> install.packages("Rgraphviz_2.7.1.tar.gz", repos=NULL)
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...
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 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
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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 library containing strerror... none required
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for sed... /bin/sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... no
checking for tclsh8.5... /usr/bin/tclsh8.5
checking whether gcc -std=gnu99 and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking for inline... inline
checking for windres... no
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... grep
checking for egrep... 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 for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uid_t in sys/types.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stddef.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for stdint.h... (cached) yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/inotify.h usability... yes
checking sys/inotify.h presence... yes
checking for sys/inotify.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for socklen_t... yes
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... yes
checking for fesetenv... yes
checking libgen.h usability... yes
checking libgen.h presence... yes
checking for libgen.h... yes
checking for basename in -lgen... no
checking for working alloca.h... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... no
checking for setenv... yes
checking for getenv... yes
checking for __freadable... yes
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... yes
checking for memset... yes
checking for nl_langinfo... yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for _NSGetEnviron... no
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... 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 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 for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
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
checking for shl_load in -ldld... no
checking for dlopen... no
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 for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
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
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
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
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 ltdl.h... no
checking where to find libltdl headers... -I${top_srcdir}/libltdl
checking where to find libltdl library... ${top_build_prefix}libltdl/libltdlc.la
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... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking for X... disabled
configure: WARNING: X11 not available.
checking tcl.h usability... no
checking tcl.h presence... no
checking for tcl.h... no
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
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for X11/Xaw/Text.h... no
configure: WARNING: Optional Xaw library not available - missing headers
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... yes
checking for GDK_PIXBUF... yes
checking for GTK... yes
checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... yes
checking for qmake-qt4... no
checking for qmake-qt3... no
checking for qmake... no
checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... yes
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
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
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
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 (/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix'  'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'LDFLAGS=-L/usr/local/lib64' '--libdir=/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib' '--includedir=/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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
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 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
checking for shl_load in -ldld... no
checking for dlopen... no
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... 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
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
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
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
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)
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/config/missing --run autoheader)
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf.  It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl'
make  install-am
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/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" )
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader)
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf.  It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
rm -f stamp-h1
touch config-h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib'
Making install in cdt
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/cdt'
  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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/cdt'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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: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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/graph'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pathplan'
  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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pathplan'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/vpsc'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/rbtree'
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/rbtree'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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
ortho.c: In function 'orthoEdges':
ortho.c:1250: warning: 'ps' may be used uninitialized in this function
  CC       partition.lo
partition.c: In function 'make_new_monotone_poly':
partition.c:212: warning: 'tp' may be used uninitialized in this function
partition.c:212: note: 'tp' was declared here
partition.c:212: warning: 'tq' may be used uninitialized in this function
partition.c:212: note: 'tq' was declared here
partition.c: In function 'monotonate_trapezoids':
partition.c:620: warning: 'size' may be used uninitialized in this function
  CC       rawgraph.lo
  CC       sgraph.lo
  CC       trapezoid.lo
trapezoid.c:22:1: warning: "__USE_ISOC99" redefined
In file included from /usr/include/string.h:27,
                 from trapezoid.c:19:
/usr/include/features.h:239:1: warning: this is the location of the previous definition
trapezoid.c:67: warning: function declaration isn't a prototype
trapezoid.c: In function 'add_segment':
trapezoid.c:434: warning: 'tfirstr' may be used uninitialized in this function
trapezoid.c:434: warning: 'tlastr' may be used uninitialized in this function
  CCLD     libortho_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/ortho'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/ortho'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/ortho'
Making install in sparse
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/sparse'
  CC       SparseMatrix.lo
  CC       general.lo
  CC       BinaryHeap.lo
  CC       IntStack.lo
  CCLD     libsparse_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/sparse'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/sparse'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/sparse'
Making install in patchwork
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/patchwork'
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/patchwork'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/patchwork'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/patchwork'
Making install in common
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/common'
  CC       arrows.lo
arrows.c: In function 'arrowOrthoClip':
arrows.c:317: warning: 'hlen' may be used uninitialized in this function
  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
postproc.c: In function 'gv_postprocess':
postproc.c:197: warning: 'pp$x' may be used uninitialized in this function
postproc.c:197: note: 'pp$x' was declared here
  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
emit.c: In function 'getObjId':
emit.c:182: warning: 'idnum' may be used uninitialized in this function
emit.c:183: warning: 'pfx' may be used uninitialized in this function
emit.c: In function 'xdotBB':
emit.c:2471: warning: 'fontsize' may be used uninitialized in this function
emit.c:2472: warning: 'fontname' may be used uninitialized in this function
emit.c: In function 'emit_edge_graphics':
emit.c:1721: warning: 'segs' may be used uninitialized in this function
emit.c:1721: note: 'segs' was declared here
emit.c:1792: warning: 'bz.list' may be used uninitialized in this function
emit.c:1792: warning: 'bz.sflag' may be used uninitialized in this function
emit.c:1792: warning: 'bz.eflag' may be used uninitialized in this function
emit.c:1792: warning: 'bz.size' may be used uninitialized in this function
emit.c:1792: warning: 'bz.sp.x' may be used uninitialized in this function
emit.c:1792: warning: 'bz.sp.y' may be used uninitialized in this function
emit.c:1792: warning: 'bz.ep.x' may be used uninitialized in this function
emit.c:1792: warning: 'bz.ep.y' may be used uninitialized in this function
  CCLD     libcommon_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/common'
make[4]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/common'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/common'
Making install in pack
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pack'
  CC       ccomps.lo
  CC       pack.lo
pack.c: In function 'putGraphs':
pack.c:920: warning: 'pts' may be used uninitialized in this function
  CCLD     libpack_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pack'
make[4]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pack.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pack.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pack.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pack'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/pack'
Making install in xdot
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/xdot'
  CC       xdot.lo
  CCLD     libxdot.la
  CCLD     libxdot_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/xdot'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libxdot.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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 xdot.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 xdot.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxdot.pc '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 xdot.h '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/xdot'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/xdot'
Making install in gvc
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/gvc'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/libgvc.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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 gvc.3 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 gvc.3.pdf '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgvc.pc '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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 '/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/gvc'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/gvc'
Making install in circogen
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/circogen'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/circogen'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/circogen'
Making install in dotgen
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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
mincross.c: In function 'mincross.clone.0':
mincross.c:581: warning: 'maxthispass' may be used uninitialized in this function
  CC       position.lo
  CC       rank.lo
  CC       sameport.lo
  CC       dotsplines.lo
dotsplines.c: In function '_dot_splines':
dotsplines.c:268: warning: 'edges' may be used uninitialized in this function
dotsplines.c:269: warning: 'P' may be used uninitialized in this function
  CC       aspect.lo
  CCLD     libdotgen_C.la
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/dotgen'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/dotgen'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/dotgen'
Making install in fdpgen
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/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
make[4]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/fdpgen'
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/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/fdpgen'
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/fdpgen'
Making install in neatogen
make[3]: Entering directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/neatogen'
  CC       adjust.lo
adjust.c: In function 'removeOverlapWith':
adjust.c:1045: warning: 'ret' may be used uninitialized in this function
adjust.c: In function 'getSizes':
adjust.c:670: warning: 'nedge_nodes' may be used uninitialized in this function
  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
voronoi.c: In function 'voronoi':
voronoi.c:26: warning: 'newintstar.y' may be used uninitialized in this function
  CC       stress.lo
stress.c: In function 'mdsModel':
stress.c:1370: warning: 'delta' may be used uninitialized in this function
  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
multispline.c:1245: error: expected specifier-qualifier-list before 'PQ'
multispline.c:1250:1: warning: "N_VAL" redefined
In file included from multispline.c:1241:
../../lib/ortho/fPQ.h:19:1: warning: this is the location of the previous definition
multispline.c:1251:1: warning: "N_IDX" redefined
../../lib/ortho/fPQ.h:20:1: warning: this is the location of the previous definition
In file included from multispline.c:1254:
../../lib/ortho/fPQ.h:19:1: warning: "N_VAL" redefined
multispline.c:1250:1: warning: this is the location of the previous definition
../../lib/ortho/fPQ.h:20:1: warning: "N_IDX" redefined
multispline.c:1251:1: warning: this is the location of the previous definition
multispline.c:1257:1: warning: "N_DAD" redefined
../../lib/ortho/fPQ.h:21:1: warning: this is the location of the previous definition
multispline.c:1258:1: warning: "E_WT" redefined
../../lib/ortho/fPQ.h:23:1: warning: this is the location of the previous definition
multispline.c:1268: error: expected declaration specifiers or '...' before 'PQ'
multispline.c: In function 'triPath':
multispline.c:1276: error: 'pq' undeclared (first use in this function)
multispline.c:1276: error: (Each undeclared identifier is reported only once
multispline.c:1276: error: for each function it appears in.)
multispline.c:1277:13: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1277: error: 'N_VAL' undeclared (first use in this function)
multispline.c:1279: error: too many arguments to function 'PQinit'
multispline.c:1281:17: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1282: warning: implicit declaration of function 'PQinsert'
multispline.c:1284: error: too many arguments to function 'PQremove'
multispline.c:1284: warning: assignment makes integer from pointer without a cast
multispline.c:1285:13: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1295:24: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1296:20: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1297:21: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1298:21: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1301:28: error: macro "N_VAL" passed 2 arguments, but takes just 1
multispline.c:1302: error: too many arguments to function 'PQupdate'
multispline.c: In function 'makeMultiSpline':
multispline.c:1339: error: 'PPQ' has no member named 'pq'
multispline.c:1339: error: too many arguments to function 'PQgen'
multispline.c:1340: error: 'PPQ' has no member named 'pq'
multispline.c:1341: error: 'PPQ' has no member named 'pq'
multispline.c:1343: error: 'PPQ' has no member named 'vals'
multispline.c:1344: error: 'PPQ' has no member named 'idxs'
multispline.c:1347: error: 'PQ' undeclared (first use in this function)
multispline.c:1347: error: expected expression before ')' token
multispline.c:1347: error: too many arguments to function 'triPath'
multispline.c:1351: error: 'PPQ' has no member named 'pq'
multispline.c:1351: error: too many arguments to function 'PQfree'
make[3]: *** [multispline.lo] Error 1
make[3]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib/neatogen'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz/lib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/graphviz'
make: *** [install] Error 2
cp: omitting directory `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/lib/pkgconfig'
cp: cannot stat `/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/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/RtmpN65SXj/R.INSTALLe73e3939bc8e/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
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c Rgraphviz.c -o Rgraphviz.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c RgraphvizInit.c -o RgraphvizInit.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c agopen.c -o agopen.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c agread.c -o agread.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c agwrite.c -o agwrite.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c bezier.c -o bezier.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c buildEdgeList.c -o buildEdgeList.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c buildNodeList.c -o buildNodeList.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c doLayout.c -o doLayout.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c graphvizVersion.c -o graphvizVersion.o
gcc -std=gnu99 -I/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN65SXj/R.INSTALLe73e3939bc8e/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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
gcc: libgvplugin_dot_layout.a: No such file or directory
gcc: libgvplugin_neato_layout.a: No such file or directory
gcc: libgvplugin_core.a: No such file or directory
make: *** [Rgraphviz.so] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/library/Rgraphviz’