh -ev
  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
  
  mkdir -p /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/lib/R/3.1/site-library
  pushd /sw/build.build/bioconductor-graph-r31-1.42.0-1/graph/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/lib/R/3.1/site-library graph
/sw/build.build/bioconductor-graph-r31-1.42.0-1 /sw/build.build/bioconductor-graph-r31-1.42.0-1/graph
* installing *source* package 'graph' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
mv graph.dylib BioC_graph.dylib
installing to /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/lib/R/3.1/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/3.1/site-library/graph/libs/BioC_graph.dylib /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/lib/R/3.1/site-library/graph/libs/BioC_graph.dylib
sudo -u fink-bld [ENV] sh -c /tmp/fink.sPS6L
/bin/rm -f /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/info/dir /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/info/dir.old /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/sw/share/info/dir /sw/build.build/root-bioconductor-graph-r31-1.42.0-1/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-r31-1.42.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods
dpkg-deb: building package `bioconductor-graph-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-graph-r31_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-r31-1.42.0-1
(Reading database ... 7664 files and directories currently installed.)
Removing fink-buildlock-bioconductor-graph-r31-1.42.0-1 ...