Multiple platform build/check report for BioC 3.15 - CHECK results for Rgraphviz on riesling1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.4 LTS)	x86_64	R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences"	4334
riesling1	Windows Server 2019 Standard	x64	R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"	4097
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences"	4083
merida1	macOS 10.14.6 Mojave	x86_64	R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences"	4134
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rgraphviz
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rgraphviz' ...
** using staged installation
configure.win: loading site script /usr/local/etc/config.site
configure.win: Using bundled Graphviz.
configure.win: Searching for the compilers specified by R.
checking for gcc... C:/rtools40/mingw64/bin/gcc
checking whether the C compiler works... yes
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checking whether C:/rtools40/mingw64/bin/gcc accepts -g... yes
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checking how to run the C preprocessor... C:/rtools40/mingw64/bin/gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether C:/rtools40/mingw64/bin/g++ -std=gnu++11 accepts -g... yes
configure.win: Preparing to compile Graphviz.
configure.win: Configuring bundled Graphviz.
checking build system type... x86_64-w64-mingw32
checking host system type... x86_64-w64-mingw32
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checking whether C:/rtools40/mingw64/bin/g++ -std=gnu++11 accepts -g... (cached) yes
checking dependency style of C:/rtools40/mingw64/bin/g++ -std=gnu++11... (cached) gcc3
checking how to run the C++ preprocessor... C:/rtools40/mingw64/bin/g++ -std=gnu++11 -E
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checking whether the C:/rtools40/mingw64/bin/gcc linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
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configure: creating ./config.status
config.status: creating Makefile
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config.status: creating lib/graph/Makefile
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config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt'  '--host=x86_64-w64-mingw32' '--build=x86_64-w64-mingw32' 'CC=C:/rtools40/mingw64/bin/gcc' 'CXX=C:/rtools40/mingw64/bin/g++ -std=gnu++11' 'CFLAGS=-fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition' 'CXXFLAGS=-O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition' 'LDFLAGS=' '--libdir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib' '--includedir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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' 'build_alias=x86_64-w64-mingw32' 'host_alias=x86_64-w64-mingw32' 'R_LIBS=D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rgraphviz/00new' '--enable-ltdl-convenience' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
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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:    No (gdk_pixbuf library not available)
  ghostscript:   No (disabled)
  glitz:         No (disabled by default - incomplete)
  gtk:           No (gtk library not available)
  lasi:          No (disabled)
  ming:          No (disabled by default - incomplete)
  pangocairo:    No (disabled)
  quartz:        No (disabled by default - Mac only)
  rsvg:          No (disabled)
  visio:         No (disabled by default - experimental)
  xlib:          No (disabled or unavailable)

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

  tcldot:        No (tcl not available)
  tclpathplan:   No (tcl not available)
  gdtclft:       No (tcl not available)
  tkspline:      No (tk not available)
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing --run aclocal-1.12 -I m4
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoconf
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: autoconf: command not found
WARNING: `autoconf' is missing on your system.  You should only need it if
         you modified `configure.ac'.  You might want to install the
         `Autoconf' and `GNU m4' packages.  Grab them from any GNU
         archive site.
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --host=x86_64-w64-mingw32 --build=x86_64-w64-mingw32 CC=C:/rtools40/mingw64/bin/gcc CXX=C:/rtools40/mingw64/bin/g++ -std=gnu++11 CFLAGS=-fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition CXXFLAGS=-O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition LDFLAGS= --prefix=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt --libdir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib --includedir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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 build_alias=x86_64-w64-mingw32 host_alias=x86_64-w64-mingw32 R_LIBS=D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rgraphviz/00new --enable-ltdl-convenience --no-create --no-recursion
checking build system type... x86_64-w64-mingw32
checking host system type... x86_64-w64-mingw32
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/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 x86_64-w64-mingw32-gcc... C:/rtools40/mingw64/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
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 C:/rtools40/mingw64/bin/gcc accepts -g... yes
checking for C:/rtools40/mingw64/bin/gcc option to accept ISO C89... none needed
checking dependency style of C:/rtools40/mingw64/bin/gcc... gcc3
checking for library containing strerror... none required
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking for gawk... (cached) gawk
checking whether ln -s works... no, using cp -pR
checking for sed... sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for x86_64-w64-mingw32-pkg-config... /mingw64/bin/x86_64-w64-mingw32-pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... no
checking for tclsh8.5... no
checking for tclsh8.4... no
checking for tclsh8.3... no
checking for tclsh... no
checking whether C:/rtools40/mingw64/bin/gcc and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether C:/rtools40/mingw64/bin/g++ -std=gnu++11 accepts -g... yes
checking dependency style of C:/rtools40/mingw64/bin/g++ -std=gnu++11... gcc3
checking for x86_64-w64-mingw32-gcc... x86_64-w64-mingw32-gcc
checking whether we are using the GNU Objective C compiler... no
checking whether x86_64-w64-mingw32-gcc accepts -g... no
checking dependency style of x86_64-w64-mingw32-gcc... gcc3
checking for inline... inline
checking for windres... windres
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... C:/rtools40/mingw64/bin/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
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uid_t in sys/types.h... no
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stddef.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for stdint.h... (cached) yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking values.h usability... no
checking values.h presence... no
checking for values.h... no
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... no
checking termios.h presence... no
checking for termios.h... no
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... no
checking sys/times.h presence... no
checking for sys/times.h... no
checking for sys/types.h... (cached) yes
checking sys/select.h usability... no
checking sys/select.h presence... no
checking for sys/select.h... no
checking fpu_control.h usability... no
checking fpu_control.h presence... no
checking for fpu_control.h... no
checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... no
checking sys/socket.h presence... no
checking for sys/socket.h... no
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... no
checking sys/mman.h presence... no
checking for sys/mman.h... no
checking sys/ioctl.h usability... no
checking sys/ioctl.h presence... no
checking for sys/ioctl.h... no
checking sys/inotify.h usability... no
checking sys/inotify.h presence... no
checking for sys/inotify.h... no
checking langinfo.h usability... no
checking langinfo.h presence... no
checking for langinfo.h... no
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
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... no
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... no
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... no
checking for alloca... yes
checking for lrand48... no
checking for drand48... no
checking for srand48... no
checking for setmode... yes
checking for setenv... no
checking for getenv... yes
checking for __freadable... no
checking for _sysconf... no
checking for getrusage... no
checking for strerror... yes
checking for cbrt... yes
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... no
checking for memset... yes
checking for nl_langinfo... no
checking for pow... yes
checking for sqrt... yes
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... no
checking for a sed that does not truncate output... sed
checking for fgrep... grep -F
checking for ld used by C:/rtools40/mingw64/bin/gcc... C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /mingw32/bin/nm -B
checking the name lister (/mingw32/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe option to reload object files... -r
checking for x86_64-w64-mingw32-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL
checking for x86_64-w64-mingw32-ar... no
checking for ar... ar
checking for x86_64-w64-mingw32-strip... no
checking for strip... strip
checking for x86_64-w64-mingw32-ranlib... no
checking for ranlib... ranlib
checking command to parse /mingw32/bin/nm -B output from C:/rtools40/mingw64/bin/gcc object... failed
checking for dlfcn.h... no
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether C:/rtools40/mingw64/bin/g++ -std=gnu++11 accepts -g... (cached) yes
checking dependency style of C:/rtools40/mingw64/bin/g++ -std=gnu++11... (cached) gcc3
checking how to run the C++ preprocessor... C:/rtools40/mingw64/bin/g++ -std=gnu++11 -E
checking for objdir... .libs
checking if C:/rtools40/mingw64/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for C:/rtools40/mingw64/bin/gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if C:/rtools40/mingw64/bin/gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if C:/rtools40/mingw64/bin/gcc static flag -static works... yes
checking if C:/rtools40/mingw64/bin/gcc supports -c -o file.o... yes
checking if C:/rtools40/mingw64/bin/gcc supports -c -o file.o... (cached) yes
checking whether the C:/rtools40/mingw64/bin/gcc linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
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 C:/rtools40/mingw64/bin/g++ -std=gnu++11... C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) is GNU ld... yes
checking whether the C:/rtools40/mingw64/bin/g++ -std=gnu++11 linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
checking for C:/rtools40/mingw64/bin/g++ -std=gnu++11 option to produce PIC... -DDLL_EXPORT -DPIC
checking if C:/rtools40/mingw64/bin/g++ -std=gnu++11 PIC flag -DDLL_EXPORT -DPIC works... yes
checking if C:/rtools40/mingw64/bin/g++ -std=gnu++11 static flag -static works... yes
checking if C:/rtools40/mingw64/bin/g++ -std=gnu++11 supports -c -o file.o... yes
checking if C:/rtools40/mingw64/bin/g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the C:/rtools40/mingw64/bin/g++ -std=gnu++11 linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .dll
checking which variable specifies run-time module search path... PATH
checking for the default library search path... /lib /usr/lib
checking for library containing dlopen... no
checking for dlopen in -lsvld... no
checking for shl_load... no
checking for shl_load in -ldld... no
checking whether cygwin_conv_path is declared... no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... unknown
checking for argz.h... no
checking for error_t... no
checking for argz_add... no
checking for argz_append... no
checking for argz_count... no
checking for argz_create_sep... no
checking for argz_insert... no
checking for argz_next... no
checking for argz_stringify... no
checking whether libtool supports -dlopen/-dlpreopen... no
checking for ltdl.h... no
checking where to find libltdl headers... -I${top_srcdir}/libltdl
checking where to find libltdl library... ${top_build_prefix}libltdl/libltdlc.la
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking for X... disabled
configure: WARNING: X11 not available.
checking tcl.h usability... no
checking tcl.h presence... no
checking for tcl.h... no
configure: WARNING: Unable to find header tcl.h. The Tcl packages will not be built
configure: WARNING: No Tcl. The Tk packages will not be built either
checking for connect... no
checking for main in -lsocket... no
checking for accept... no
checking for gethostbyname... no
checking for main in -lnsl... no
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... no
checking X11/Intrinsic.h presence... no
checking for X11/Intrinsic.h... no
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
checking for GDK_PIXBUF... no
checking for GTK... no
checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... no
checking for qmake-qt4... no
checking for qmake-qt3... no
checking for qmake... no
checking for sincos... yes
checking if FILE struct contains _cnt... yes
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... no
checking if errno externs are declared... no
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... C:\rtools40\mingw32\bin\nm.exe: conftest.o: file format not recognized
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:    No (gdk_pixbuf library not available)
  ghostscript:   No (disabled)
  glitz:         No (disabled by default - incomplete)
  gtk:           No (gtk library not available)
  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/sh ./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="${ZSH_VERSION+.}:" && cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoheader)
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: autoheader: command not found
WARNING: `autoheader' is missing on your system.  You should only need it if
         you modified `acconfig.h' or `configure.ac'.  You might want
         to install the `Autoconf' and `GNU m4' packages.  Grab them
         from any GNU archive site.
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run aclocal-1.12 -I m4
/d/biocbuild/bbs-3.15-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/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run automake-1.12 --foreign
/d/biocbuild/bbs-3.15-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/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoconf
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: autoconf: command not found
WARNING: `autoconf' is missing on your system.  You should only need it if
         you modified `configure.ac'.  You might want to install the
         `Autoconf' and `GNU m4' packages.  Grab them from any GNU
         archive site.
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --disable-option-checking --prefix=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt --host=x86_64-w64-mingw32 --build=x86_64-w64-mingw32 CC=C:/rtools40/mingw64/bin/gcc CXX=C:/rtools40/mingw64/bin/g++ -std=gnu++11 CFLAGS=-fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition CXXFLAGS=-O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition LDFLAGS= --libdir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib --includedir=/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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 build_alias=x86_64-w64-mingw32 host_alias=x86_64-w64-mingw32 R_LIBS=D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rgraphviz/00new --enable-ltdl-convenience --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... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-w64-mingw32
checking host system type... x86_64-w64-mingw32
checking for style of include used by make... GNU
checking for x86_64-w64-mingw32-gcc... C:/rtools40/mingw64/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
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 C:/rtools40/mingw64/bin/gcc accepts -g... yes
checking for C:/rtools40/mingw64/bin/gcc option to accept ISO C89... none needed
checking dependency style of C:/rtools40/mingw64/bin/gcc... gcc3
checking for a sed that does not truncate output... sed
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checking if the linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /mingw32/bin/nm -B
checking the name lister (/mingw32/bin/nm -B) interface... BSD nm
checking whether ln -s works... no, using cp -pR
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
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checking command to parse /mingw32/bin/nm -B output from C:/rtools40/mingw64/bin/gcc object... failed
checking how to run the C preprocessor... C:/rtools40/mingw64/bin/gcc -E
checking for ANSI C header files... yes
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checking for objdir... .libs
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checking for C:/rtools40/mingw64/bin/gcc option to produce PIC... -DDLL_EXPORT -DPIC
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checking if C:/rtools40/mingw64/bin/gcc supports -c -o file.o... (cached) yes
checking whether the C:/rtools40/mingw64/bin/gcc linker (C:/rtools40/mingw64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
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checking which extension is used for runtime loadable modules... .dll
checking which variable specifies run-time module search path... PATH
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checking whether deplibs are loaded by dlopen... unknown
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checking whether libtool supports -dlopen/-dlpreopen... no
checking for unistd.h... (cached) yes
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checking for closedir... yes
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checking for strlcat... no
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checking that generated files are newer than configure... done
configure: creating ./config.status
 /bin/sh ./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
/bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/install-sh -d . 
cp ./argz_.h argz.h-t
mv argz.h-t argz.h
make  install-am
make[3]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT loadlibrary.lo -MD -MP -MF .deps/loadlibrary.Tpo -c -o loadlibrary.lo `test -f 'loaders/loadlibrary.c' || echo './'`loaders/loadlibrary.c
libtool: compile:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT loadlibrary.lo -MD -MP -MF .deps/loadlibrary.Tpo -c loaders/loadlibrary.c -o loadlibrary.o
In file included from libltdl/lt__private.h:57,
                 from loaders/loadlibrary.c:32:
loaders/loadlibrary.c: In function 'vm_open':
./ltdl.h:44:24: warning: the address of 'wpath' will always evaluate as 'true' [-Waddress]
 #define LT_STRLEN(s) (((s) && (s)[0]) ? strlen (s) : 0)
                        ^
loaders/loadlibrary.c:159:12: note: in expansion of macro 'LT_STRLEN'
      len = LT_STRLEN (wpath);
            ^~~~~~~~~
mv -f .deps/loadlibrary.Tpo .deps/loadlibrary.Plo
/bin/sh ./libtool --tag=CC   --mode=link C:/rtools40/mingw64/bin/gcc  -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -module -avoid-version  -o loadlibrary.la  loadlibrary.lo  
libtool: link: ar cru .libs/loadlibrary.a  loadlibrary.o
libtool: link: ranlib .libs/loadlibrary.a
libtool: link: ( cd ".libs" && rm -f "loadlibrary.la" && cp -pR "../loadlibrary.la" "loadlibrary.la" )
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c -o libltdlc_la-preopen.o
mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c -o libltdlc_la-lt__alloc.o
mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c -o libltdlc_la-lt_dlloader.o
mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c -o libltdlc_la-lt_error.o
mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c -o libltdlc_la-ltdl.o
In file included from libltdl/lt__private.h:51,
                 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/sh ./libtool  --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c -o libltdlc_la-slist.o
mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo
/bin/sh ./libtool --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c -o argz.lo argz.c
libtool: compile:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c argz.c -o argz.o
mv -f .deps/argz.Tpo .deps/argz.Plo
/bin/sh ./libtool --tag=CC   --mode=compile C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c -o lt__strl.lo lt__strl.c
libtool: compile:  C:/rtools40/mingw64/bin/gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -MT lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c lt__strl.c -o lt__strl.o
mv -f .deps/lt__strl.Tpo .deps/lt__strl.Plo
/bin/sh ./libtool --tag=CC   --mode=link C:/rtools40/mingw64/bin/gcc  -fcommon -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -no-undefined -dlpreopen loadlibrary.la   -o libltdlc.la  libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo argz.lo lt__strl.lo 
libtool: link: not configured to extract global symbols from dlpreopened files
libtool: link: (cd .libs/libltdlc.lax/loadlibrary.a && ar x "/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/loadlibrary.a")
libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o argz.o lt__strl.o  .libs/libltdlc.lax/loadlibrary.a/loadlibrary.o 
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && cp -pR "../libltdlc.la" "libltdlc.la" )
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader)
/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: autoheader: command not found
WARNING: `autoheader' is missing on your system.  You should only need it if
         you modified `acconfig.h' or `configure.ac'.  You might want
         to install the `Autoconf' and `GNU m4' packages.  Grab them
         from any GNU archive site.
rm -f stamp-h1
touch config-h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make[4]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib'
Making install in cdt
make[3]: Entering directory '/d/biocbuild/bbs-3.15-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
  CCLD     libcdt_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libcdt.a
libtool: install: chmod 644 /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libcdt.a
libtool: install: ranlib /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libcdt.a
----------------------------------------------------------------------
Libraries have been installed in:
   /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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 `PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-LLIBDIR' linker flag

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
make[4]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
  CC       attribs.lo
attribs.c: In function 'agcopydict':
attribs.c:286:18: warning: zero-length ms_printf format string [-Wformat-zero-length]
  fprintf(stderr, "", a->name, a->value);
                  ^~
attribs.c:286:18: warning: zero-length ms_printf format string [-Wformat-zero-length]
  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 returning 'unsigned char *' from a function with return type 'char *' 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:
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)
              ^~~~~~~~~~
  CC       node.lo
sed "s/yy/ag/g" < y.tab.c > parser.c
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
  CCLD     libgraph_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libgraph.a
libtool: install: chmod 644 /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libgraph.a
libtool: install: ranlib /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libgraph.a
----------------------------------------------------------------------
Libraries have been installed in:
   /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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 `PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-LLIBDIR' linker flag

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
make[4]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory '/d/biocbuild/bbs-3.15-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
  CC       shortestpth.lo
  CC       solvers.lo
  CC       triang.lo
  CC       util.lo
  CC       visibility.lo
  CCLD     libpathplan.la
  CCLD     libpathplan_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libpathplan.a
libtool: install: chmod 644 /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libpathplan.a
libtool: install: ranlib /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/libpathplan.a
----------------------------------------------------------------------
Libraries have been installed in:
   /d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/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 `PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-LLIBDIR' linker flag

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/man/man3'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/share/graphviz/doc/pdf'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
 /usr/bin/mkdir -p '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz'
make[4]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory '/d/biocbuild/bbs-3.15-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 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-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 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory '/d/biocbuild/bbs-3.15-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 'putSeg':
ortho.c:545:5: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->p.p1,seg->comm_coord,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       seg->p.p2, seg->comm_coord, bendToStr (seg->l1), bendToStr (seg->l2));
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:545:5: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
ortho.c:542:5: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
     fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->comm_coord, seg->p.p1,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       seg->comm_coord, seg->p.p2, bendToStr (seg->l1), bendToStr (seg->l2));
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:542:5: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
ortho.c: In function 'decide_point':
ortho.c:878:11: warning: 'prec' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return(ret);
           ^
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: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
make[4]: Entering directory '/d/biocbuild/bbs-3.15-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 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
Making install in sparse
make[3]: Entering directory '/d/biocbuild/bbs-3.15-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
  CC       IntStack.lo
  CCLD     libsparse_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-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 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
Making install in patchwork
make[3]: Entering directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
make[4]: Entering directory '/d/biocbuild/bbs-3.15-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 '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
Making install in common
make[3]: Entering directory '/d/biocbuild/bbs-3.15-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
sed "s/yy/html/g" < y.tab.h > htmlparse.h
  CC       htmllex.lo
In file included from render.h:47,
                 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));
                                   ^~~~~~~
sed "s/yy/html/g" < y.tab.c > htmlparse.c
  CC       htmlparse.lo
In file included from render.h:47,
                 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,
                 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,
                 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
postproc.c: In function 'gv_postprocess':
postproc.c:24:1: warning: ' translate } def
/arrowlengt...' directive writing 560 bytes into a region of size between 230 and 296 [-Wformat-overflow=]
 "/pathbox {\n\
 ^~~~~~~~~~~~~~
     /Y exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /X exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /y exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /x exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     newpath x y moveto\n\
     ~~~~~~~~~~~~~~~~~~~~~
     X y lineto\n\
     ~~~~~~~~~~~~~
     X Y lineto\n\
     ~~~~~~~~~~~~~
     x Y lineto\n\
     ~~~~~~~~~~~~~
     closepath stroke\n \
     ~~~~~~~~~~~~~~~~~~~~
 } def\n\
 ~~~~~~~~
 /dbgstart { gsave %.5g %.5g translate } def\n\
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 /arrowlength 10 def\n\
 ~~~~~~~~~~~~~~~~~~~~~~
 /arrowwidth arrowlength 2 div def\n\
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 /arrowhead {\n\
 ~~~~~~~~~~~~~~~
     gsave\n\
     ~~~~~~~~
     rotate\n\
     ~~~~~~~~~
     currentpoint\n\
     ~~~~~~~~~~~~~~~
     newpath\n\
     ~~~~~~~~~~
     moveto\n\
     ~~~~~~~~~
     arrowlength arrowwidth 2 div rlineto\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     0 arrowwidth neg rlineto\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
     closepath fill\n\
     ~~~~~~~~~~~~~~~~~
     grestore\n\
     ~~~~~~~~~~~
 } bind def\n\
 ~~~~~~~~~~~~~
 /makearrow {\n\
 ~~~~~~~~~~~~~~~
     currentpoint exch pop sub exch currentpoint pop sub atan\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     arrowhead\n\
     ~~~~~~~~~~~~
 } bind def\n\
 ~~~~~~~~~~~~~
 /point {\
 ~~~~~~~~~
     newpath\
     ~~~~~~~~
     2 0 360 arc fill\
     ~~~~~~~~~~~~~~~~~
 } def\
 ~~~~~~
 /makevec {\n\
 ~~~~~~~~~~~~~
     /Y exch def\n\
     ~~~~~~~~~~~~~~
     /X exch def\n\
     ~~~~~~~~~~~~~~
     /y exch def\n\
     ~~~~~~~~~~~~~~
     /x exch def\n\
     ~~~~~~~~~~~~~~
     newpath x y moveto\n\
     ~~~~~~~~~~~~~~~~~~~~~
     X Y lineto stroke\n\
     ~~~~~~~~~~~~~~~~~~~~
     X Y moveto\n\
     ~~~~~~~~~~~~~
     x y makearrow\n\
     ~~~~~~~~~~~~~~~~
 } def\n"
 ~~~~~~~~
postproc.c:24:1: note: in definition of macro 'M1'
 "/pathbox {\n\
 ^~~~~~~~~~~~~~
     /Y exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /X exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /y exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     /x exch %.5g sub def\n\
     ~~~~~~~~~~~~~~~~~~~~~~~
     newpath x y moveto\n\
     ~~~~~~~~~~~~~~~~~~~~~
     X y lineto\n\
     ~~~~~~~~~~~~~
     X Y lineto\n\
     ~~~~~~~~~~~~~
     x Y lineto\n\
     ~~~~~~~~~~~~~
     closepath stroke\n \
     ~~~~~~~~~~~~~~~~~~~~
 } def\n\
 ~~~~~~~~
 /dbgstart { gsave %.5g %.5g translate } def\n\
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 /arrowlength 10 def\n\
 ~~~~~~~~~~~~~~~~~~~~~~
 /arrowwidth arrowlength 2 div def\n\
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 /arrowhead {\n\
 ~~~~~~~~~~~~~~~
     gsave\n\
     ~~~~~~~~
     rotate\n\
     ~~~~~~~~~
     currentpoint\n\
     ~~~~~~~~~~~~~~~
     newpath\n\
     ~~~~~~~~~~
     moveto\n\
     ~~~~~~~~~
     arrowlength arrowwidth 2 div rlineto\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     0 arrowwidth neg rlineto\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
     closepath fill\n\
     ~~~~~~~~~~~~~~~~~
     grestore\n\
     ~~~~~~~~~~~
 } bind def\n\
 ~~~~~~~~~~~~~
 /makearrow {\n\
 ~~~~~~~~~~~~~~~
     currentpoint exch pop sub exch currentpoint pop sub atan\n\
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     arrowhead\n\
     ~~~~~~~~~~~~
 } bind def\n\
 ~~~~~~~~~~~~~
 /point {\
 ~~~~~~~~~
     newpath\
     ~~~~~~~~
     2 0 360 arc fill\
     ~~~~~~~~~~~~~~~~~
 } def\
 ~~~~~~
 /makevec {\n\
 ~~~~~~~~~~~~~
     /Y exch def\n\
     ~~~~~~~~~~~~~~
     /X exch def\n\
     ~~~~~~~~~~~~~~
     /y exch def\n\
     ~~~~~~~~~~~~~~
     /x exch def\n\
     ~~~~~~~~~~~~~~
     newpath x y moveto\n\
     ~~~~~~~~~~~~~~~~~~~~~
     X Y lineto stroke\n\
     ~~~~~~~~~~~~~~~~~~~~
     X Y moveto\n\
     ~~~~~~~~~~~~~
     x y makearrow\n\
     ~~~~~~~~~~~~~~~~
 } def\n"
 ~~~~~~~~
postproc.c:296:6: note: 'sprintf' output between 777 and 843 bytes into a destination of size 512
      sprintf(buf, M1, Offset.y, Offset.x, Offset.y, Offset.x,
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                  -Offset.x, -Offset.y);
                  ~~~~~~~~~~~~~~~~~~~~~
  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,
                 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:22:10: fatal error: libltdl/lt_system.h: No such file or directory
 #include "libltdl/lt_system.h"
          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [Makefile:631: utils.lo] Error 1
make[3]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib/common'
make[2]: *** [Makefile:524: install-recursive] Error 1
make[2]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz/lib'
make[1]: *** [Makefile:743: install-recursive] Error 1
make[1]: Leaving directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/graphviz'
make: *** [Makefile:1106: install] Error 2
cp: -r not specified; omitting directory '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/pkgconfig'
cp: cannot stat '/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/lib/graphviz/*': No such file or directory
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... 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.win: Using the following compilation and linking flags for Rgraphviz
configure.win:    PKG_CFLAGS= -I/d/biocbuild/bbs-3.15-bioc/meat/Rgraphviz/src/libwinucrt/include/graphviz
configure.win:    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.win:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure.win: Compiling using Graphviz version: '2.28.0'.
configure.win: Using bundled Graphviz: 'TRUE'.
configure.win: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
                             ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rgraphviz.c -o Rgraphviz.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RgraphvizInit.c -o RgraphvizInit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c agopen.c -o agopen.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c agread.c -o agread.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c agwrite.c -o agwrite.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bezier.c -o bezier.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c buildEdgeList.c -o buildEdgeList.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c buildNodeList.c -o buildNodeList.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c doLayout.c -o doLayout.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c graphvizVersion.c -o graphvizVersion.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c init.c -o init.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 libwin/x64/lib/libxdot.a libwin/x64/lib/libgvplugin_dot_layout.a libwin/x64/lib/libgvplugin_neato_layout.a libwin/x64/lib/libgvplugin_core.a libwin/x64/lib/libgvc.a libwin/x64/lib/libpathplan.a libwin/x64/lib/libgraph.a libwin/x64/lib/libcdt.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
sed "s!@GRAPHVIZ_VERSION@!"2.28.0"!" ../R/graphviz_build_version.R.in |\
  sed "s!@GRAPHVIZ_BUNDLED@!TRUE!" > ../R/graphviz_build_version.R
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rgraphviz/00new/Rgraphviz/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rgraphviz'
    finding HTML links ... done
    AgEdge-class                            html  
    AgNode-class                            html  
    AgTextLabel-class                       html  
    BezierCurve-class                       html  
    GraphvizAttributes                      html  
    GraphvizLayouts                         html  
    Ragraph-class                           html  
    agopen                                  html  
    agopenSimple                            html  
    agwrite                                 html  
    boundingBox-class                       html  
    buildNodeList                           html  
    clusterData-methods                     html  
    getDefaultAttrs                         html  
    graphData-methods                       html  
    graphDataDefaults-methods               html  
    graphLayout                             html  
    graphvizCapabilities                    html  
    graphvizVersion                         html  
    layoutGraph                             html  
    makeNodeAttrs                           html  
    pEdge-class                             html  
    pNode-class                             html  
    pieGlyph                                html  
    plot-methods                            html  
    removedEdges                            html  
    renderGraph                             html  
    toDot-methods                           html  
    toFile                                  html  
    xyPoint-class                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rgraphviz)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'goSTAG' is missing or broken
 done
name	user	system	elapsed
AgEdge-class	0.03	0.00	0.03
AgNode-class	0.02	0.00	0.00
AgTextLabel-class	0.00	0.02	0.01
BezierCurve-class	0	0	0
GraphvizLayouts	0	0	0
Ragraph-class	0.01	0.01	0.04
agopen	0	0	0
agopenSimple	0.04	0.00	0.03
agwrite	0.01	0.00	0.02
boundingBox-class	0	0	0
buildNodeList	0	0	0
clusterData-methods	0.20	0.01	0.22
getDefaultAttrs	0	0	0
graphLayout	0	0	0
graphvizCapabilities	0	0	0
graphvizVersion	0	0	0
layoutGraph	0.24	0.00	0.24
makeNodeAttrs	0.01	0.00	0.01
pEdge-class	0	0	0
pNode-class	0	0	0
pieGlyph	0.02	0.00	0.02
plot-methods	0	0	0
removedEdges	0	0	0
renderGraph	0.11	0.00	0.11
toDot-methods	0	0	0
toFile	0.04	0.00	0.05
xyPoint-class	0	0	0
CHECK results for Rgraphviz on riesling1

Summary

Command output

Installation output

Tests output

Example timings
