BioC 3.0: CHECK report for Rgraphviz on perceval

Package: Rgraphviz

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rgraphviz_2.10.0.tar.gz

StartedAt: 2015-04-10 05:41:45 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:45:02 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 197.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rgraphviz.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rgraphviz_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘2.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/libwin/i386/lib/libcdt.a src/libwin/i386/lib/libcdt.la
  src/libwin/i386/lib/libgraph.a src/libwin/i386/lib/libgraph.la
  src/libwin/i386/lib/libgvc.a src/libwin/i386/lib/libgvc.la
  src/libwin/i386/lib/libgvplugin_core.a
  src/libwin/i386/lib/libgvplugin_core.la
  src/libwin/i386/lib/libgvplugin_dot_layout.a
  src/libwin/i386/lib/libgvplugin_dot_layout.la
  src/libwin/i386/lib/libgvplugin_neato_layout.a
  src/libwin/i386/lib/libgvplugin_neato_layout.la
  src/libwin/i386/lib/libpathplan.a src/libwin/i386/lib/libpathplan.la
  src/libwin/i386/lib/libxdot.a src/libwin/i386/lib/libxdot.la
  src/libwin/x64/lib/libcdt.a src/libwin/x64/lib/libcdt.la
  src/libwin/x64/lib/libgraph.a src/libwin/x64/lib/libgraph.la
  src/libwin/x64/lib/libgvc.a src/libwin/x64/lib/libgvc.la
  src/libwin/x64/lib/libgvplugin_core.a
  src/libwin/x64/lib/libgvplugin_core.la
  src/libwin/x64/lib/libgvplugin_dot_layout.a
  src/libwin/x64/lib/libgvplugin_dot_layout.la
  src/libwin/x64/lib/libgvplugin_neato_layout.a
  src/libwin/x64/lib/libgvplugin_neato_layout.la
  src/libwin/x64/lib/libpathplan.a src/libwin/x64/lib/libpathplan.la
  src/libwin/x64/lib/libxdot.a src/libwin/x64/lib/libxdot.la
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rgraphviz’ can be installed ... [109s/134s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.graphviz_build_version’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/4s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00check.log’
for details.

* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
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checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether llvm-g++-4.2 -arch x86_64 accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-apple-darwin10.8.0
checking host system type... x86_64-apple-darwin10.8.0
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configure: WARNING: X11 not available.
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configure: WARNING: Optional Xpm library not available
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configure: WARNING: Optional Xaw library not available
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
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config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix'  'CC=llvm-gcc-4.2 -arch x86_64 -std=gnu99' 'CXX=llvm-g++-4.2 -arch x86_64' 'CFLAGS=-mtune=core2 -g -O2 -Wall' 'CXXFLAGS=-mtune=core2 -g -O2 -Wall' 'LDFLAGS=-L/usr/local/lib -L/usr/local/lib' '--libdir=/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib' '--includedir=/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'PKG_CONFIG_PATH=/Library/Frameworks/GTK+.framework/Resources/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/X11/lib/pkgconfig:/usr/local/ggobi/lib/pkgconfig' 'R_LIBS=/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck:/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck' '--enable-ltdl-convenience' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
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checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-apple-darwin10.8.0
checking host system type... x86_64-apple-darwin10.8.0
checking for style of include used by make... GNU
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking dependency style of llvm-gcc-4.2 -arch x86_64 -std=gnu99... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by llvm-gcc-4.2 -arch x86_64 -std=gnu99... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from llvm-gcc-4.2 -arch x86_64 -std=gnu99 object... rm: conftest.dSYM: is a directory
ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if llvm-gcc-4.2 -arch x86_64 -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to produce PIC... -fno-common -DPIC
checking if llvm-gcc-4.2 -arch x86_64 -std=gnu99 PIC flag -fno-common -DPIC works... yes
checking if llvm-gcc-4.2 -arch x86_64 -std=gnu99 static flag -static works... no
checking if llvm-gcc-4.2 -arch x86_64 -std=gnu99 supports -c -o file.o... yes
checking if llvm-gcc-4.2 -arch x86_64 -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the llvm-gcc-4.2 -arch x86_64 -std=gnu99 linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... DYLD_LIBRARY_PATH
checking for the default library search path... /usr/local/lib /lib /usr/lib
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... yes
checking whether we have to add an underscore for dlsym... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... no
checking for error_t... no
checking for argz_add... no
checking for argz_append... no
checking for argz_count... no
checking for argz_create_sep... no
checking for argz_insert... no
checking for argz_next... no
checking for argz_stringify... no
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... yes
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

----------------------------------------------------------------

graphviz-2.28.0 will be compiled with the following:

options:
  cgraph:        No (disabled by default - experimental)
  digcola:       Yes
  expat:         No (disabled)
  fontconfig:    No (disabled)
  freetype:      No (disabled)
  glut:          No (disabled)
  gts:           No (disabled)
  ipsepcola:     No (disabled by default - C++ portability issues)
  ltdl:          No (disabled)
  ortho:         Yes
  png:           No (disabled)
  jpeg:          No (disabled)
  sfdp:          Yes
  shared:        No (disabled)
  static:        Yes
  qt:            No (qmake not found)

commands:
  dot:           Yes (always enabled)
  neato:         Yes (always enabled)
  fdp:           Yes (always enabled)
  circo:         Yes (always enabled)
  twopi:         Yes (always enabled)
  gvpr:          Yes (always enabled)
  gvmap:         Yes (always enabled)
  lefty:         No (missing Xaw library)
  smyrna:        No (disabled by default - experimental)
  gvedit:        No (qmake not found)

plugin libraries:
  dot_layout:    Yes (always enabled)
  neato_layout:  Yes (always enabled)
  core:          Yes (always enabled)
  devil:         No (disabled)
  gd:            No (disabled)
  gdiplus:       No (disabled by default - Windows only)
  gdk_pixbuf:    Yes
  ghostscript:   No (disabled)
  glitz:         No (disabled by default - incomplete)
  gtk:           Yes
  lasi:          No (disabled)
  ming:          No (disabled by default - incomplete)
  pangocairo:    No (disabled)
  quartz:        No (disabled by default - Mac only)
  rsvg:          No (disabled)
  visio:         No (disabled by default - experimental)
  xlib:          No (disabled or unavailable)

language extensions:
  gv_sharp:      No (swig not available)
  gv_go:         No (disabled by default - experimental)
  gv_guile:      No (swig not available)
  gv_io:         No (disabled by default - no swig support yet)
  gv_java:       No (swig not available)
  gv_lua:        No (swig not available)
  gv_ocaml:      No (swig not available)
  gv_perl:       No (swig not available)
  gv_php:        No (swig not available)
  gv_python:     No (swig not available)
  gv_python23:   No (disabled by default - for multiversion installs)
  gv_python24:   No (disabled by default - for multiversion installs)
  gv_python25:   No (disabled by default - for multiversion installs)
  gv_python26:   No (disabled by default - for multiversion installs)
  gv_python27:   No (disabled by default - for multiversion installs)
  gv_R:          No (swig not available)
  gv_ruby:       No (swig not available)
  gv_tcl:        No (swig not available)

  tcldot:        Yes
  tclpathplan:   Yes
  gdtclft:       No (gd not available)
  tkspline:      Yes
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
Making install in libltdl
/bin/sh /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl/config/install-sh -d . 
cp ./argz_.h argz.h-t
mv argz.h-t argz.h
make  install-am
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c  -fno-common -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/sh ./libtool --tag=CC   --mode=link llvm-gcc-4.2 -arch x86_64 -std=gnu99  -mtune=core2 -g -O2 -Wall -module -avoid-version -L/usr/local/lib -L/usr/local/lib -o dlopen.la  dlopen.lo  
libtool: link: ar cru .libs/dlopen.a  dlopen.o
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c  -fno-common -DPIC -o libltdlc_la-preopen.o
mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c  -fno-common -DPIC -o libltdlc_la-lt__alloc.o
mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c  -fno-common -DPIC -o libltdlc_la-lt_dlloader.o
mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c  -fno-common -DPIC -o libltdlc_la-lt_error.o
mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c  -fno-common -DPIC -o libltdlc_la-ltdl.o
ltdl.c: In function 'try_dlopen':
ltdl.c:1268: warning: the address of 'libext' will always evaluate as 'true'
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c  -fno-common -DPIC -o libltdlc_la-slist.o
mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo
/bin/sh ./libtool --tag=CC   --mode=compile llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -mtune=core2 -g -O2 -Wall -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c -o argz.lo argz.c
libtool: compile:  llvm-gcc-4.2 -arch x86_64 -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -mtune=core2 -g -O2 -Wall -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c argz.c  -fno-common -DPIC -o argz.o
mv -f .deps/argz.Tpo .deps/argz.Plo
/bin/sh ./libtool --tag=CC   --mode=link llvm-gcc-4.2 -arch x86_64 -std=gnu99  -mtune=core2 -g -O2 -Wall -no-undefined -dlpreopen dlopen.la  -L/usr/local/lib -L/usr/local/lib -o libltdlc.la  libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo argz.lo 
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && llvm-gcc-4.2 -arch x86_64 -std=gnu99 -mtune=core2 -g -O2 -Wall -c -fno-builtin  -fno-common -DPIC "libltdlcS.c")
libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT"
libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")
libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o argz.o .libs/libltdlcS.o  .libs/libltdlc.lax/dlopen.a/dlopen.o 
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
Making install in lib
Making install in cdt
  CC       dtclose.lo
  CC       dtdisc.lo
  CC       dtextract.lo
  CC       dtflatten.lo
  CC       dthash.lo
  CC       dtlist.lo
  CC       dtmethod.lo
  CC       dtopen.lo
  CC       dtrenew.lo
  CC       dtrestore.lo
  CC       dtsize.lo
  CC       dtstat.lo
  CC       dtstrhash.lo
  CC       dttree.lo
  CC       dttreeset.lo
  CC       dtview.lo
  CC       dtwalk.lo
  CCLD     libcdt.la
  CCLD     libcdt_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in graph
  CC       attribs.lo
  CC       agxbuf.lo
  CC       edge.lo
  CC       graph.lo
  CC       graphio.lo
  CC       lexer.lo
lexer.c: In function 'scan_token':
lexer.c:147: warning: pointer targets in return differ in signedness
lexer.c: In function 'aglex':
lexer.c:435: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness
lexer.c:435: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness
  CC       node.lo
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
  CCLD     libgraph_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in pathplan
  CC       cvt.lo
  CC       inpoly.lo
  CC       route.lo
  CC       shortest.lo
  CC       shortestpth.lo
  CC       solvers.lo
  CC       triang.lo
  CC       util.lo
  CC       visibility.lo
  CCLD     libpathplan.la
  CCLD     libpathplan_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in vpsc
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in rbtree
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in ortho
  CC       fPQ.lo
  CC       intset.lo
  CC       maze.lo
maze.c: In function 'mkMazeGraph':
maze.c:411: warning: value computed is not used
  CC       ortho.lo
  CC       partition.lo
  CC       rawgraph.lo
  CC       sgraph.lo
  CC       trapezoid.lo
  CCLD     libortho_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sparse
  CC       SparseMatrix.lo
SparseMatrix.c: In function 'SparseMatrix_multiply':
SparseMatrix.c:1291: warning: assuming signed overflow does not occur when assuming that (X + c) <= X is always false
SparseMatrix.c: In function 'SparseMatrix_multiply3':
SparseMatrix.c:1461: warning: assuming signed overflow does not occur when assuming that (X + c) <= X is always false
  CC       general.lo
  CC       BinaryHeap.lo
  CC       IntStack.lo
  CCLD     libsparse_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in patchwork
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in common
  CC       arrows.lo
  CC       colxlate.lo
  CC       fontmetrics.lo
  CC       args.lo
  CC       memory.lo
  CC       globals.lo
  CC       htmllex.lo
  CC       htmlparse.lo
  CC       htmltable.lo
  CC       input.lo
  CC       pointset.lo
  CC       postproc.lo
  CC       routespl.lo
  CC       splines.lo
  CC       psusershape.lo
  CC       timing.lo
  CC       labels.lo
  CC       ns.lo
  CC       shapes.lo
  CC       utils.lo
  CC       geom.lo
  CC       output.lo
  CC       emit.lo
  CCLD     libcommon_C.la
make[4]: Nothing to be done for `install-exec-am'.
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in pack
  CC       ccomps.lo
  CC       pack.lo
  CCLD     libpack_C.la
make[4]: Nothing to be done for `install-exec-am'.
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pack.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pack.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pack.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in xdot
  CC       xdot.lo
  CCLD     libxdot.la
  CCLD     libxdot_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 xdot.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 xdot.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxdot.pc '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 xdot.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in gvc
  CC       gvrender.lo
  CC       gvlayout.lo
  CC       gvdevice.lo
  CC       gvloadimage.lo
  CC       gvcontext.lo
  CC       gvjobs.lo
  CC       gvevent.lo
  CC       gvplugin.lo
  CC       gvconfig.lo
  CC       gvtextlayout.lo
  CC       gvusershape.lo
  CC       gvc.lo
  CCLD     libgvc.la
  CCLD     libgvc_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 gvc.3 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 gvc.3.pdf '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgvc.pc '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
Making install in circogen
  CC       circularinit.lo
  CC       nodelist.lo
  CC       block.lo
  CC       edgelist.lo
  CC       circular.lo
  CC       deglist.lo
  CC       blocktree.lo
  CC       blockpath.lo
  CC       circpos.lo
  CC       nodeset.lo
  CCLD     libcircogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in dotgen
  CC       acyclic.lo
  CC       class1.lo
  CC       class2.lo
  CC       cluster.lo
  CC       compound.lo
  CC       conc.lo
  CC       decomp.lo
  CC       fastgr.lo
  CC       flat.lo
  CC       dotinit.lo
  CC       mincross.lo
  CC       position.lo
  CC       rank.lo
  CC       sameport.lo
  CC       dotsplines.lo
  CC       aspect.lo
  CCLD     libdotgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in fdpgen
  CC       comp.lo
  CC       dbg.lo
  CC       grid.lo
  CC       fdpinit.lo
  CC       layout.lo
  CC       tlayout.lo
  CC       xlayout.lo
  CC       clusteredges.lo
  CCLD     libfdpgen_C.la
/usr/bin/ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in neatogen
  CC       adjust.lo
  CC       circuit.lo
  CC       edges.lo
  CC       geometry.lo
  CC       heap.lo
  CC       hedges.lo
  CC       info.lo
  CC       neatoinit.lo
  CC       legal.lo
  CC       lu.lo
  CC       matinv.lo
  CC       memory.lo
  CC       poly.lo
  CC       printvis.lo
  CC       site.lo
  CC       solve.lo
  CC       neatosplines.lo
neatosplines.c: In function '_spline_edges':
neatosplines.c:603: warning: unused variable 'rtr'
  CC       stuff.lo
  CC       voronoi.lo
  CC       stress.lo
  CC       kkutils.lo
  CC       matrix_ops.lo
  CC       embed_graph.lo
  CC       dijkstra.lo
  CC       conjgrad.lo
  CC       pca.lo
  CC       closest.lo
  CC       bfs.lo
  CC       constraint.lo
  CC       quad_prog_solve.lo
  CC       smart_ini_x.lo
  CC       constrained_majorization.lo
  CC       opt_arrangement.lo
  CC       overlap.lo
  CC       call_tri.lo
  CC       compute_hierarchy.lo
  CC       delaunay.lo
  CC       multispline.lo
  CCLD     libneatogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in twopigen
  CC       twopiinit.lo
  CC       circle.lo
  CCLD     libtwopigen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sfdpgen
  CC       sfdpinit.lo
  CC       spring_electrical.lo
  CC       LinkedList.lo
  CC       sparse_solve.lo
  CC       post_process.lo
  CC       stress_model.lo
  CC       uniform_stress.lo
  CC       QuadTree.lo
  CC       Multilevel.lo
  CC       PriorityQueue.lo
  CCLD     libsfdpgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in osage
  CC       osageinit.lo
  CCLD     libosage_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in plugin
Making install in core
  CC       gvplugin_core.lo
  CC       gvrender_core_dot.lo
  CC       gvrender_core_fig.lo
  CC       gvrender_core_map.lo
  CC       gvrender_core_ps.lo
  CC       gvrender_core_svg.lo
  CC       gvrender_core_tk.lo
  CC       gvrender_core_vml.lo
  CC       gvloadimage_core.lo
  CCLD     libgvplugin_core_C.la
  CCLD     libgvplugin_core.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_core.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in dot_layout
  CC       gvplugin_dot_layout.lo
  CC       gvlayout_dot_layout.lo
gvlayout_dot_layout.c:45: warning: ignoring #pragma comment 
gvlayout_dot_layout.c:46: warning: ignoring #pragma comment 
  CCLD     libgvplugin_dot_layout_C.la
  CCLD     libgvplugin_dot_layout.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in neato_layout
  CC       gvplugin_neato_layout.lo
  CC       gvlayout_neato_layout.lo
  CCLD     libgvplugin_neato_layout_C.la
/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
  CCLD     libgvplugin_neato_layout.la
/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
ranlib: file: /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a(dbg.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[3]: Nothing to be done for `install-exec-am'.
 config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man7'
 /usr/bin/install -c -m 644 graphviz.7 '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man7'
 config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graphviz_version.h '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 config/install-sh -c -d '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc'
 /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc'
cp: /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz is a directory (not copied).
cp: /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig is a directory (not copied).
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for deflateBound in -lz... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CFLAGS= -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c LL_funcs.c -o LL_funcs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c Rgraphviz.c -o Rgraphviz.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c RgraphvizInit.c -o RgraphvizInit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c agopen.c -o agopen.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c agread.c -o agread.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c agwrite.c -o agwrite.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c bezier.c -o bezier.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c buildEdgeList.c -o buildEdgeList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c buildNodeList.c -o buildNodeList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c doLayout.c -o doLayout.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c graphvizVersion.c -o graphvizVersion.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I/Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘Rgraphviz’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rgraphviz)

name	user	system	elapsed
AgEdge-class	0.024	0.002	0.026
AgNode-class	0.024	0.001	0.025
AgTextLabel-class	0.019	0.001	0.019
BezierCurve-class	0.117	0.000	0.118
GraphvizLayouts	0.006	0.000	0.007
Ragraph-class	0.047	0.011	0.057
agopen	0.023	0.001	0.023
agopenSimple	0.057	0.004	0.060
agwrite	0.016	0.001	0.023
boundingBox-class	0.013	0.001	0.013
buildNodeList	0.011	0.001	0.011
clusterData-methods	0.474	0.015	0.536
getDefaultAttrs	0.003	0.000	0.003
graphLayout	0.011	0.000	0.012
graphvizCapabilities	0.002	0.000	0.003
graphvizVersion	0.002	0.001	0.002
layoutGraph	0.339	0.009	0.370
makeNodeAttrs	0.005	0.002	0.007
pEdge-class	0.009	0.000	0.009
pNode-class	0.007	0.001	0.008
pieGlyph	0.013	0.002	0.025
plot-methods	0.001	0.000	0.001
removedEdges	0.009	0.000	0.009
renderGraph	0.137	0.004	0.183
toDot-methods	0.014	0.001	0.017
toFile	0.069	0.005	0.075
xyPoint-class	0.003	0.000	0.002