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- > 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
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- checking lex output file root... lex.yy
- checking lex library... -lfl
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- 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... 98304
- 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... yes
- 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... no
- 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... yes
- 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
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- 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/lib/mysql /usr/lib64/mysql /usr/lib/xulrunner /usr/lib64/xulrunner
- checking for library containing dlopen... -ldl
- checking for dlerror... yes
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- checking for _ prefix in compiled symbols... no
- checking whether deplibs are loaded by dlopen... yes
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- checking if argz actually works... yes
- checking whether libtool supports -dlopen/-dlpreopen... yes
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- 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
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- checking for X... disabled
- configure: WARNING: X11 not available.
- checking tcl.h usability... no
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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
- checking for connect... yes
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- configure: WARNING: Optional Xpm library not available
- checking X11/Intrinsic.h usability... yes
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- configure: WARNING: Optional Xaw library not available - missing headers
- checking zlib.h usability... yes
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- checking for QTCORE... no
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- 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
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- 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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl)
- configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix' 'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'LDFLAGS=-L/usr/local/lib64' '--libdir=/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib' '--includedir=/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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... 98304
- 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... yes
- 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... no
- 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/lib/mysql /usr/lib64/mysql /usr/lib/xulrunner /usr/lib64/xulrunner
- 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
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- 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 (QtCore not available)
- 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 (QtCore not available)
- 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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/config/missing --run autoheader)
- aclocal.m4:20: 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'.
- configure.ac:5: error: Autoconf version 2.61 or higher is required
- configure.ac:5: the top level
- autom4te: /usr/bin/m4 failed with exit status: 63
- autoheader: /usr/bin/autom4te failed with exit status: 63
- WARNING: `autoheader' is probably too old. You should only need it if
- you modified `acconfig.h' or `configure.ac'. You might want
- to install the `Autoconf' and `GNU m4' packages. Grab them
- from any GNU archive site.
- rm -f stamp-h1
- touch config.h.in
- cd . && /bin/sh ./config.status config.h
- config.status: creating config.h
- config.status: config.h is unchanged
- grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
- make install-recursive
- make[1]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz'
- Making install in libltdl
- make[2]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl'
- make install-am
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader)
- aclocal.m4:20: 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'.
- configure.ac:55: error: Autoconf version 2.62 or higher is required
- aclocal.m4:537: AM_INIT_AUTOMAKE is expanded from...
- configure.ac:55: the top level
- autom4te: /usr/bin/m4 failed with exit status: 63
- autoheader: /usr/bin/autom4te failed with exit status: 63
- WARNING: `autoheader' is probably too old. You should only need it if
- you modified `acconfig.h' or `configure.ac'. You might want
- to install the `Autoconf' and `GNU m4' packages. Grab them
- from any GNU archive site.
- rm -f stamp-h1
- touch config-h.in
- cd . && /bin/sh ./config.status config.h
- config.status: creating config.h
- config.status: config.h is unchanged
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl'
- make[2]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/libltdl'
- Making install in lib
- make[2]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib'
- Making install in cdt
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/cdt'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- /bin/sh ../../libtool --mode=install /usr/bin/install -c libcdt.la '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- libtool: install: /usr/bin/install -c .libs/libcdt.lai /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libcdt.la
- libtool: install: /usr/bin/install -c .libs/libcdt.a /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libcdt.a
- libtool: install: chmod 644 /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libcdt.a
- libtool: install: ranlib /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/2.6.18-371.3.1.el5/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib
- ----------------------------------------------------------------------
- Libraries have been installed in:
- /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 cdt.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 cdt.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /usr/bin/install -c -m 644 libcdt.pc '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 cdt.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/cdt'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/cdt'
- Making install in graph
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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:435: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness
- CC node.lo
- CC parser.lo
- CC refstr.lo
- CC trie.lo
- CCLD libgraph.la
- CCLD libgraph_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/graph'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- /bin/sh ../../libtool --mode=install /usr/bin/install -c libgraph.la '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- libtool: install: /usr/bin/install -c .libs/libgraph.lai /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgraph.la
- libtool: install: /usr/bin/install -c .libs/libgraph.a /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgraph.a
- libtool: install: chmod 644 /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgraph.a
- libtool: install: ranlib /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/2.6.18-371.3.1.el5/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib
- ----------------------------------------------------------------------
- Libraries have been installed in:
- /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 graph.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 graph.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /usr/bin/install -c -m 644 libgraph.pc '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 graph.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/graph'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/graph'
- Making install in pathplan
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pathplan'
- CC cvt.lo
- CC inpoly.lo
- CC route.lo
- CC shortest.lo
- CC shortestpth.lo
- CC solvers.lo
- CC triang.lo
- CC util.lo
- CC visibility.lo
- CCLD libpathplan.la
- CCLD libpathplan_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pathplan'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- /bin/sh ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- libtool: install: /usr/bin/install -c .libs/libpathplan.lai /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libpathplan.la
- libtool: install: /usr/bin/install -c .libs/libpathplan.a /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libpathplan.a
- libtool: install: chmod 644 /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libpathplan.a
- libtool: install: ranlib /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/2.6.18-371.3.1.el5/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib
- ----------------------------------------------------------------------
- Libraries have been installed in:
- /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 pathplan.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 pathplan.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /usr/bin/install -c -m 644 libpathplan.pc '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pathplan'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pathplan'
- Making install in vpsc
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/vpsc'
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/vpsc'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/vpsc'
- Making install in rbtree
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/rbtree'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/rbtree'
- Making install in ortho
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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 'bendToStr':
- ortho.c:518: warning: 's' may be used uninitialized in this function
- ortho.c: In function 'emitSearchGraph':
- ortho.c:1409: warning: 'p.x' may be used uninitialized in this function
- ortho.c:1409: warning: 'p.y' may be used uninitialized in this function
- ortho.c: In function 'orthoEdges':
- ortho.c:1250: warning: 'ps' may be used uninitialized in this function
- ortho.c:152: warning: 'prevbp.y' may be used uninitialized in this function
- ortho.c:152: warning: 'prevbp.x' 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: warning: 'tq' may be used uninitialized in this function
- 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:26,
- from trapezoid.c:19:
- /usr/include/features.h:185:1: 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: 'tlastr' may be used uninitialized in this function
- trapezoid.c:434: warning: 'tfirstr' may be used uninitialized in this function
- CCLD libortho_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/ortho'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/ortho'
- Making install in sparse
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/sparse'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/sparse'
- Making install in patchwork
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/patchwork'
- CC patchwork.lo
- CC patchworkinit.lo
- CC tree_map.lo
- CCLD libpatchwork_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/patchwork'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/patchwork'
- Making install in common
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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
- 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:183: warning: 'pfx' may be used uninitialized in this function
- emit.c:182: warning: 'idnum' may be used uninitialized in this function
- emit.c: In function 'emit_edge':
- emit.c:1721: warning: 'segs' may be used uninitialized in this function
- emit.c:1723: warning: 'endcolor' may be used uninitialized in this function
- emit.c:1792: warning: 'bz.ep.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.sp.y' 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.size' may be used uninitialized in this function
- 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: In function 'xdotBB':
- emit.c:2437: warning: 'bb.LL.x' may be used uninitialized in this function
- emit.c:2437: warning: 'bb.UR.x' may be used uninitialized in this function
- emit.c:2472: warning: 'fontname' may be used uninitialized in this function
- emit.c:2471: warning: 'fontsize' may be used uninitialized in this function
- CCLD libcommon_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/common'
- make[4]: Nothing to be done for `install-exec-am'.
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/common'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/common'
- Making install in pack
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pack'
- make[4]: Nothing to be done for `install-exec-am'.
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 pack.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 pack.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 pack.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pack'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/pack'
- Making install in xdot
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/xdot'
- CC xdot.lo
- CCLD libxdot.la
- CCLD libxdot_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/xdot'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- /bin/sh ../../libtool --mode=install /usr/bin/install -c libxdot.la '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- libtool: install: /usr/bin/install -c .libs/libxdot.lai /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libxdot.la
- libtool: install: /usr/bin/install -c .libs/libxdot.a /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libxdot.a
- libtool: install: chmod 644 /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libxdot.a
- libtool: install: ranlib /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/2.6.18-371.3.1.el5/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib
- ----------------------------------------------------------------------
- Libraries have been installed in:
- /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 xdot.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 xdot.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /usr/bin/install -c -m 644 libxdot.pc '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- /usr/bin/install -c -m 644 xdot.h '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/xdot'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/xdot'
- Making install in gvc
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/gvc'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- /bin/sh ../../libtool --mode=install /usr/bin/install -c libgvc.la '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib'
- libtool: install: /usr/bin/install -c .libs/libgvc.lai /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgvc.la
- libtool: install: /usr/bin/install -c .libs/libgvc.a /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgvc.a
- libtool: install: chmod 644 /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/libgvc.a
- libtool: install: ranlib /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/2.6.18-371.3.1.el5/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib
- ----------------------------------------------------------------------
- Libraries have been installed in:
- /tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /usr/bin/install -c -m 644 gvc.3 '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/man/man3'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /usr/bin/install -c -m 644 gvc.3.pdf '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /usr/bin/install -c -m 644 libgvc.pc '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- /bin/mkdir -p '/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/include/graphviz'
- make[4]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/gvc'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/gvc'
- Making install in circogen
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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
- circpos.c: In function 'doBlock':
- circpos.c:264: warning: 'midAngle' may be used uninitialized in this function
- CC nodeset.lo
- CCLD libcircogen_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/circogen'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/circogen'
- Making install in dotgen
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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':
- mincross.c:581: warning: 'maxthispass' may be used uninitialized in this function
- mincross.c:374: warning: 'sepIndex' 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:269: warning: 'P' may be used uninitialized in this function
- dotsplines.c:268: warning: 'edges' may be used uninitialized in this function
- dotsplines.c: In function 'make_flat_edge':
- dotsplines.c:882: warning: 'lmaxx' may be used uninitialized in this function
- dotsplines.c:882: warning: 'lminx' may be used uninitialized in this function
- CC aspect.lo
- aspect.c: In function 'rank3':
- aspect.c:707: warning: 'fstNdGrp' may be used uninitialized in this function
- aspect.c:703: warning: 'nextMaxWidth' may be used uninitialized in this function
- aspect.c:702: warning: 'maxLayerIndex' may be used uninitialized in this function
- CCLD libdotgen_C.la
- make[4]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/dotgen'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/dotgen'
- Making install in fdpgen
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/fdpgen'
- make[3]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/fdpgen'
- Making install in neatogen
- make[3]: Entering directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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
- 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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib/neatogen'
- make[2]: *** [install-recursive] Error 1
- make[2]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz/lib'
- make[1]: *** [install-recursive] Error 1
- make[1]: Leaving directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/graphviz'
- make: *** [install] Error 2
- cp: omitting directory `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/Rgraphviz/src/libunix/lib/pkgconfig'
- cp: cannot stat `/tmp/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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/Rtmp5lnUVa/R.INSTALL71c64d6a2eca/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’
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