BioC 2.12: CHECK report for Rgraphviz on george2

Package: Rgraphviz

Version: 2.4.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rgraphviz_2.4.1.tar.gz

StartedAt: 2013-10-09 04:31:39 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:35:15 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 215.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rgraphviz.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘2.4.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/graphviz/libltdl/lt__strl.lo src/graphviz/libltdl/lt__strl.o
  src/libwin/i386/lib/libcdt.a src/libwin/i386/lib/libcdt.la
  src/libwin/i386/lib/libgraph.a src/libwin/i386/lib/libgraph.la
  src/libwin/i386/lib/libgvc.a src/libwin/i386/lib/libgvc.la
  src/libwin/i386/lib/libgvplugin_core.a
  src/libwin/i386/lib/libgvplugin_core.la
  src/libwin/i386/lib/libgvplugin_dot_layout.a
  src/libwin/i386/lib/libgvplugin_dot_layout.la
  src/libwin/i386/lib/libgvplugin_neato_layout.a
  src/libwin/i386/lib/libgvplugin_neato_layout.la
  src/libwin/i386/lib/libpathplan.a src/libwin/i386/lib/libpathplan.la
  src/libwin/i386/lib/libxdot.a src/libwin/i386/lib/libxdot.la
  src/libwin/x64/lib/libcdt.a src/libwin/x64/lib/libcdt.la
  src/libwin/x64/lib/libgraph.a src/libwin/x64/lib/libgraph.la
  src/libwin/x64/lib/libgvc.a src/libwin/x64/lib/libgvc.la
  src/libwin/x64/lib/libgvplugin_core.a
  src/libwin/x64/lib/libgvplugin_core.la
  src/libwin/x64/lib/libgvplugin_dot_layout.a
  src/libwin/x64/lib/libgvplugin_dot_layout.la
  src/libwin/x64/lib/libgvplugin_neato_layout.a
  src/libwin/x64/lib/libgvplugin_neato_layout.la
  src/libwin/x64/lib/libpathplan.a src/libwin/x64/lib/libpathplan.la
  src/libwin/x64/lib/libxdot.a src/libwin/x64/lib/libxdot.la
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  src/graphviz/libltdl/m4/lt˜obsolete.m4
  src/graphviz/m4/lt˜obsolete.m4
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rgraphviz’ can be installed ... [90s/133s] OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/7s]
 [5s/8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00check.log’
for details.

* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... 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
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checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
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checking for suffix of object files... o
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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 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... 1572864
checking whether the shell understands some XSI constructs... yes
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checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
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checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
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checking whether we are using the GNU C++ compiler... (cached) yes
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checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
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checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
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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
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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
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checking if g++ PIC flag -fPIC -DPIC works... yes
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checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/local/root/lib/root /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa /lib32 /usr/lib32 
checking for library containing dlopen... -ldl
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checking whether lt_dlinterface_register is declared... yes
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checking where to find libltdl headers... 
checking where to find libltdl library... -lltdl
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checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/usr/include/tcl8.5 -I/usr/include/tcl8.5/generic
checking tcl.h usability... yes
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using /usr/lib/tclConfig.sh
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using /usr/lib/tkConfig.sh
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
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checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix'  'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2 -Wall' 'CXXFLAGS=-g -O2 -Wall' 'LDFLAGS=-L/usr/local/lib' '--libdir=/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib' '--includedir=/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'R_LIBS=/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck:/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck' --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... 1572864
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/local/root/lib/root /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa /lib32 /usr/lib32 
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

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

graphviz-2.28.0 will be compiled with the following:

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

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

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

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

  tcldot:        Yes
  tclpathplan:   Yes
  gdtclft:       No (gd not available)
  tkspline:      Yes
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
make  install-am
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
/bin/bash ./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 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -Wall -module -avoid-version -L/usr/local/lib -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/bash ./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 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./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 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./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 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./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 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./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 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c  -fPIC -DPIC -o libltdlc_la-ltdl.o
ltdl.c: In function 'try_dlopen':
ltdl.c:1268:19: warning: the address of 'libext' will always evaluate as 'true' [-Waddress]
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/bash ./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 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -Wall -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/bash ./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 -Wall -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 -Wall -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/bash ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -Wall -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 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 -Wall -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 "/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")
libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o lt__strl.o .libs/libltdlcS.o  .libs/libltdlc.lax/dlopen.a/dlopen.o 
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
Making install in cdt
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/cdt'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       dtclose.lo
  CC       dtdisc.lo
dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CC       dtextract.lo
  CC       dtflatten.lo
  CC       dthash.lo
dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dthash.c: In function 'dthash':
dthash.c:276:11: warning: 's' may be used uninitialized in this function [-Wuninitialized]
dthash.c:306:19: warning: 'r' may be used uninitialized in this function [-Wuninitialized]
  CC       dtlist.lo
dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CC       dtmethod.lo
  CC       dtopen.lo
  CC       dtrenew.lo
  CC       dtrestore.lo
  CC       dtsize.lo
dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CC       dtstat.lo
dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CC       dtstrhash.lo
  CC       dttree.lo
dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dttree.c: In function 'dttree':
dttree.c:294:15: warning: 'me' may be used uninitialized in this function [-Wuninitialized]
dttree.c:231:6: warning: 'root' may be used uninitialized in this function [-Wuninitialized]
  CC       dttreeset.lo
dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CC       dtview.lo
dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtview.c: In function 'dtvsearch':
dtview.c:20:12: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
dtview.c:19:11: warning: 'o' may be used uninitialized in this function [-Wuninitialized]
  CC       dtwalk.lo
dtwalk.c: In function 'dtwalk':
dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  CCLD     libcdt.la
  CCLD     libcdt_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/cdt'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libcdt.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/graph'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       attribs.lo
  CC       agxbuf.lo
  CC       edge.lo
  CC       graph.lo
  CC       graphio.lo
  CC       lexer.lo
lexer.c: In function 'scan_token':
lexer.c:147:5: warning: pointer targets in return differ in signedness [-Wpointer-sign]
lexer.c: In function 'html_pair':
lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
lexer.c: In function 'aglex':
lexer.c:435:6: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]
lexer.c:136:14: note: expected 'unsigned char *' but argument is of type 'char *'
lexer.c:435:6: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]
lexer.c:136:14: note: expected 'unsigned char *' but argument is of type 'char *'
lexer.c: In function 'aglasterr':
lexer.c:527:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  CC       node.lo
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
  CCLD     libgraph_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/graph'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgraph.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pathplan'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       cvt.lo
cvt.c:276:13: warning: 'append_bezier' defined but not used [-Wunused-function]
  CC       inpoly.lo
  CC       route.lo
  CC       shortest.lo
shortest.c: In function 'loadtriangle':
shortest.c:539:8: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
  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 `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pathplan'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/vpsc'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/rbtree'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/rbtree'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/ortho'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       fPQ.lo
  CC       intset.lo
  CC       maze.lo
maze.c: In function 'mkMazeGraph':
maze.c:411:5: warning: value computed is not used [-Wunused-value]
maze.c:325:20: warning: variable 'ncnt' set but not used [-Wunused-but-set-variable]
  CC       ortho.lo
ortho.c: In function 'addLoop':
ortho.c:461:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable]
ortho.c: In function 'addNodeEdges':
ortho.c:497:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable]
ortho.c: In function 'emitGraph':
ortho.c:1523:5: warning: format not a string literal and no format arguments [-Wformat-security]
ortho.c: In function 'orthoEdges':
ortho.c:192:11: warning: 'prevbp.x' may be used uninitialized in this function [-Wuninitialized]
ortho.c:152:22: note: 'prevbp.x' was declared here
ortho.c:179:11: warning: 'prevbp.y' may be used uninitialized in this function [-Wuninitialized]
ortho.c:152:22: note: 'prevbp.y' was declared here
ortho.c:1356:9: warning: 'ps' may be used uninitialized in this function [-Wuninitialized]
  CC       partition.lo
partition.c: In function 'traverse_polygon':
partition.c:328:7: warning: variable 'do_switch' set but not used [-Wunused-but-set-variable]
partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
partition.c: In function 'partition':
partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable]
partition.c: In function 'make_new_monotone_poly':
partition.c:274:5: warning: 'tq' may be used uninitialized in this function [-Wuninitialized]
partition.c:273:5: warning: 'tp' may be used uninitialized in this function [-Wuninitialized]
partition.c: In function 'monotonate_trapezoids':
partition.c:665:3: warning: 'size' may be used uninitialized in this function [-Wuninitialized]
  CC       rawgraph.lo
  CC       sgraph.lo
  CC       trapezoid.lo
trapezoid.c:22:0: warning: "__USE_ISOC99" redefined [enabled by default]
/usr/include/features.h:241:0: note: this is the location of the previous definition
trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
trapezoid.c: In function 'add_segment':
trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable]
trapezoid.c:996:19: warning: 'tlastr' may be used uninitialized in this function [-Wuninitialized]
trapezoid.c:996:19: warning: 'tfirstr' may be used uninitialized in this function [-Wuninitialized]
  CCLD     libortho_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/ortho'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/ortho'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/ortho'
Making install in sparse
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sparse'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       SparseMatrix.lo
SparseMatrix.c: In function 'SparseMatrix_import_binary':
SparseMatrix.c:629:48: warning: variable 'iread' set but not used [-Wunused-but-set-variable]
  CC       general.lo
  CC       BinaryHeap.lo
  CC       IntStack.lo
  CCLD     libsparse_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sparse'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sparse'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sparse'
Making install in patchwork
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/patchwork'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/patchwork'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/patchwork'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/patchwork'
Making install in common
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/common'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       arrows.lo
arrows.c: In function 'arrowOrthoClip':
arrows.c:397:21: warning: 'hlen' may be used uninitialized in this function [-Wuninitialized]
  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
psusershape.c: In function 'user_init':
psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
psusershape.c: In function 'ps_string':
psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
  CC       timing.lo
  CC       labels.lo
labels.c: In function 'xml_url_string':
labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
  CC       ns.lo
  CC       shapes.lo
  CC       utils.lo
utils.c: In function 'htmlEntityUTF8':
utils.c:1455:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
utils.c: In function 'latin1ToUTF8':
utils.c:1530:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
utils.c: In function 'utf8ToLatin1':
utils.c:1572:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
  CC       geom.lo
  CC       output.lo
  CC       emit.lo
emit.c: In function 'emit_xdot':
emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable]
emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable]
emit.c: In function 'nodeIntersect':
emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable]
emit.c: In function 'xdotBB':
emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable]
emit.c: In function 'style_token':
emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
emit.c: In function 'emit_edge_graphics':
emit.c:1932:44: warning: 'bz.list' may be used uninitialized in this function [-Wuninitialized]
emit.c:1932:44: warning: 'bz.size' may be used uninitialized in this function [-Wuninitialized]
emit.c:1921:12: warning: 'bz.sflag' may be used uninitialized in this function [-Wuninitialized]
emit.c:1932:12: warning: 'bz.eflag' may be used uninitialized in this function [-Wuninitialized]
emit.c:1776:32: warning: 'endcolor' may be used uninitialized in this function [-Wuninitialized]
emit.c:1723:11: note: 'endcolor' was declared here
emit.c:1744:9: warning: 'segs' may be used uninitialized in this function [-Wuninitialized]
emit.c:1721:18: note: 'segs' was declared here
emit.c: In function 'getObjId':
emit.c:214:13: warning: 'pfx' may be used uninitialized in this function [-Wuninitialized]
emit.c: In function 'xdotBB':
emit.c:2515:9: warning: 'fontname' may be used uninitialized in this function [-Wuninitialized]
emit.c:2515:9: warning: 'fontsize' may be used uninitialized in this function [-Wuninitialized]
  CCLD     libcommon_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/common'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/common'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/common'
Making install in pack
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pack'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       ccomps.lo
  CC       pack.lo
pack.c: In function 'putGraphs':
pack.c:920:12: warning: 'pts' may be used uninitialized in this function [-Wuninitialized]
  CCLD     libpack_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pack'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pack.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pack.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pack.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pack'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/pack'
Making install in xdot
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/xdot'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       xdot.lo
  CCLD     libxdot.la
  CCLD     libxdot_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/xdot'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libxdot.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 xdot.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 xdot.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxdot.pc '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 xdot.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/xdot'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/xdot'
Making install in gvc
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/gvc'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  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 `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/gvc'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/libgvc.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 gvc.3 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 gvc.3.pdf '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgvc.pc '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/gvc'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/gvc'
Making install in circogen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/circogen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  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:338:13: warning: 'midAngle' may be used uninitialized in this function [-Wuninitialized]
circpos.c:264:39: note: 'midAngle' was declared here
  CC       nodeset.lo
  CCLD     libcircogen_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/circogen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/circogen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/circogen'
Making install in dotgen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/dotgen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  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.constprop.12':
mincross.c:421:12: warning: 'sepIndex' may be used uninitialized in this function [-Wuninitialized]
mincross.c:374:9: note: 'sepIndex' was declared here
mincross.c:637:2: warning: 'maxthispass' may be used uninitialized in this function [-Wuninitialized]
  CC       position.lo
  CC       rank.lo
  CC       sameport.lo
  CC       dotsplines.lo
dotsplines.c: In function 'completeregularpath':
dotsplines.c:1866:9: warning: variable 'pn' set but not used [-Wunused-but-set-variable]
dotsplines.c:1865:13: warning: variable 'pp' set but not used [-Wunused-but-set-variable]
dotsplines.c: In function '_dot_splines':
dotsplines.c:490:6: warning: 'P' may be used uninitialized in this function [-Wuninitialized]
dotsplines.c:488:6: warning: 'edges' may be used uninitialized in this function [-Wuninitialized]
dotsplines.c: In function 'make_flat_edge':
dotsplines.c:993:18: warning: 'lmaxx' may be used uninitialized in this function [-Wuninitialized]
dotsplines.c:882:19: note: 'lmaxx' was declared here
dotsplines.c:997:18: warning: 'lminx' may be used uninitialized in this function [-Wuninitialized]
dotsplines.c:882:12: note: 'lminx' was declared here
  CC       aspect.lo
aspect.c: In function 'computeCombiAR':
aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable]
aspect.c: In function 'rank3':
aspect.c:799:30: warning: 'fstNdGrp' may be used uninitialized in this function [-Wuninitialized]
aspect.c:707:18: note: 'fstNdGrp' was declared here
aspect.c:750:2: warning: 'nextMaxWidth' may be used uninitialized in this function [-Wuninitialized]
aspect.c:703:12: note: 'nextMaxWidth' was declared here
aspect.c:737:18: warning: 'maxLayerIndex' may be used uninitialized in this function [-Wuninitialized]
aspect.c:702:9: note: 'maxLayerIndex' was declared here
  CCLD     libdotgen_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/dotgen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/dotgen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/dotgen'
Making install in fdpgen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/fdpgen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  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 `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/fdpgen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/fdpgen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/fdpgen'
Making install in neatogen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/neatogen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       adjust.lo
adjust.c: In function 'getSizes':
adjust.c:681:17: warning: 'nedge_nodes' may be used uninitialized in this function [-Wuninitialized]
adjust.c: In function 'removeOverlapWith':
adjust.c:1045:9: warning: 'ret' may be used uninitialized in this function [-Wuninitialized]
  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 'makeObstacle':
neatosplines.c:363:13: warning: variable 'desc' set but not used [-Wunused-but-set-variable]
neatosplines.c: In function '_spline_edges':
neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable]
  CC       stuff.lo
  CC       voronoi.lo
voronoi.c: In function 'voronoi':
voronoi.c:48:7: warning: 'newintstar.y' may be used uninitialized in this function [-Wuninitialized]
  CC       stress.lo
stress.c: In function 'mdsModel':
stress.c:1383:12: warning: 'delta' may be used uninitialized in this function [-Wuninitialized]
  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]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/neatogen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/neatogen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/neatogen'
Making install in twopigen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/twopigen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       twopiinit.lo
  CC       circle.lo
circle.c: In function 'circleLayout':
circle.c:285:5: warning: 'delx' may be used uninitialized in this function [-Wuninitialized]
circle.c:268:20: note: 'delx' was declared here
  CCLD     libtwopigen_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/twopigen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/twopigen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/twopigen'
Making install in sfdpgen
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sfdpgen'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       sfdpinit.lo
  CC       spring_electrical.lo
spring_electrical.c: In function 'rotate':
spring_electrical.c:1850:8: warning: variable 'y' set but not used [-Wunused-but-set-variable]
  CC       LinkedList.lo
  CC       sparse_solve.lo
  CC       post_process.lo
post_process.c: In function 'StressMajorizationSmoother2_new':
post_process.c:110:36: warning: variable 'dd' set but not used [-Wunused-but-set-variable]
post_process.c: In function 'StressMajorizationSmoother_smooth':
post_process.c:578:102: warning: variable 'res' set but not used [-Wunused-but-set-variable]
post_process.c:578:9: warning: variable 'w' set but not used [-Wunused-but-set-variable]
post_process.c:577:32: warning: variable 'jw' set but not used [-Wunused-but-set-variable]
post_process.c:577:27: warning: variable 'iw' set but not used [-Wunused-but-set-variable]
post_process.c: In function 'TriangleSmoother_new':
post_process.c:698:68: warning: variable 'jd' set but not used [-Wunused-but-set-variable]
post_process.c:698:63: warning: variable 'id' set but not used [-Wunused-but-set-variable]
  CC       stress_model.lo
  CC       uniform_stress.lo
uniform_stress.c: In function 'uniform_stress':
uniform_stress.c:112:8: warning: variable 'res' set but not used [-Wunused-but-set-variable]
  CC       QuadTree.lo
  CC       Multilevel.lo
Multilevel.c: In function 'maximal_independent_vertex_set':
Multilevel.c:87:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Multilevel.c: In function 'maximal_independent_vertex_set_RS':
Multilevel.c:138:57: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
Multilevel.c:138:48: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_leaves_first':
Multilevel.c:327:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_supernodes_first':
Multilevel.c:502:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]
Multilevel.c: In function 'maximal_independent_edge_set_heavest_cluster_pernode_leaves_first':
Multilevel.c:646:30: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  CC       PriorityQueue.lo
  CCLD     libsfdpgen_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sfdpgen'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sfdpgen'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/sfdpgen'
Making install in osage
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/osage'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       osageinit.lo
  CCLD     libosage_C.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/osage'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/osage'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib/osage'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/lib'
Making install in plugin
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
Making install in core
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/core'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       gvplugin_core.lo
  CC       gvrender_core_dot.lo
gvrender_core_dot.c: In function 'xdot_points':
gvrender_core_dot.c:107:12: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
  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
gvrender_core_tk.c: In function 'tkgen_print_tags':
gvrender_core_tk.c:58:18: warning: variable 'ObjId' set but not used [-Wunused-but-set-variable]
gvrender_core_tk.c:57:21: warning: variable 'ObjPart' set but not used [-Wunused-but-set-variable]
  CC       gvrender_core_vml.lo
gvrender_core_vml.c: In function 'vml_ellipse':
gvrender_core_vml.c:452:38: warning: variable 'bottom' set but not used [-Wunused-but-set-variable]
gvrender_core_vml.c:452:26: warning: variable 'right' set but not used [-Wunused-but-set-variable]
  CC       gvloadimage_core.lo
  CCLD     libgvplugin_core_C.la
  CCLD     libgvplugin_core.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/core'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_core.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/core'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/core'
Making install in dot_layout
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/dot_layout'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       gvplugin_dot_layout.lo
  CC       gvlayout_dot_layout.lo
gvlayout_dot_layout.c:45:0: warning: ignoring #pragma comment  [-Wunknown-pragmas]
gvlayout_dot_layout.c:46:0: warning: ignoring #pragma comment  [-Wunknown-pragmas]
  CCLD     libgvplugin_dot_layout_C.la
  CCLD     libgvplugin_dot_layout.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/dot_layout'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/dot_layout'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/dot_layout'
Making install in neato_layout
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/neato_layout'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
  CC       gvplugin_neato_layout.lo
  CC       gvlayout_neato_layout.lo
  CCLD     libgvplugin_neato_layout_C.la
  CCLD     libgvplugin_neato_layout.la
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/neato_layout'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: finish: PATH="/home/biocbuild/bin:/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[5]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[5]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz/plugin'
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[3]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man7'
 /usr/bin/install -c -m 644 graphviz.7 '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/man/man7'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graphviz_version.h '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc'
 /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/share/graphviz/doc'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
make[1]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/graphviz'
cp: omitting directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/graphviz'
cp: omitting directory `/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/lib/pkgconfig'
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/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c LL_funcs.c -o LL_funcs.o
LL_funcs.c: In function ‘Rgraphviz_agopenSimple’:
LL_funcs.c:430:29: warning: variable ‘curNode’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c Rgraphviz.c -o Rgraphviz.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c RgraphvizInit.c -o RgraphvizInit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c agopen.c -o agopen.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c agread.c -o agread.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c agwrite.c -o agwrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c bezier.c -o bezier.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c buildEdgeList.c -o buildEdgeList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c buildNodeList.c -o buildNodeList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c doLayout.c -o doLayout.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c graphvizVersion.c -o graphvizVersion.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -I/home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -shared -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘Rgraphviz’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rgraphviz)

name	user	system	elapsed
AgEdge-class	0.088	0.000	0.087
AgNode-class	0.060	0.000	0.057
AgTextLabel-class	0.076	0.000	0.075
BezierCurve-class	0.060	0.000	0.058
GraphvizLayouts	0.028	0.000	0.029
Ragraph-class	0.120	0.004	0.126
agopen	0.052	0.000	0.054
agopenSimple	0.256	0.000	0.261
agwrite	0.036	0.000	0.043
boundingBox-class	0.028	0.004	0.033
buildNodeList	0.024	0.000	0.027
clusterData-methods	0.448	0.016	0.469
getDefaultAttrs	0.016	0.000	0.016
graphLayout	0.040	0.000	0.039
graphvizCapabilities	0.016	0.000	0.015
graphvizVersion	0.012	0.000	0.012
layoutGraph	0.448	0.004	0.452
makeNodeAttrs	0.012	0.004	0.017
pEdge-class	0.024	0.012	0.034
pNode-class	0.020	0.012	0.030
pieGlyph	0.028	0.000	0.026
plot-methods	0.016	0.000	0.016
removedEdges	0.028	0.000	0.026
renderGraph	0.288	0.008	0.309
toDot-methods	0.040	0.008	0.046
toFile	0.084	0.004	0.121
xyPoint-class	0.012	0.012	0.025