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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rgraphviz_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘2.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rgraphviz’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: `aclocal-1.12' is missing on your system.  You should only need it if
  WARNING: `automake-1.12' is missing on your system.  You should only need it if
  lexer.c:527:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.graphviz_build_version’
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/Rgraphviz/libs/Rgraphviz.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rgraphviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Rgraphviz’ ...
** using staged installation
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for flex... no
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checking for gawk... (cached) gawk
checking whether ln -s works... yes
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checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/bin/tclsh8.6
checking whether gcc and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking dependency style of g++ -std=gnu++11... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking for inline... inline
checking for windres... no
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... grep
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
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checking stdarg.h usability... yes
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checking malloc.h usability... yes
checking malloc.h presence... yes
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checking search.h usability... yes
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checking values.h usability... yes
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checking float.h usability... yes
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checking time.h usability... yes
checking time.h presence... yes
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checking setjmp.h usability... yes
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checking sys/time.h usability... yes
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checking sys/select.h usability... yes
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checking fpu_control.h usability... yes
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checking sys/fpu.h usability... no
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checking sys/socket.h usability... yes
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checking sys/mman.h usability... yes
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checking sys/ioctl.h usability... yes
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checking sys/inotify.h usability... yes
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checking langinfo.h usability... yes
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checking libintl.h usability... yes
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checking crt_externs.h usability... no
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checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for socklen_t... yes
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checking for struct dioattr... no
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checking libgen.h usability... yes
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checking for basename in -lgen... no
checking for working alloca.h... yes
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checking for __freadable... yes
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
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checking for pow... no
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checking for a sed that does not truncate output... /bin/sed
checking for fgrep... grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 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 object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking dependency style of g++ -std=gnu++11... (cached) gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc 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 for ld used by g++ -std=gnu++11... /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++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 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/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu 
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
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checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
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checking whether lt_dlinterface_register is declared... yes
checking for lt_dladvise_preload in -lltdl... yes
checking where to find libltdl headers... 
checking where to find libltdl library... -lltdl
checking for unistd.h... (cached) yes
checking for dl.h... no
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checking for dld.h... no
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checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking for X... disabled
configure: WARNING: X11 not available.
checking tcl.h usability... no
checking tcl.h presence... no
checking for tcl.h... no
configure: WARNING: Unable to find header tcl.h. The Tcl packages will not be built
configure: WARNING: No Tcl. The Tk packages will not be built either
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for X11/Xaw/Text.h... no
configure: WARNING: Optional Xaw library not available - missing headers
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... no
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checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... no
checking for qmake-qt4... no
checking for qmake-qt3... no
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checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... yes
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix'  'CC=gcc' 'CXX=g++ -std=gnu++11' 'CFLAGS=-g -O2 -Wall' 'CXXFLAGS=-g -O2 -Wall' 'LDFLAGS=-L/usr/local/lib' '--libdir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'R_LIBS=/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rgraphviz/00new' --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
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... 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... /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 object... ok
checking how to run the C preprocessor... gcc -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 supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc 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/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu 
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

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

graphviz-2.28.0 will be compiled with the following:

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

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

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

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

  tcldot:        No (tcl not available)
  tclpathplan:   No (tcl not available)
  gdtclft:       No (tcl not available)
  tkspline:      No (tk not available)
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing --run aclocal-1.12 -I m4
/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu
/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoconf
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5343: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
m4/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure CC=gcc CXX=g++ -std=gnu++11 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --prefix=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix --libdir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib --includedir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg R_LIBS=/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rgraphviz/00new --no-create --no-recursion
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... byacc
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for sed... /bin/sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/bin/tclsh8.6
checking whether gcc and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking dependency style of g++ -std=gnu++11... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking for inline... inline
checking for windres... no
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... grep
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
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checking for unistd.h... yes
checking for mode_t... yes
checking for pid_t... yes
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checking for uid_t in sys/types.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
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checking stddef.h usability... yes
checking stddef.h presence... yes
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checking for stddef.h... (cached) yes
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checking for stdint.h... (cached) yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking search.h usability... yes
checking search.h presence... yes
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checking getopt.h usability... yes
checking getopt.h presence... yes
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checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/inotify.h usability... yes
checking sys/inotify.h presence... yes
checking for sys/inotify.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for socklen_t... yes
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... yes
checking for fesetenv... yes
checking libgen.h usability... yes
checking libgen.h presence... yes
checking for libgen.h... yes
checking for basename in -lgen... no
checking for working alloca.h... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... no
checking for setenv... yes
checking for getenv... yes
checking for __freadable... yes
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... yes
checking for memset... yes
checking for nl_langinfo... yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for _NSGetEnviron... no
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 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 object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking dependency style of g++ -std=gnu++11... (cached) gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc 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 for ld used by g++ -std=gnu++11... /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++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 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/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu 
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
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checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for ltdl.h... yes
checking whether lt_dlinterface_register is declared... yes
checking for lt_dladvise_preload in -lltdl... yes
checking where to find libltdl headers... 
checking where to find libltdl library... -lltdl
checking for unistd.h... (cached) yes
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checking for closedir... yes
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checking for X... disabled
configure: WARNING: X11 not available.
checking tcl.h usability... no
checking tcl.h presence... no
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configure: WARNING: Unable to find header tcl.h. The Tcl packages will not be built
configure: WARNING: No Tcl. The Tk packages will not be built either
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
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configure: WARNING: Optional Xaw library not available - missing headers
checking zlib.h usability... yes
checking zlib.h presence... yes
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checking for main in -lz... yes
checking for deflateBound... no
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checking for qmake... no
checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... yes
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
configure: creating ./config.status

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

graphviz-2.28.0 will be compiled with the following:

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

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

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

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

  tcldot:        No (tcl not available)
  tclpathplan:   No (tcl not available)
  gdtclft:       No (tcl not available)
  tkspline:      No (tk not available)
 /bin/bash ./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: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoheader)
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5343: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
m4/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run aclocal-1.12 -I m4
/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run automake-1.12 --foreign
/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoconf
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure --disable-option-checking --prefix=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix CC=gcc CXX=g++ -std=gnu++11 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --libdir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib --includedir=/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg R_LIBS=/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rgraphviz/00new --cache-file=/dev/null --srcdir=. --no-create --no-recursion
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
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... 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... /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 object... ok
checking how to run the C preprocessor... gcc -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 supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc 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/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu 
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
 /bin/bash ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
make  install-am
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -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 -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  -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
ar: `u' modifier ignored since `D' is the default (see `U')
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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
In file included from libltdl/lt__private.h:51:0,
                 from ltdl.c:32:
ltdl.c: In function 'try_dlopen':
./ltdl.h:44:24: warning: the address of 'libext' will always evaluate as 'true' [-Waddress]
 #define LT_STRLEN(s) (((s) && (s)[0]) ? strlen (s) : 0)
                        ^
libltdl/lt__alloc.h:38:42: note: in definition of macro 'MALLOC'
 #define MALLOC(tp, n)  (tp*) lt__malloc((n) * sizeof(tp))
                                          ^
ltdl.c:1268:52: note: in expansion of macro 'LT_STRLEN'
    archive_name = MALLOC (char, LT_STRLEN (name) + LT_STRLEN (libext) + 2);
                                                    ^~~~~~~~~
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -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 -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 -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 -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  -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 -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-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")
libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o lt__strl.o .libs/libltdlcS.o  .libs/libltdlc.lax/dlopen.a/dlopen.o 
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader)
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
rm -f stamp-h1
touch config-h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
Making install in cdt
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
  CC       dtclose.lo
  CC       dtdisc.lo
dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Void_t* dtmemory(dt, addr, size, disc)
                ^~~~~~~~
  CC       dtextract.lo
  CC       dtflatten.lo
  CC       dthash.lo
dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static void dthtab(dt)
             ^~~~~~
dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Void_t* dthash(dt,obj,type)
                ^~~~~~
dthash.c: In function 'dthash':
dthash.c:306:6: warning: 'r' may be used uninitialized in this function [-Wmaybe-uninitialized]
     (*dt->memoryf)(dt,(Void_t*)r,0,disc);
     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  CC       dtlist.lo
dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Void_t* dtlist(dt, obj, type)
                ^~~~~~
  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]
 static int treecount(e)
            ^~~~~~~~~
  CC       dtstat.lo
dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static void dttstat(ds,root,depth,level)
             ^~~~~~~
dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static void dthstat(data, ds, count)
             ^~~~~~~
  CC       dtstrhash.lo
  CC       dttree.lo
dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Void_t* dttree(dt,obj,type)
                ^~~~~~
dttree.c: In function 'dttree':
dttree.c:218:16: warning: 'me' may be used uninitialized in this function [-Wmaybe-uninitialized]
    root->right = link.left;
  CC       dttreeset.lo
dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Dtlink_t* treebalance(list, size)
                  ^~~~~~~~~~~
  CC       dtview.lo
dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static Void_t* dtvsearch(dt,obj,type)
                ^~~~~~~~~
dtview.c: In function 'dtvsearch':
dtview.c:20:12: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
  int  cmp, lk, sz, ky;
            ^~
  CC       dtwalk.lo
dtwalk.c: In function 'dtwalk':
dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 int(*  userf)();
 ^~~
  CCLD     libcdt.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libcdt_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
  CC       attribs.lo
  CC       agxbuf.lo
  CC       edge.lo
  CC       graph.lo
graph.c: In function 'agclose':
graph.c:374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if (g->attr)
     ^~
graph.c:376:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  if (g->didset)
  ^~
  CC       graphio.lo
  CC       lexer.lo
lexer.c: In function 'scan_token':
lexer.c:141:11: warning: comparison between pointer and zero character constant [-Wpointer-compare]
     if (p == '\0')
           ^~
lexer.c:141:9: note: did you mean to dereference the pointer?
     if (p == '\0')
         ^
lexer.c:147:12: warning: pointer targets in return differ in signedness [-Wpointer-sign]
     return p;
            ^
lexer.c: In function 'html_pair':
lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int rc, depth = 1;
         ^~
In file included from lexer.c:20:0:
lexer.c: In function 'aglex':
agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
lexer.c:413:29: note: in expansion of macro 'agxbuse'
  aglval.str = agstrdup_html(agxbuse(&xb));
                             ^~~~~~~
lexer.c:435:26: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]
      LexPtr = scan_token(LexPtr, tbuf);
                          ^~~~~~
lexer.c:136:14: note: expected 'unsigned char *' but argument is of type 'char *'
 static char *scan_token(unsigned char *p, unsigned char *token)
              ^~~~~~~~~~
lexer.c:435:34: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]
      LexPtr = scan_token(LexPtr, tbuf);
                                  ^~~~
lexer.c:136:14: note: expected 'unsigned char *' but argument is of type 'char *'
 static char *scan_token(unsigned char *p, unsigned char *token)
              ^~~~~~~~~~
lexer.c: In function 'aglasterr':
lexer.c:527:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread(buf, sizeof(char), len, agerrout);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  CC       node.lo
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libgraph_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
  CC       cvt.lo
cvt.c:276:13: warning: 'append_bezier' defined but not used [-Wunused-function]
 static void append_bezier(Ppoint_t * bezier)
             ^~~~~~~~~~~~~
  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]
     if (newtrin <= trin)
        ^
  CC       shortestpth.lo
  CC       solvers.lo
  CC       triang.lo
  CC       util.lo
  CC       visibility.lo
  CCLD     libpathplan.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libpathplan_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
  CC       fPQ.lo
  CC       intset.lo
  CC       maze.lo
maze.c: In function 'mkMazeGraph':
maze.c:325:20: warning: variable 'ncnt' set but not used [-Wunused-but-set-variable]
     int nsides, i, ncnt, maxdeg;
                    ^~~~
  CC       ortho.lo
ortho.c: In function 'addLoop':
ortho.c:461:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable]
  double wt;
         ^~
ortho.c: In function 'addNodeEdges':
ortho.c:497:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable]
  double wt;
         ^~
ortho.c: In function 'orthoEdges':
ortho.c:192:11: warning: 'prevbp.x' may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if (prevbp.x > bp1.x) l1 = B_RIGHT;
           ^
ortho.c:152:22: note: 'prevbp.x' was declared here
     pointf bp1, bp2, prevbp;  /* bend points */
                      ^~~~~~
ortho.c:179:11: warning: 'prevbp.y' may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if (prevbp.y > bp1.y) l1 = B_UP;
           ^
ortho.c:152:22: note: 'prevbp.y' was declared here
     pointf bp1, bp2, prevbp;  /* bend points */
                      ^~~~~~
ortho.c:1356:2: warning: 'ps' may be used uninitialized in this function [-Wmaybe-uninitialized]
  freePS (ps);
  ^~~~~~~~~~~
  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]
   int do_switch = FALSE;
       ^~~~~~~~~
partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
   int retval;
       ^~~~~~
partition.c: In function 'partition':
partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable]
     int nt;
         ^~
partition.c: In function 'make_new_monotone_poly':
partition.c:274:5: warning: 'tq' may be used uninitialized in this function [-Wmaybe-uninitialized]
   q = vp1->vpos[iq];
   ~~^~~~~~~~~~~~~~~
partition.c:212:7: warning: 'tp' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int tp, tq;
       ^~
partition.c: In function 'monotonate_trapezoids':
partition.c:665:10: warning: 'size' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return size;
          ^~~~
  CC       rawgraph.lo
  CC       sgraph.lo
  CC       trapezoid.lo
trapezoid.c:22:0: warning: "__USE_ISOC99" redefined
 #define __USE_ISOC99
 
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:0,
                 from /usr/include/string.h:26,
                 from trapezoid.c:19:
/usr/include/features.h:320:0: note: this is the location of the previous definition
 # define __USE_ISOC99  1
 
trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static int newnode()
            ^~~~~~~
trapezoid.c: In function 'add_segment':
trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable]
   int tritop = 0, tribot = 0, is_swapped;
       ^~~~~~
trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CCLD     libortho_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
Making install in sparse
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
  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]
   int m, n, nz, nzmax, type, format, property, iread;
                                                ^~~~~
  CC       general.lo
  CC       BinaryHeap.lo
In file included from general.h:21:0,
                 from BinaryHeap.h:17,
                 from BinaryHeap.c:14:
BinaryHeap.c: In function 'BinaryHeap_sanity_check':
BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for (i = 0; i < h->len + IntStack_get_length(h->id_stack); i++) assert(mask[i] =- 1);
                                                                          ^
  CC       IntStack.lo
  CCLD     libsparse_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
Making install in patchwork
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
Making install in common
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/common'
  CC       arrows.lo
arrows.c: In function 'arrowOrthoClip':
arrows.c:392:21: warning: 'hlen' may be used uninitialized in this function [-Wmaybe-uninitialized]
      else r.x = p.x - hlen;
                 ~~~~^~~~~~
cat brewer_lib svgcolor_lib ../../lib/common/color_names | LC_ALL=C sort > color_lib
gawk -f ../../awk/colortbl.awk color_lib > colortbl.h
  CC       colxlate.lo
  CC       fontmetrics.lo
  CC       args.lo
  CC       memory.lo
  CC       globals.lo
  CC       htmllex.lo
In file included from render.h:47:0,
                 from htmllex.c:15:
htmllex.c: In function 'error_context':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
htmllex.c:57:35: note: in expansion of macro 'agxbuse'
     agerr(AGPREV, "... %s ...\n", agxbuse(state.xb));
                                   ^~~~~~~
  CC       htmlparse.lo
In file included from render.h:47:0,
                 from ../../lib/common/htmlparse.y:16:
../../lib/common/htmlparse.y: In function 'appendFItemList':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse'
     fi->ti.str = strdup(agxbuse(ag));
                         ^~~~~~~
../../lib/common/htmlparse.y: In function 'htmlparse':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse'
           if (nonSpace(agxbuse(HTMLstate.str))) {
                        ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse'
           if (nonSpace(agxbuse(HTMLstate.str))) {
                        ^~~~~~~
  CC       htmltable.lo
In file included from render.h:47:0,
                 from htmltable.c:35:
htmltable.c: In function 'initAnchor':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
htmltable.c:299:7: note: in expansion of macro 'agxbuse'
  id = agxbuse (&xb);
       ^~~~~~~
htmltable.c: In function 'nameOf':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
htmltable.c:1665:12: note: in expansion of macro 'agxbuse'
     return agxbuse(xb);
            ^~~~~~~
  CC       input.lo
input.c: In function 'dotneato_basename':
input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation]
     while (*s) s++; s--;
     ^~~~~
input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while'
     while (*s) s++; s--;
                     ^
In file included from render.h:47:0,
                 from input.c:15:
input.c: In function 'global_def':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
input.c:200:24: note: in expansion of macro 'agxbuse'
     sym = dclfun(NULL, agxbuse (xb), rhs);
                        ^~~~~~~
  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]
     int saw_bb, must_inline, rc;
                              ^~
In file included from render.h:47:0,
                 from psusershape.c:20:
psusershape.c: In function 'ps_string':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
psusershape.c:303:5: note: in expansion of macro 'agxbputc'
     agxbputc (&xb, RPAREN);
     ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
psusershape.c:305:9: note: in expansion of macro 'agxbuse'
     s = agxbuse(&xb);
         ^~~~~~~
psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int rc;
         ^~
  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]
     char *p, *sub, *prev = NULL;
                     ^~~~
  CC       ns.lo
  CC       shapes.lo
  CC       utils.lo
utils.c: In function 'chkPort':
utils.c:689:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
     else
     ^~~~
utils.c:691:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  pt.name = s;
  ^~
In file included from render.h:47:0,
                 from utils.c:14:
utils.c: In function 'clustNode':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:949:5: note: in expansion of macro 'agxbputc'
     agxbputc(xb, ':');
     ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
utils.c:953:29: note: in expansion of macro 'agxbuse'
     cn = agnode(agroot(cg), agxbuse(xb));
                             ^~~~~~~
utils.c: In function 'scanEntity':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1358:5: note: in expansion of macro 'agxbputc'
     agxbputc(xb, '&');
     ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1368:5: note: in expansion of macro 'agxbputc'
     agxbputc(xb, '#');
     ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1370:5: note: in expansion of macro 'agxbputc'
     agxbputc(xb, ';');
     ^~~~~~~~
utils.c: In function 'htmlEntityUTF8':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
utils.c:1514:18: note: in expansion of macro 'agxbuse'
     ns = strdup (agxbuse(&xb));
                  ^~~~~~~
utils.c:1455:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int rc;
         ^~
In file included from render.h:47:0,
                 from utils.c:14:
utils.c: In function 'latin1ToUTF8':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
utils.c:1554:18: note: in expansion of macro 'agxbuse'
     ns = strdup (agxbuse(&xb));
                  ^~~~~~~
utils.c:1530:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int rc;
         ^~
In file included from render.h:47:0,
                 from utils.c:14:
utils.c: In function 'utf8ToLatin1':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
utils.c:1586:18: note: in expansion of macro 'agxbuse'
     ns = strdup (agxbuse(&xb));
                  ^~~~~~~
utils.c:1572:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int rc;
         ^~
  CC       geom.lo
  CC       output.lo
In file included from render.h:47:0,
                 from output.c:14:
output.c: In function 'attach_attrs_and_arrows':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
output.c:350:22: note: in expansion of macro 'agxbuse'
      agset(n, "pos", agxbuse(&xb));
                      ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
output.c:373:24: note: in expansion of macro 'agxbuse'
      agset(n, "rects", agxbuse(&xb));
                        ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:391:4: note: in expansion of macro 'agxbputc'
    agxbputc(&xb, ' ');
    ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
output.c:403:32: note: in expansion of macro 'agxbuse'
   agxset(n, N_vertices->index, agxbuse(&xb));
                                ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:417:4: note: in expansion of macro 'agxbputc'
    agxbputc(&xb, ';');
    ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:434:8: note: in expansion of macro 'agxbputc'
        agxbputc(&xb, ' ');
        ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
output.c:440:19: note: in expansion of macro 'agxbuse'
   agset(e, "pos", agxbuse(&xb));
                   ^~~~~~~
  CC       emit.lo
In file included from render.h:47:0,
                 from emit.c:25:
emit.c: In function 'getObjId':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:212:2: note: in expansion of macro 'agxbputc'
  agxbputc (xb, '_');
  ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
emit.c:218:12: note: in expansion of macro 'agxbuse'
     return agxbuse(xb);
            ^~~~~~~
emit.c: In function 'emit_xdot':
emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable]
     char* fontname;
           ^~~~~~~~
emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable]
     double fontsize;
            ^~~~~~~~
In file included from render.h:47:0,
                 from emit.c:25:
emit.c: In function 'selectedlayer':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
emit.c:1152:22: note: in expansion of macro 'agxbuse'
     w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims);
                      ^~~~~~~
emit.c: In function 'nodeIntersect':
emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
     char* target;
           ^~~~~~
emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable]
     char* tooltip;
           ^~~~~~~
emit.c: In function 'xdotBB':
emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable]
     pointf sz;
            ^~
emit.c: In function 'style_token':
emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
     int token, rc;
                ^~
In file included from render.h:47:0,
                 from emit.c:25:
emit.c: In function 'parse_style':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:3356:3: note: in expansion of macro 'agxbputc'
   agxbputc(&ps_xb, '\0'); /* terminate previous */
   ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
emit.c:3359:22: note: in expansion of macro 'agxbuse'
      agxbput(&ps_xb, agxbuse(&xb));
                      ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:3360:6: note: in expansion of macro 'agxbputc'
      agxbputc(&ps_xb, '\0');
      ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
emit.c:3372:11: note: in expansion of macro 'agxbuse'
     (void)agxbuse(&ps_xb);  /* adds final '\0' to buffer */
           ^~~~~~~
emit.c: In function 'emit_edge_graphics':
emit.c:1932:3: warning: 'bz.eflag' may be used uninitialized in this function [-Wmaybe-uninitialized]
   arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1],
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    arrowsize, penwidth, bz.eflag);
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:1921:3: warning: 'bz.sflag' may be used uninitialized in this function [-Wmaybe-uninitialized]
   arrow_gen(job, EMIT_TDRAW, bz.sp, bz.list[0],
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    arrowsize, penwidth, bz.sflag);
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:1932:47: warning: 'bz.size' may be used uninitialized in this function [-Wmaybe-uninitialized]
   arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1],
                                             ~~^~~~~
emit.c:1932:44: warning: 'bz.list' may be used uninitialized in this function [-Wmaybe-uninitialized]
   arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1],
                                            ^
emit.c:1776:10: warning: 'endcolor' may be used uninitialized in this function [-Wmaybe-uninitialized]
          gvrender_set_fillcolor(job, endcolor);
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:1723:11: note: 'endcolor' was declared here
     char* endcolor;
           ^~~~~~~~
emit.c:1746:19: warning: 'segs' may be used uninitialized in this function [-Wmaybe-uninitialized]
      if (s == segs->segs) {
               ~~~~^~~~~~
emit.c:1721:18: note: 'segs' was declared here
     colorsegs_t* segs;
                  ^~~~
emit.c: In function 'getObjId':
emit.c:214:5: warning: 'pfx' may be used uninitialized in this function [-Wmaybe-uninitialized]
     agxbput (xb, pfx);
     ^~~~~~~~~~~~~~~~~
emit.c: In function 'xdotBB':
emit.c:2515:9: warning: 'fontname' may be used uninitialized in this function [-Wmaybe-uninitialized]
      sz = textsize (g, op->para, fontname, fontsize);
      ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:2515:9: warning: 'fontsize' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CCLD     libcommon_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/common'
make[4]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/common'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/common'
Making install in pack
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
  CC       ccomps.lo
  CC       pack.lo
pack.c: In function 'putGraphs':
pack.c:953:12: warning: 'pts' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return pts;
            ^~~
  CCLD     libpack_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
make[4]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pack.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pack.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pack.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
Making install in xdot
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
  CC       xdot.lo
xdot.c: In function 'sprintXDot':
xdot.c:537:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xdot.c:538:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
xdot.c:606:16: note: in expansion of macro 'agxbuse'
     s = strdup(agxbuse(&xb));
                ^~~~~~~
  CCLD     libxdot.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libxdot_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 xdot.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 xdot.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxdot.pc '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 xdot.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
Making install in gvc
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
  CC       gvrender.lo
  CC       gvlayout.lo
  CC       gvdevice.lo
In file included from ../../lib/common/types.h:18:0,
                 from gvplugin_device.h:17,
                 from gvdevice.c:55:
gvdevice.c: In function 'gvfwrite':
gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     assert(size = sizeof(char));
            ^
  CC       gvloadimage.lo
  CC       gvcontext.lo
  CC       gvjobs.lo
  CC       gvevent.lo
  CC       gvplugin.lo
In file included from gvplugin.c:23:0:
gvplugin.c: In function 'gvplugin_list':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvplugin.c:392:3: note: in expansion of macro 'agxbputc'
   agxbputc(&xb,' '); agxbput(&xb, (*pnext)->typestr);
   ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvplugin.c:393:3: note: in expansion of macro 'agxbputc'
   agxbputc(&xb,':'); agxbput(&xb, (*pnext)->package->name);
   ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvplugin.c:410:3: note: in expansion of macro 'agxbputc'
   agxbputc(&xb,' '); agxbput(&xb, q);
   ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvplugin.c:423:7: note: in expansion of macro 'agxbuse'
  bp = agxbuse(&xb);
       ^~~~~~~
  CC       gvconfig.lo
  CC       gvtextlayout.lo
  CC       gvusershape.lo
gvusershape.c: In function 'gvusershape_open':
gvusershape.c:415:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!(us->data = (void*)find_user_shape(us->name)))
   ^~
gvusershape.c:417:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
       free(us);
       ^~~~
  CC       gvc.lo
  CCLD     libgvc.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libgvc_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 gvc.3 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 gvc.3.pdf '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgvc.pc '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
Making install in circogen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
  CC       circularinit.lo
  CC       nodelist.lo
  CC       block.lo
  CC       edgelist.lo
  CC       circular.lo
  CC       deglist.lo
  CC       blocktree.lo
  CC       blockpath.lo
  CC       circpos.lo
circpos.c: In function 'doBlock':
circpos.c:338:13: warning: 'midAngle' may be used uninitialized in this function [-Wmaybe-uninitialized]
  PSI(pi->n) = midAngle;
circpos.c:264:39: note: 'midAngle' was declared here
     double mindistAngle, rotateAngle, midAngle;
                                       ^~~~~~~~
  CC       nodeset.lo
  CCLD     libcircogen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
Making install in dotgen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
  CC       acyclic.lo
  CC       class1.lo
  CC       class2.lo
  CC       cluster.lo
  CC       compound.lo
  CC       conc.lo
  CC       decomp.lo
  CC       fastgr.lo
  CC       flat.lo
  CC       dotinit.lo
  CC       mincross.lo
mincross.c: In function 'mincross.constprop':
mincross.c:421:12: warning: 'sepIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
     for (i = sepIndex + 1; i < GD_rank(g)[r].n; i++) {
          ~~^~~~~~~~~~~~~~
mincross.c:374:9: note: 'sepIndex' was declared here
     int sepIndex;
         ^~~~~~~~
  CC       position.lo
  CC       rank.lo
  CC       sameport.lo
  CC       dotsplines.lo
dotsplines.c: In function 'makeLineEdge':
dotsplines.c:1604:23: warning: right-hand operand of comma expression has no effect [-Wunused-value]
  lp = ED_label(e)->pos, lp;
                       ^
dotsplines.c: In function 'completeregularpath':
dotsplines.c:1866:9: warning: variable 'pn' set but not used [-Wunused-but-set-variable]
     int pn;
         ^~
dotsplines.c:1865:13: warning: variable 'pp' set but not used [-Wunused-but-set-variable]
     pointf *pp;
             ^~
dotsplines.c: In function '_dot_splines':
dotsplines.c:490:2: warning: 'P' may be used uninitialized in this function [-Wmaybe-uninitialized]
  free(P);
  ^~~~~~~
dotsplines.c: In function 'make_flat_edge':
dotsplines.c:993:18: warning: 'lmaxx' may be used uninitialized in this function [-Wmaybe-uninitialized]
      points[5].x = lmaxx;
      ~~~~~~~~~~~~^~~~~~~
dotsplines.c:882:19: note: 'lmaxx' was declared here
     double lminx, lmaxx;
                   ^~~~~
dotsplines.c:997:18: warning: 'lminx' may be used uninitialized in this function [-Wmaybe-uninitialized]
      points[7].x = lminx;
      ~~~~~~~~~~~~^~~~~~~
dotsplines.c:882:12: note: 'lminx' was declared here
     double lminx, lmaxx;
            ^~~~~
  CC       aspect.lo
aspect.c: In function 'computeCombiAR':
aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable]
     int i, maxLayerIndex;
            ^~~~~~~~~~~~~
aspect.c: In function 'rank3':
aspect.c:702:9: warning: 'maxLayerIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int maxLayerIndex;
         ^~~~~~~~~~~~~
aspect.c:750:2: warning: 'nextMaxWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (nextMaxWidth <= layerWidthInfo[maxLayerIndex].width / 4
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  || nextMaxWidth >= layerWidthInfo[maxLayerIndex].width * 3 / 4)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aspect.c:703:12: note: 'nextMaxWidth' was declared here
     double nextMaxWidth;
            ^~~~~~~~~~~~
  CCLD     libdotgen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
Making install in fdpgen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
  CC       comp.lo
  CC       dbg.lo
  CC       grid.lo
  CC       fdpinit.lo
  CC       layout.lo
  CC       tlayout.lo
  CC       xlayout.lo
  CC       clusteredges.lo
  CCLD     libfdpgen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
Making install in neatogen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
  CC       adjust.lo
In file included from ../../lib/common/render.h:44:0,
                 from neato.h:37,
                 from adjust.c:19:
adjust.c: In function 'getSizes':
../../lib/common/memory.h:39:30: warning: 'nedge_nodes' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define N_GNEW(n,t)      (t*)gmalloc((n)*sizeof(t))
                              ^~~~~~~
adjust.c:670:12: note: 'nedge_nodes' was declared here
     int i, nedge_nodes;
            ^~~~~~~~~~~
adjust.c: In function 'removeOverlapWith':
adjust.c:1045:9: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int ret;
         ^~~
  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]
     epsf_t *desc;
             ^~~~
neatosplines.c: In function '_spline_edges':
neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable]
     router_t* rtr = 0;
               ^~~
  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 [-Wmaybe-uninitialized]
  if (newsite != (struct Site *) NULL && (PQempty()
                                         ~~~~~~~~~~
       || newsite->coord.y <
       ~~~~~~~~~~~~~~~~~~~~~
       newintstar.y
       ~~~~~~~~~~~~
       || (newsite->coord.y ==
       ^~~~~~~~~~~~~~~~~~~~~~~
           newintstar.y
           ~~~~~~~~~~~~
           && newsite->coord.x <
           ~~~~~~~~~~~~~~~~~~~~~
           newintstar.x))) {
           ~~~~~~~~~~~~~~
  CC       stress.lo
stress.c: In function 'mdsModel':
stress.c:1383:12: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized]
      delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);
      ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  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
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
Making install in twopigen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
  CC       twopiinit.lo
  CC       circle.lo
circle.c: In function 'circleLayout':
circle.c:285:5: warning: 'delx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  xf += delx;
  ~~~^~~~~~~
circle.c:268:20: note: 'delx' was declared here
     double xf = 0, delx, d;
                    ^~~~
  CCLD     libtwopigen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
Making install in sfdpgen
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
  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]
   real y[4], axis[2], center[2], x0, x1;
        ^
  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]
   real *avg_dist, diag_d, diag_w, *dd, dist, s = 0, stop = 0, sbot = 0;
                                    ^~
post_process.c: In function 'StressMajorizationSmoother_smooth':
post_process.c:578:102: warning: variable 'res' set but not used [-Wunused-but-set-variable]
   real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.;
                                                                                                      ^~~
post_process.c:578:9: warning: variable 'w' set but not used [-Wunused-but-set-variable]
   real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.;
         ^
post_process.c:577:32: warning: variable 'jw' set but not used [-Wunused-but-set-variable]
   int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0;
                                ^~
post_process.c:577:27: warning: variable 'iw' set but not used [-Wunused-but-set-variable]
   int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0;
                           ^~
post_process.c: In function 'TriangleSmoother_new':
post_process.c:698:68: warning: variable 'jd' set but not used [-Wunused-but-set-variable]
   int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz;
                                                                    ^~
post_process.c:698:63: warning: variable 'id' set but not used [-Wunused-but-set-variable]
   int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz;
                                                               ^~
  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]
   real res;
        ^~~
  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]
   int i, ii, j, *ia, *ja, m, n, *p = NULL;
                              ^
Multilevel.c: In function 'maximal_independent_vertex_set_RS':
Multilevel.c:138:57: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
   int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0;
                                                         ^~~~~~~
Multilevel.c:138:48: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0;
                                                ^
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]
   int i, ii, j, *ia, *ja, m, n, *p = NULL, q;
                              ^
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]
   int i, ii, j, *ia, *ja, m, n, *p = NULL;
                              ^
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]
   int i, ii, j, *ia, *ja, m, n, *p = NULL, q, iv;
                              ^
  CC       PriorityQueue.lo
  CCLD     libsfdpgen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
Making install in osage
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
  CC       osageinit.lo
  CCLD     libosage_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/lib'
Making install in plugin
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
Making install in core
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
  CC       gvplugin_core.lo
  CC       gvrender_core_dot.lo
In file included from gvrender_core_dot.c:32:0:
gvrender_core_dot.c: In function 'xdot_str':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvrender_core_dot.c:100:5: note: in expansion of macro 'agxbputc'
     agxbputc(xbufs[emit_state], ' ');
     ^~~~~~~~
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]
     int i, rc;
            ^~
In file included from gvrender_core_dot.c:32:0:
gvrender_core_dot.c: In function 'xdot_style':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvrender_core_dot.c:162:13: note: in expansion of macro 'agxbputc'
             agxbputc(&xbuf, '(');
             ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvrender_core_dot.c:166:21: note: in expansion of macro 'agxbputc'
                     agxbputc(&xbuf, ',');
                     ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gvrender_core_dot.c:172:13: note: in expansion of macro 'agxbputc'
             agxbputc(&xbuf, ')');
             ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:174:30: note: in expansion of macro 'agxbuse'
         xdot_str (job, "S ", agxbuse(&xbuf));
                              ^~~~~~~
gvrender_core_dot.c: In function 'xdot_end_node':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:186:31: note: in expansion of macro 'agxbuse'
  agxset(n, xd->n_draw->index, agxbuse(xbufs[EMIT_NDRAW]));
                               ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:192:33: note: in expansion of macro 'agxbuse'
  agxset(n, xd->n_l_draw->index, agxbuse(xbufs[EMIT_NLABEL]));
                                 ^~~~~~~
gvrender_core_dot.c: In function 'xdot_end_edge':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:206:31: note: in expansion of macro 'agxbuse'
  agxset(e, xd->e_draw->index, agxbuse(xbufs[EMIT_EDRAW]));
                               ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:212:31: note: in expansion of macro 'agxbuse'
  agxset(e, xd->t_draw->index, agxbuse(xbufs[EMIT_TDRAW]));
                               ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:218:31: note: in expansion of macro 'agxbuse'
  agxset(e, xd->h_draw->index, agxbuse(xbufs[EMIT_HDRAW]));
                               ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:224:32: note: in expansion of macro 'agxbuse'
  agxset(e, xd->e_l_draw->index,agxbuse(xbufs[EMIT_ELABEL]));
                                ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:230:32: note: in expansion of macro 'agxbuse'
  agxset(e, xd->tl_draw->index, agxbuse(xbufs[EMIT_TLABEL]));
                                ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:236:32: note: in expansion of macro 'agxbuse'
  agxset(e, xd->hl_draw->index, agxbuse(xbufs[EMIT_HLABEL]));
                                ^~~~~~~
gvrender_core_dot.c: In function 'xdot_end_cluster':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:289:42: note: in expansion of macro 'agxbuse'
     agxset(cluster_g, xd->g_draw->index, agxbuse(xbufs[EMIT_CDRAW]));
                                          ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:295:41: note: in expansion of macro 'agxbuse'
  agxset(cluster_g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_CLABEL]));
                                         ^~~~~~~
gvrender_core_dot.c: In function 'xdot_end_graph':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:436:31: note: in expansion of macro 'agxbuse'
  agxset(g, xd->g_draw->index, agxbuse(xbufs[EMIT_GDRAW]));
                               ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
           (int)(*(X)->ptr++ = ((unsigned char)C)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
 #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
                     ^~~~~~~~
gvrender_core_dot.c:444:33: note: in expansion of macro 'agxbuse'
  agxset(g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_GLABEL]));
                                 ^~~~~~~
  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]
     unsigned int ObjId;
                  ^~~~~
gvrender_core_tk.c:57:21: warning: variable 'ObjPart' set but not used [-Wunused-but-set-variable]
     char *ObjType, *ObjPart;
                     ^~~~~~~
  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]
     double dx, dy, left, right, top, bottom;
                                      ^~~~~~
gvrender_core_vml.c:452:26: warning: variable 'right' set but not used [-Wunused-but-set-variable]
     double dx, dy, left, right, top, bottom;
                          ^~~~~
  CC       gvloadimage_core.lo
  CCLD     libgvplugin_core_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libgvplugin_core.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_core.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
Making install in dot_layout
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
  CC       gvplugin_dot_layout.lo
  CC       gvlayout_dot_layout.lo
  CCLD     libgvplugin_dot_layout_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libgvplugin_dot_layout.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
Making install in neato_layout
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
  CC       gvplugin_neato_layout.lo
  CC       gvlayout_neato_layout.lo
  CCLD     libgvplugin_neato_layout_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
  CCLD     libgvplugin_neato_layout.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/bash ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `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-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[4]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
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-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
make[3]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
make[3]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
 /usr/bin/install -c -m 644 graphviz.7 '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graphviz_version.h '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /bin/mkdir -p '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
 /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/graphviz'
cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.11-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.11-bioc/meat/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-3.11-bioc/meat/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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]
     Agnode_t *head, *tail, *curNode;
                             ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include  -I/home/biocbuild/bbs-3.11-bioc/meat/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 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rgraphviz/00new/Rgraphviz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rgraphviz)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("Rgraphviz") || stop("unable to load Rgraphviz")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: grid
[1] TRUE
> BiocGenerics:::testPackage("Rgraphviz")
plotting different layout types
   dot  .... done
   circo  .... done
   fdp  .... done
   neato  .... done
   osage  .... done
   twopi  .... done
using toFile with various device types
   canon . done
   cmap . done
   cmapx . done
   cmapx_np . done
   dot . done
   eps . done
   fig . done
   gv . done
   imap . done
   imap_np . done
   ismap . done
   plain . done
   plain-ext . done
   ps . done
   ps2 . done
   svg . done
   tk . done
   vml . done
   xdot . done


RUNIT TEST PROTOCOL -- Sat Oct 17 04:46:44 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.820   0.075   1.918