> biocLite("Rgraphviz")
BioC_mirror: http://mirrors.ebi.ac.uk/bioconductor/
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'Rgraphviz'
trying URL 'http://mirrors.ebi.ac.uk/bioconductor//packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0.tar.gz'
Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb)
opened URL
==================================================
downloaded 7.1 Mb

Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

   Welcome to R!

* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/atlas /usr/lib64/mysql /usr/lib64/qt-3.3/lib
checking for library containing dlopen... -ldl
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configure: WARNING: X11 not available.
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configure: WARNING: Unable to find header tcl.h. The Tcl packages will not be built
configure: WARNING: No Tcl. The Tk packages will not be built either
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configure: WARNING: Optional Xpm library not available
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configure: WARNING: Optional Xaw library not available - missing headers
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checking that generated files are newer than configure... done
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
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config.status: creating lib/dotgen/Makefile
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config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
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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 (/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix'  'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'LDFLAGS=-L/usr/local/lib64' '--libdir=/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib' '--includedir=/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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' 'R_LIBS=/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/library' '--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... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu99... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1966080
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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 -B output from gcc -std=gnu99 object... ok
checking how to run the C preprocessor... gcc -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
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checking for inttypes.h... yes
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checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... no
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
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checking for dlopen... no
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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... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/atlas /usr/lib64/mysql /usr/lib64/qt-3.3/lib
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
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checking for argz_count... yes
checking for argz_create_sep... yes
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checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
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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 headers)
  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 (tcl not available)

  tcldot:        No (tcl not available)
  tclpathplan:   No (tcl not available)
  gdtclft:       No (tcl not available)
  tkspline:      No (tk not available)
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
make  install-am
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
/bin/sh ./libtool  --tag=CC   --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c  -fPIC -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/sh ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -module -avoid-version -L/usr/local/lib64 -o dlopen.la  dlopen.lo -ldl -ldl
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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c  -fPIC -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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c  -fPIC -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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c  -fPIC -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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c  -fPIC -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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c  -fPIC -DPIC -o libltdlc_la-ltdl.o
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -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:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c  -fPIC -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 gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -MT lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c -o lt__strl.lo lt__strl.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c lt__strl.c  -fPIC -DPIC -o lt__strl.o
mv -f .deps/lt__strl.Tpo .deps/lt__strl.Plo
/bin/sh ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -no-undefined -dlpreopen dlopen.la  -L/usr/local/lib64 -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 lt__strl.lo -ldl
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && gcc -std=gnu99 -g -O2 -c -fno-builtin  -fPIC -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 "/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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 lt__strl.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" )
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib'
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
Making install in cdt
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/cdt'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
  CC       dtclose.lo
  CC       dtdisc.lo
dtdisc.c:14: warning: function declaration isn't a prototype
  CC       dtextract.lo
  CC       dtflatten.lo
  CC       dthash.lo
dthash.c:16: warning: function declaration isn't a prototype
dthash.c:82: warning: function declaration isn't a prototype
dthash.c: In function 'dthash':
dthash.c:87: warning: 'r' may be used uninitialized in this function
dthash.c:93: warning: 's' may be used uninitialized in this function
  CC       dtlist.lo
dtlist.c:12: warning: function declaration isn't a prototype
  CC       dtmethod.lo
  CC       dtopen.lo
  CC       dtrenew.lo
  CC       dtrestore.lo
  CC       dtsize.lo
dtsize.c:12: warning: function declaration isn't a prototype
  CC       dtstat.lo
dtstat.c:12: warning: function declaration isn't a prototype
dtstat.c:32: warning: function declaration isn't a prototype
  CC       dtstrhash.lo
  CC       dttree.lo
dttree.c:15: warning: function declaration isn't a prototype
dttree.c: In function 'dttree':
dttree.c:23: warning: 'me' may be used uninitialized in this function
  CC       dttreeset.lo
dttreeset.c:12: warning: function declaration isn't a prototype
  CC       dtview.lo
dtview.c:13: warning: function declaration isn't a prototype
dtview.c: In function 'dtvsearch':
dtview.c:19: warning: 'o' may be used uninitialized in this function
  CC       dtwalk.lo
dtwalk.c: In function 'dtwalk':
dtwalk.c:14: warning: function declaration isn't a prototype
  CCLD     libcdt.la
  CCLD     libcdt_C.la
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/cdt'
make[5]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libcdt.a
libtool: finish: PATH="/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/share/scripts:/GWD/bioinfo/apps/bin:/GWD/bioinfo/common/scripts:/GWD/bioinfo/tools/bin:/usr/local/bin:/usr/reg-central/bin:/usr/central/bin:/usr/reg-common/scripts:/usr/common/scripts:/home/ef884766/bin:/home/ef884766/bin/Linux:/bioinfo/apps/2.6.32-358.18.1.el6.x86_64/bin:/bioinfo/apps/bin:/bioinfo/apps/gene/bin:/bioinfo/apps/unsupported/bin:/bioinfo/share/bin:/bioinfo/share/unsupported/bin:/bioinfo/apps/sybase/bin:/bin:/usr/bin:/usr/bin/X11:/sbin:/usr/sbin:/opt/TWWfsw/TWW/bin:/sbin" ldconfig -n /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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 `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/graph'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
  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:136: note: expected 'unsigned char *' but argument is of type 'char *'
lexer.c:435: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness
lexer.c:136: note: expected 'unsigned char *' but argument is of type 'char *'
  CC       node.lo
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
  CCLD     libgraph_C.la
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/graph'
make[5]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libgraph.a
libtool: finish: PATH="/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/share/scripts:/GWD/bioinfo/apps/bin:/GWD/bioinfo/common/scripts:/GWD/bioinfo/tools/bin:/usr/local/bin:/usr/reg-central/bin:/usr/central/bin:/usr/reg-common/scripts:/usr/common/scripts:/home/ef884766/bin:/home/ef884766/bin/Linux:/bioinfo/apps/2.6.32-358.18.1.el6.x86_64/bin:/bioinfo/apps/bin:/bioinfo/apps/gene/bin:/bioinfo/apps/unsupported/bin:/bioinfo/share/bin:/bioinfo/share/unsupported/bin:/bioinfo/apps/sybase/bin:/bin:/usr/bin:/usr/bin/X11:/sbin:/usr/sbin:/opt/TWWfsw/TWW/bin:/sbin" ldconfig -n /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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 `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/pathplan'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
  CC       cvt.lo
cvt.c:276: warning: 'append_bezier' defined but not used
  CC       inpoly.lo
  CC       route.lo
  CC       shortest.lo
shortest.c: In function 'loadtriangle':
shortest.c:539: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
  CC       shortestpth.lo
  CC       solvers.lo
  CC       triang.lo
  CC       util.lo
  CC       visibility.lo
  CCLD     libpathplan.la
  CCLD     libpathplan_C.la
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/pathplan'
make[5]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: finish: PATH="/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/projects/cb-software/personal/ef884766/bin/:/GWD/bioinfo/share/scripts:/GWD/bioinfo/apps/bin:/GWD/bioinfo/common/scripts:/GWD/bioinfo/tools/bin:/usr/local/bin:/usr/reg-central/bin:/usr/central/bin:/usr/reg-common/scripts:/usr/common/scripts:/home/ef884766/bin:/home/ef884766/bin/Linux:/bioinfo/apps/2.6.32-358.18.1.el6.x86_64/bin:/bioinfo/apps/bin:/bioinfo/apps/gene/bin:/bioinfo/apps/unsupported/bin:/bioinfo/share/bin:/bioinfo/share/unsupported/bin:/bioinfo/apps/sybase/bin:/bin:/usr/bin:/usr/bin/X11:/sbin:/usr/sbin:/opt/TWWfsw/TWW/bin:/sbin" ldconfig -n /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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 `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/vpsc'
make[5]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/rbtree'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/rbtree'
make[5]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/ortho'
make[4]: Entering directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
  CC       fPQ.lo
fPQ.c:24: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
fPQ.c:26: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'guard'
fPQ.c: In function 'PQgen':
fPQ.c:32: error: 'pq' undeclared (first use in this function)
fPQ.c:32: error: (Each undeclared identifier is reported only once
fPQ.c:32: error: for each function it appears in.)
fPQ.c:33: error: 'snode' undeclared (first use in this function)
fPQ.c:33: error: expected expression before ')' token
fPQ.c:34: error: 'guard' undeclared (first use in this function)
fPQ.c: In function 'PQfree':
fPQ.c:43: error: 'pq' undeclared (first use in this function)
fPQ.c: In function 'PQcheck':
fPQ.c:60: warning: implicit declaration of function 'N_IDX'
fPQ.c:60: error: 'pq' undeclared (first use in this function)
fPQ.c: In function 'PQupheap':
fPQ.c:69: error: 'snode' undeclared (first use in this function)
fPQ.c:69: error: 'x' undeclared (first use in this function)
fPQ.c:69: error: 'pq' undeclared (first use in this function)
fPQ.c:72: error: 'n' undeclared (first use in this function)
fPQ.c:74: warning: implicit declaration of function 'N_VAL'
fPQ.c: At top level:
fPQ.c:85: error: expected ')' before '*' token
fPQ.c: In function 'PQdownheap':
fPQ.c:100: error: 'snode' undeclared (first use in this function)
fPQ.c:100: error: 'x' undeclared (first use in this function)
fPQ.c:100: error: 'pq' undeclared (first use in this function)
fPQ.c:103: error: 'n' undeclared (first use in this function)
fPQ.c: At top level:
fPQ.c:124: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
fPQ.c:141: error: expected ')' before '*' token
fPQ.c: In function 'PQprint':
fPQ.c:152: error: 'snode' undeclared (first use in this function)
fPQ.c:152: error: 'n' undeclared (first use in this function)
fPQ.c:156: error: 'pq' undeclared (first use in this function)
make[3]: *** [fPQ.lo] Error 1
make[3]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib/ortho'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz/lib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/graphviz'
make: *** [install] Error 2
cp: omitting directory `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/pkgconfig'
cp: cannot stat `/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/lib/graphviz/*': No such file or directory
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -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 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/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/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
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/Rtmpzpj10B/R.INSTALL116e437a03262/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:
common.h:16:17: error: gvc.h: No such file or directory
common.h:17:22: error: gvplugin.h: No such file or directory
common.h:18:20: error: gvcext.h: No such file or directory
common.h:19:20: error: gvcjob.h: No such file or directory
In file included from LL_funcs.c:1:
common.h:22: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
common.h:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
In file included from LL_funcs.c:2:
util.h:18: error: expected ‘)’ before ‘*’ token
LL_funcs.c:5: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
LL_funcs.c:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
LL_funcs.c: In function ‘getDefAttrs’:
LL_funcs.c:31: error: ‘Agdict_t’ undeclared (first use in this function)
LL_funcs.c:31: error: (Each undeclared identifier is reported only once
LL_funcs.c:31: error: for each function it appears in.)
LL_funcs.c:31: error: ‘dict’ undeclared (first use in this function)
LL_funcs.c:31: warning: implicit declaration of function ‘agdictof’
LL_funcs.c:34: warning: implicit declaration of function ‘dtsize’
LL_funcs.c: In function ‘Rgraphviz_getDefAttrsGraph’:
LL_funcs.c:61: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:61: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:61: warning: implicit declaration of function ‘getAgraphPtr’
LL_funcs.c: In function ‘Rgraphviz_setDefAttrsGraph’:
LL_funcs.c:88: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:88: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:93: error: ‘Agsym_t’ undeclared (first use in this function)
LL_funcs.c:93: error: ‘r’ undeclared (first use in this function)
LL_funcs.c:93: warning: implicit declaration of function ‘agraphattr’
LL_funcs.c: In function ‘Rgraphviz_getAttrsGraph’:
LL_funcs.c:105: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:105: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:109: warning: implicit declaration of function ‘agget’
LL_funcs.c: In function ‘Rgraphviz_setAttrsGraph’:
LL_funcs.c:129: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:129: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:136: warning: implicit declaration of function ‘agsafeset’
LL_funcs.c: In function ‘Rgraphviz_getAttrsCluster’:
LL_funcs.c:148: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:148: error: ‘sg’ undeclared (first use in this function)
LL_funcs.c:148: warning: implicit declaration of function ‘getClusterPtr’
LL_funcs.c: In function ‘Rgraphviz_setAttrsCluster’:
LL_funcs.c:172: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:172: error: ‘sg’ undeclared (first use in this function)
LL_funcs.c: In function ‘Rgraphviz_getDefAttrsNode’:
LL_funcs.c:191: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:191: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:194: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:194: error: ‘n’ undeclared (first use in this function)
LL_funcs.c: In function ‘Rgraphviz_setDefAttrsNode’:
LL_funcs.c:219: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:219: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:224: error: ‘Agsym_t’ undeclared (first use in this function)
LL_funcs.c:224: error: ‘r’ undeclared (first use in this function)
LL_funcs.c:224: warning: implicit declaration of function ‘agnodeattr’
LL_funcs.c: In function ‘Rgraphviz_getAttrsNode’:
LL_funcs.c:236: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:236: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:240: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:240: error: ‘n’ undeclared (first use in this function)
LL_funcs.c:240: warning: implicit declaration of function ‘agfindnode’
LL_funcs.c: In function ‘Rgraphviz_setAttrsNode’:
LL_funcs.c:265: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:265: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:269: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:269: error: ‘n’ undeclared (first use in this function)
LL_funcs.c: In function ‘Rgraphviz_getDefAttrsEdge’:
LL_funcs.c:288: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:288: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:291: error: ‘Agedge_t’ undeclared (first use in this function)
LL_funcs.c:291: error: ‘e’ undeclared (first use in this function)
LL_funcs.c: In function ‘Rgraphviz_setDefAttrsEdge’:
LL_funcs.c:316: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:316: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:321: error: ‘Agsym_t’ undeclared (first use in this function)
LL_funcs.c:321: error: ‘r’ undeclared (first use in this function)
LL_funcs.c:321: warning: implicit declaration of function ‘agedgeattr’
LL_funcs.c: In function ‘Rgraphviz_getAttrsEdge’:
LL_funcs.c:333: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:333: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:338: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:338: error: ‘u’ undeclared (first use in this function)
LL_funcs.c:341: error: ‘v’ undeclared (first use in this function)
LL_funcs.c:345: error: ‘Agedge_t’ undeclared (first use in this function)
LL_funcs.c:345: error: ‘e’ undeclared (first use in this function)
LL_funcs.c:345: warning: implicit declaration of function ‘agfindedge’
LL_funcs.c: In function ‘Rgraphviz_setAttrsEdge’:
LL_funcs.c:369: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:369: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:374: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:374: error: ‘u’ undeclared (first use in this function)
LL_funcs.c:377: error: ‘v’ undeclared (first use in this function)
LL_funcs.c:381: error: ‘Agedge_t’ undeclared (first use in this function)
LL_funcs.c:381: error: ‘e’ undeclared (first use in this function)
LL_funcs.c: In function ‘Rgraphviz_toFile’:
LL_funcs.c:399: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:399: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:404: warning: implicit declaration of function ‘gvLayout’
LL_funcs.c:404: error: ‘gvc’ undeclared (first use in this function)
LL_funcs.c:408: warning: implicit declaration of function ‘gvRenderFilename’
LL_funcs.c:409: warning: implicit declaration of function ‘gvFreeLayout’
LL_funcs.c: In function ‘Rgraphviz_agopenSimple’:
LL_funcs.c:428: error: ‘Agraph_t’ undeclared (first use in this function)
LL_funcs.c:428: error: ‘g’ undeclared (first use in this function)
LL_funcs.c:428: error: ‘tmpGraph’ undeclared (first use in this function)
LL_funcs.c:429: error: ‘sgs’ undeclared (first use in this function)
LL_funcs.c:430: error: ‘Agnode_t’ undeclared (first use in this function)
LL_funcs.c:430: error: ‘head’ undeclared (first use in this function)
LL_funcs.c:430: error: ‘tail’ undeclared (first use in this function)
LL_funcs.c:430: error: ‘curNode’ undeclared (first use in this function)
LL_funcs.c:431: error: ‘Agedge_t’ undeclared (first use in this function)
LL_funcs.c:431: error: ‘curEdge’ undeclared (first use in this function)
LL_funcs.c:456: warning: implicit declaration of function ‘aginit’
LL_funcs.c:458: warning: implicit declaration of function ‘agopen’
LL_funcs.c:462: error: expected expression before ‘)’ token
LL_funcs.c:476: warning: implicit declaration of function ‘agsubg’
LL_funcs.c:501: warning: implicit declaration of function ‘agnode’
LL_funcs.c:531: warning: implicit declaration of function ‘agedge’
LL_funcs.c:535: warning: implicit declaration of function ‘buildRagraph’
make: *** [LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/library/Rgraphviz’

The downloaded source packages are in
        ‘/tmp/RtmpyORfmB/downloaded_packages’
Updating HTML index of packages in '.Library'