Rgraphviz 2.18.0
Kasper Daniel Hansen
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Rgraphviz | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | [ OK ] | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rgraphviz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
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checking whether we are cross compiling... no
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checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-apple-darwin13.4.0
checking host system type... x86_64-apple-darwin13.4.0
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checking whether build environment is sane... yes
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checking if assert needs __eprintf... clang: warning: argument unused during compilation: '-L/usr/local/lib'
clang: warning: argument unused during compilation: '-L/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
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
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config.status: creating lib/graph/Makefile
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config.status: creating plugin/Makefile
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config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix' 'CC=clang' 'CXX=clang++' 'CFLAGS=-Wall -mtune=core2 -g -O2' 'CXXFLAGS=-Wall -mtune=core2 -g -O2' 'LDFLAGS=-L/usr/local/lib' '--libdir=/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/pkgconfig' --cache-file=/dev/null --srcdir=.
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checking host system type... x86_64-apple-darwin13.4.0
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checking the name lister (/usr/bin/nm) interface... rm: conftest.dSYM: is a directory
BSD nm
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ok
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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 (swig not available)
tcldot: Yes
tclpathplan: Yes
gdtclft: No (gd not available)
tkspline: No (tk not available)
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make install-recursive
Making install in libltdl
/bin/sh /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/install-sh -d .
cp ./argz_.h argz.h-t
mv argz.h-t argz.h
make install-am
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fno-common -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -mtune=core2 -g -O2 -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo
libtool: link: ar cru .libs/dlopen.a dlopen.o
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c -fno-common -DPIC -o libltdlc_la-preopen.o
mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c -fno-common -DPIC -o libltdlc_la-lt__alloc.o
mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c -fno-common -DPIC -o libltdlc_la-lt_dlloader.o
mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c -fno-common -DPIC -o libltdlc_la-lt_error.o
mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c -fno-common -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 clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -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: clang -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c -fno-common -DPIC -o libltdlc_la-slist.o
mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo
/bin/sh ./libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c -o argz.lo argz.c
libtool: compile: clang -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -mtune=core2 -g -O2 -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c argz.c -fno-common -DPIC -o argz.o
mv -f .deps/argz.Tpo .deps/argz.Plo
/bin/sh ./libtool --tag=CC --mode=link clang -Wall -mtune=core2 -g -O2 -no-undefined -dlpreopen dlopen.la -L/usr/local/lib -o libltdlc.la libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo argz.lo
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && clang -Wall -mtune=core2 -g -O2 -c -fno-builtin -fno-rtti -fno-exceptions -fno-common -DPIC "libltdlcS.c")
libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT"
libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")
libtool: link: ar cru .libs/libltdlc.a libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o argz.o .libs/libltdlcS.o .libs/libltdlc.lax/dlopen.a/dlopen.o
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
Making install in lib
cd .. && /bin/sh /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu lib/Makefile
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system. You should only need it if
you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
You might want to install the `Automake' and `Perl' packages.
Grab them from any GNU archive site.
cd .. && /bin/sh ./config.status lib/Makefile
config.status: creating lib/Makefile
Making install in cdt
cd ../.. && /bin/sh ./config.status lib/cdt/Makefile depfiles
config.status: creating lib/cdt/Makefile
config.status: executing depfiles commands
CC dtclose.lo
CC dtdisc.lo
CC dtextract.lo
CC dtflatten.lo
CC dthash.lo
CC dtlist.lo
CC dtmethod.lo
CC dtopen.lo
CC dtrenew.lo
CC dtrestore.lo
CC dtsize.lo
CC dtstat.lo
CC dtstrhash.lo
CC dttree.lo
CC dttreeset.lo
CC dtview.lo
CC dtwalk.lo
CCLD libcdt.la
CCLD libcdt_C.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libcdt.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 cdt.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 cdt.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libcdt.pc '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 cdt.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in graph
cd ../.. && /bin/sh ./config.status lib/graph/Makefile depfiles
config.status: creating lib/graph/Makefile
config.status: executing depfiles commands
CC attribs.lo
attribs.c:240:7: warning: explicitly assigning a variable of type 'Agraph_t *' (aka 'struct Agraph_t *') to itself [-Wself-assign]
g = g;
˜ ^ ˜
1 warning generated.
CC agxbuf.lo
CC edge.lo
edge.c:271:10: warning: explicitly assigning a variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
dict = dict;
˜˜˜˜ ^ ˜˜˜˜
1 warning generated.
CC graph.lo
CC graphio.lo
CC lexer.lo
lexer.c:147:12: warning: returning 'unsigned char *' from a function with result type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return p;
^
lexer.c:435:26: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
LexPtr = scan_token(LexPtr, tbuf);
^˜˜˜˜˜
lexer.c:136:40: note: passing argument to parameter 'p' here
static char *scan_token(unsigned char *p, unsigned char *token)
^
lexer.c:435:34: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
LexPtr = scan_token(LexPtr, tbuf);
^˜˜˜
lexer.c:136:58: note: passing argument to parameter 'token' here
static char *scan_token(unsigned char *p, unsigned char *token)
^
3 warnings generated.
CC node.lo
node.c:138:10: warning: explicitly assigning a variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
dict = dict;
˜˜˜˜ ^ ˜˜˜˜
1 warning generated.
CC parser.lo
CC refstr.lo
CC trie.lo
CCLD libgraph.la
CCLD libgraph_C.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgraph.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 graph.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 graph.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libgraph.pc '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 graph.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in pathplan
cd ../.. && /bin/sh ./config.status lib/pathplan/Makefile depfiles
config.status: creating lib/pathplan/Makefile
config.status: executing depfiles commands
CC cvt.lo
cvt.c:276:13: warning: function 'append_bezier' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void append_bezier(Ppoint_t * bezier)
^
1 warning generated.
CC inpoly.lo
CC route.lo
CC shortest.lo
CC shortestpth.lo
CC solvers.lo
CC triang.lo
CC util.lo
CC visibility.lo
CCLD libpathplan.la
CCLD libpathplan_C.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 pathplan.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 pathplan.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libpathplan.pc '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 pathgeom.h pathplan.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in vpsc
cd ../.. && /bin/sh ./config.status lib/vpsc/Makefile depfiles
config.status: creating lib/vpsc/Makefile
config.status: executing depfiles commands
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in rbtree
cd ../.. && /bin/sh ./config.status lib/rbtree/Makefile depfiles
config.status: creating lib/rbtree/Makefile
config.status: executing depfiles commands
CC misc.lo
CC red_black_tree.lo
CC stack.lo
CCLD librbtree_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in ortho
cd ../.. && /bin/sh ./config.status lib/ortho/Makefile depfiles
config.status: creating lib/ortho/Makefile
config.status: executing depfiles commands
CC fPQ.lo
CC intset.lo
CC maze.lo
CC ortho.lo
CC partition.lo
partition.c:656:14: warning: variable 'size' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (tr[tr_start].d0 > 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
partition.c:665:10: note: uninitialized use occurs here
return size;
^˜˜˜
partition.c:656:10: note: remove the 'if' if its condition is always true
else if (tr[tr_start].d0 > 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
partition.c:620:16: note: initialize the variable 'size' to silence this warning
int i, size;
^
= 0
1 warning generated.
CC rawgraph.lo
CC sgraph.lo
CC trapezoid.lo
CCLD libortho_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sparse
cd ../.. && /bin/sh ./config.status lib/sparse/Makefile depfiles
config.status: creating lib/sparse/Makefile
config.status: executing depfiles commands
CC SparseMatrix.lo
CC general.lo
CC BinaryHeap.lo
CC IntStack.lo
CCLD libsparse_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in patchwork
cd ../.. && /bin/sh ./config.status lib/patchwork/Makefile depfiles
config.status: creating lib/patchwork/Makefile
config.status: executing depfiles commands
CC patchwork.lo
CC patchworkinit.lo
CC tree_map.lo
CCLD libpatchwork_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in common
cd ../.. && /bin/sh ./config.status lib/common/Makefile depfiles
config.status: creating lib/common/Makefile
config.status: executing depfiles commands
CC arrows.lo
CC colxlate.lo
CC fontmetrics.lo
CC args.lo
CC memory.lo
CC globals.lo
CC htmllex.lo
CC htmlparse.lo
CC htmltable.lo
CC input.lo
CC pointset.lo
CC postproc.lo
CC routespl.lo
CC splines.lo
CC psusershape.lo
CC timing.lo
CC labels.lo
CC ns.lo
CC shapes.lo
shapes.c:1253:12: warning: explicitly assigning a variable of type 'double' to itself [-Wself-assign]
angle = angle;
˜˜˜˜˜ ^ ˜˜˜˜˜
shapes.c:1261:12: warning: explicitly assigning a variable of type 'double' to itself [-Wself-assign]
angle = angle;
˜˜˜˜˜ ^ ˜˜˜˜˜
2 warnings generated.
CC utils.lo
CC geom.lo
CC output.lo
CC emit.lo
CCLD libcommon_C.la
make[4]: Nothing to be done for `install-exec-am'.
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in pack
cd ../.. && /bin/sh ./config.status lib/pack/Makefile depfiles
config.status: creating lib/pack/Makefile
config.status: executing depfiles commands
CC ccomps.lo
CC pack.lo
pack.c:936:9: warning: variable 'pts' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (pinfo->mode == l_array) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pack.c:953:12: note: uninitialized use occurs here
return pts;
^˜˜
pack.c:936:5: note: remove the 'if' if its condition is always true
if (pinfo->mode == l_array) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pack.c:920:15: note: initialize the variable 'pts' to silence this warning
point* pts;
^
= NULL
1 warning generated.
CCLD libpack_C.la
make[4]: Nothing to be done for `install-exec-am'.
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 pack.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 pack.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 pack.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in xdot
cd ../.. && /bin/sh ./config.status lib/xdot/Makefile depfiles
config.status: creating lib/xdot/Makefile
config.status: executing depfiles commands
CC xdot.lo
CCLD libxdot.la
CCLD libxdot_C.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libxdot.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 xdot.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 xdot.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libxdot.pc '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 xdot.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in gvc
cd ../.. && /bin/sh ./config.status lib/gvc/Makefile depfiles
config.status: creating lib/gvc/Makefile
config.status: executing depfiles commands
CC gvrender.lo
CC gvlayout.lo
CC gvdevice.lo
CC gvloadimage.lo
CC gvcontext.lo
CC gvjobs.lo
CC gvevent.lo
CC gvplugin.lo
gvplugin.c:62:13: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
if (api < 0 || api >= ARRAY_SIZE(api_names))
˜˜˜ ^ ˜
gvplugin.c:80:13: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
if (api < 0)
˜˜˜ ^ ˜
gvplugin.c:137:13: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
if (api < 0)
˜˜˜ ^ ˜
gvplugin.c:268:13: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
if (api < 0)
˜˜˜ ^ ˜
gvplugin.c:362:13: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
if (api < 0)
˜˜˜ ^ ˜
5 warnings generated.
CC gvconfig.lo
CC gvtextlayout.lo
CC gvusershape.lo
CC gvc.lo
CCLD libgvc.la
CCLD libgvc_C.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvc.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 gvc.3 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 gvc.3.pdf '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libgvc.pc '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in circogen
cd ../.. && /bin/sh ./config.status lib/circogen/Makefile depfiles
config.status: creating lib/circogen/Makefile
config.status: executing depfiles commands
CC circularinit.lo
CC nodelist.lo
CC block.lo
CC edgelist.lo
CC circular.lo
CC deglist.lo
CC blocktree.lo
CC blockpath.lo
CC circpos.lo
CC nodeset.lo
CCLD libcircogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in dotgen
cd ../.. && /bin/sh ./config.status lib/dotgen/Makefile depfiles
config.status: creating lib/dotgen/Makefile
config.status: executing depfiles commands
CC acyclic.lo
CC class1.lo
CC class2.lo
class2.c:53:10: warning: explicitly assigning a variable of type 'edge_t *' (aka 'struct Agedge_t *') to itself [-Wself-assign]
orig = orig;
˜˜˜˜ ^ ˜˜˜˜
1 warning generated.
CC cluster.lo
CC compound.lo
CC conc.lo
CC decomp.lo
CC fastgr.lo
CC flat.lo
CC dotinit.lo
CC mincross.lo
CC position.lo
CC rank.lo
CC sameport.lo
CC dotsplines.lo
dotsplines.c:1604:25: warning: expression result unused [-Wunused-value]
lp = ED_label(e)->pos, lp;
^˜
1 warning generated.
CC aspect.lo
CCLD libdotgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in fdpgen
cd ../.. && /bin/sh ./config.status lib/fdpgen/Makefile depfiles
config.status: creating lib/fdpgen/Makefile
config.status: executing depfiles commands
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
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in neatogen
cd ../.. && /bin/sh ./config.status lib/neatogen/Makefile depfiles
config.status: creating lib/neatogen/Makefile
config.status: executing depfiles commands
CC adjust.lo
adjust.c:674:30: warning: variable 'nedge_nodes' is uninitialized when used here [-Wuninitialized]
if (elabels && IS_LNODE(n)) nedge_nodes++;
^˜˜˜˜˜˜˜˜˜˜
adjust.c:670:23: note: initialize the variable 'nedge_nodes' to silence this warning
int i, nedge_nodes;
^
= 0
adjust.c:1073:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PORTHO_YX:
^˜˜˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1074:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PORTHO:
^˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1075:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PORTHOXY:
^˜˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1076:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PORTHOYX:
^˜˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1077:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_ORTHO_YX:
^˜˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1078:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_ORTHO:
^˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1079:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_ORTHOXY:
^˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1080:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_ORTHOYX:
^˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1070:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PUSHPULL:
^˜˜˜˜˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1067:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case AM_PUSH:
^˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1099:2: warning: variable 'ret' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default: /* to silence warnings */
^˜˜˜˜˜˜
adjust.c:1105:9: note: uninitialized use occurs here
return ret;
^˜˜
adjust.c:1045:12: note: initialize the variable 'ret' to silence this warning
int ret;
^
= 0
12 warnings generated.
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:603:15: warning: unused variable 'rtr' [-Wunused-variable]
router_t* rtr = 0;
^
1 warning generated.
CC stuff.lo
CC voronoi.lo
CC stress.lo
stress.c:1383:6: warning: variable 'delta' is uninitialized when used here [-Wuninitialized]
delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);
^˜˜˜˜
stress.c:1370:17: note: initialize the variable 'delta' to silence this warning
double delta;
^
= 0.0
1 warning generated.
CC kkutils.lo
CC matrix_ops.lo
CC embed_graph.lo
CC dijkstra.lo
CC conjgrad.lo
CC pca.lo
CC closest.lo
CC bfs.lo
CC constraint.lo
CC quad_prog_solve.lo
CC smart_ini_x.lo
CC constrained_majorization.lo
CC opt_arrangement.lo
CC overlap.lo
CC call_tri.lo
CC compute_hierarchy.lo
CC delaunay.lo
CC multispline.lo
CCLD libneatogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in twopigen
cd ../.. && /bin/sh ./config.status lib/twopigen/Makefile depfiles
config.status: creating lib/twopigen/Makefile
config.status: executing depfiles commands
CC twopiinit.lo
CC circle.lo
CCLD libtwopigen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sfdpgen
cd ../.. && /bin/sh ./config.status lib/sfdpgen/Makefile depfiles
config.status: creating lib/sfdpgen/Makefile
config.status: executing depfiles commands
CC sfdpinit.lo
CC spring_electrical.lo
spring_electrical.c:287:10: warning: explicitly assigning a variable of type 'double' to itself [-Wself-assign]
step = step;
˜˜˜˜ ^ ˜˜˜˜
spring_electrical.c:1308:16: warning: use of unary operator that may be intended as compound assignment (-=)
nsuper_avg =- 0;
^˜
spring_electrical.c:1548:16: warning: use of unary operator that may be intended as compound assignment (-=)
nsuper_avg =- 0;
^˜
3 warnings generated.
CC LinkedList.lo
CC sparse_solve.lo
CC post_process.lo
CC stress_model.lo
CC uniform_stress.lo
CC QuadTree.lo
CC Multilevel.lo
CC PriorityQueue.lo
CCLD libsfdpgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in osage
cd ../.. && /bin/sh ./config.status lib/osage/Makefile depfiles
config.status: creating lib/osage/Makefile
config.status: executing depfiles commands
CC osageinit.lo
CCLD libosage_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in plugin
cd .. && /bin/sh ./config.status plugin/Makefile
config.status: creating plugin/Makefile
Making install in core
cd ../.. && /bin/sh ./config.status plugin/core/Makefile depfiles
config.status: creating plugin/core/Makefile
config.status: executing depfiles commands
CC gvplugin_core.lo
CC gvrender_core_dot.lo
CC gvrender_core_fig.lo
CC gvrender_core_map.lo
CC gvrender_core_ps.lo
CC gvrender_core_svg.lo
CC gvrender_core_tk.lo
CC gvrender_core_vml.lo
CC gvloadimage_core.lo
CCLD libgvplugin_core_C.la
CCLD libgvplugin_core.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_core.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in dot_layout
cd ../.. && /bin/sh ./config.status plugin/dot_layout/Makefile depfiles
config.status: creating plugin/dot_layout/Makefile
config.status: executing depfiles commands
CC gvplugin_dot_layout.lo
CC gvlayout_dot_layout.lo
gvlayout_dot_layout.c:45:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma comment( lib, "graph.lib" )
^
gvlayout_dot_layout.c:46:13: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma comment( lib, "dotgen.lib" )
^
2 warnings generated.
CCLD libgvplugin_dot_layout_C.la
CCLD libgvplugin_dot_layout.la
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_dot_layout.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in neato_layout
cd ../.. && /bin/sh ./config.status plugin/neato_layout/Makefile depfiles
config.status: creating plugin/neato_layout/Makefile
config.status: executing depfiles commands
CC gvplugin_neato_layout.lo
CC gvlayout_neato_layout.lo
CCLD libgvplugin_neato_layout_C.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
CCLD libgvplugin_neato_layout.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
../../config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_neato_layout.la '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a(dbg.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
cd . && /bin/sh ./config.status Makefile
config.status: creating Makefile
make[3]: Nothing to be done for `install-exec-am'.
config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
/usr/bin/install -c -m 644 graphviz.7 '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 graphviz_version.h '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
config/install-sh -c -d '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
/usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
cp: /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/graphviz is a directory (not copied).
cp: /Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig is a directory (not copied).
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for deflateBound in -lz... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure: PKG_CFLAGS= -I/Users/biocbuild/bbs-3.4-bioc/meat/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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c LL_funcs.c -o LL_funcs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c Rgraphviz.c -o Rgraphviz.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c agopen.c -o agopen.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c agread.c -o agread.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c agwrite.c -o agwrite.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c bezier.c -o bezier.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c buildEdgeList.c -o buildEdgeList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c buildNodeList.c -o buildNodeList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c doLayout.c -o doLayout.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c graphvizVersion.c -o graphvizVersion.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/Users/biocbuild/bbs-3.4-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rgraphviz)