Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-08-02 15:05:55 -0400 (Mon, 02 Aug 2021).

CHECK results for Rgraphviz on machv2

To the developers/maintainers of the Rgraphviz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rgraphviz.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1569/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rgraphviz 2.36.0  (landing page)
Kasper Daniel Hansen
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/Rgraphviz
Branch: RELEASE_3_13
Last Commit: 1ea05ef
Last Changed Date: 2021-05-19 11:33:11 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rgraphviz
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rgraphviz_2.36.0.tar.gz
StartedAt: 2021-08-01 22:43:22 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 22:44:19 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 57.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rgraphviz.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rgraphviz_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘2.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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:
  checking if assert needs __eprintf... clang: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
  clang: warning: argument unused during compilation: '-L/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib' [-Wunused-command-line-argument]
  attribs.c:240:7: warning: explicitly assigning value of variable of type 'Agraph_t *' (aka 'struct Agraph_t *') to itself [-Wself-assign]
  edge.c:271:10: warning: explicitly assigning value of variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
  node.c:138:10: warning: explicitly assigning value of variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
  ortho.c:474:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ortho.c:474:28: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ortho.c:504:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ortho.c:504:28: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  shapes.c:758:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  shapes.c:758:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  shapes.c:1253:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  shapes.c:1261:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  gvevent.c:546:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gvevent.c:546:30: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  class2.c:53:10: warning: explicitly assigning value of variable of type 'edge_t *' (aka 'struct Agedge_t *') to itself [-Wself-assign]
  neatoinit.c:744:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  neatoinit.c:744:74: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  stress.c:1383:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spring_electrical.c:287:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rgraphviz/libs/Rgraphviz.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (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)

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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz.Rcheck/00check.log’
for details.



Installation output

Rgraphviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rgraphviz
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Rgraphviz’ ...
** using staged installation
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... clang -mmacosx-version-min=10.13
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 clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
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... clang -mmacosx-version-min=10.13
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 clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking for library containing strerror... none required
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -ll
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking for gawk... (cached) awk
checking whether ln -s works... yes
checking for sed... /usr/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/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/local/bin/tclsh8.6
checking whether clang -mmacosx-version-min=10.13 and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++14... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
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... clang -mmacosx-version-min=10.13 -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... yes
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... no
checking malloc.h presence... no
checking for malloc.h... no
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... 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... 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... 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... no
checking sys/inotify.h presence... no
checking for sys/inotify.h... no
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... yes
checking crt_externs.h presence... yes
checking for crt_externs.h... yes
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... 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... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... yes
checking for setenv... yes
checking for getenv... yes
checking for __freadable... no
checking for _sysconf... no
checking for getrusage... yes
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... yes
checking for memset... yes
checking for nl_langinfo... yes
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... yes
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
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... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /Library/Developer/CommandLineTools/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 clang -mmacosx-version-min=10.13 object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... no
checking for -exported_symbols_list linker flag... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... (cached) yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++14... (cached) gcc3
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++14 -E
checking for objdir... .libs
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
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 clang++ -mmacosx-version-min=10.13 -std=gnu++14... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to produce PIC... -fno-common -DPIC
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 PIC flag -fno-common -DPIC works... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 static flag -static works... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
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... DYLD_LIBRARY_PATH
checking for the default library search path... /usr/local/lib /lib /usr/lib
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... yes
checking whether we have to add an underscore for dlsym... no
checking whether deplibs are loaded by dlopen... yes
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... yes
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... yes
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/usr/local/include
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
using /usr/local/lib/tclConfig.sh
checking for wish8.6... /usr/local/bin/wish8.6
using tk headers from -I/usr/local/include
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking for tk.h... (cached) yes
checking tkInt.h usability... no
checking tkInt.h presence... no
checking for tkInt.h... no
using /usr/local/lib/tkConfig.sh
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... yes
checking for main in -lXaw... no
configure: WARNING: Optional Xaw library not available
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... yes
checking for GDK_PIXBUF... yes
checking for GTK... yes
checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... yes
checking for qmake-qt4... no
checking for qmake-qt3... no
checking for qmake... no
checking for sincos... no
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... yes
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... no
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... clang: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-L/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib' [-Wunused-command-line-argument]
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 (/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix'  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++14' 'CFLAGS=-Wall -g -O2' 'CXXFLAGS=-Wall -g -O2' 'LDFLAGS=-L/usr/local/lib' '--libdir=/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Resources/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/X11/lib/pkgconfig:/usr/local/opt/openssl@1.1/lib/pkgconfig:/usr/local/opt/mysql-client/lib/pkgconfig' 'R_LIBS=/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rgraphviz/00new' '--enable-ltdl-convenience' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking for style of include used by make... GNU
checking for gcc... clang -mmacosx-version-min=10.13
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 clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /Library/Developer/CommandLineTools/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 clang -mmacosx-version-min=10.13 object... rm: conftest.dSYM: is a directory
ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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 clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
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... DYLD_LIBRARY_PATH
checking for the default library search path... /usr/local/lib /lib /usr/lib
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... yes
checking whether we have to add an underscore for dlsym... no
checking whether deplibs are loaded by dlopen... yes
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... 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... yes
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
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 library)
  smyrna:        No (disabled by default - experimental)
  gvedit:        No (qmake not found)

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

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

  tcldot:        Yes
  tclpathplan:   Yes
  gdtclft:       No (gd not available)
  tkspline:      Yes
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
Making install in libltdl
/bin/sh /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/install-sh -d . 
cp ./argz_.h argz.h-t
mv argz.h-t argz.h
make  install-am
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c  -fno-common -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/sh ./libtool --tag=CC   --mode=link clang -mmacosx-version-min=10.13  -Wall -g -O2 -module -avoid-version -L/usr/local/lib -o dlopen.la  dlopen.lo  
libtool: link: ar cru .libs/dlopen.a  dlopen.o
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c  -fno-common -DPIC -o libltdlc_la-preopen.o
mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c  -fno-common -DPIC -o libltdlc_la-lt__alloc.o
mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c  -fno-common -DPIC -o libltdlc_la-lt_dlloader.o
mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c  -fno-common -DPIC -o libltdlc_la-lt_error.o
mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c  -fno-common -DPIC -o libltdlc_la-ltdl.o
ltdl.c:1343:14: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
          if (!file && *sys_dlsearch_path)
                    ^  ~~~~~~~~~~~~~~~~~~
ltdl.c:1343:14: note: use '&' for a bitwise operation
          if (!file && *sys_dlsearch_path)
                    ^~
                    &
ltdl.c:1343:14: note: remove constant to silence this warning
          if (!file && *sys_dlsearch_path)
                   ~^~~~~~~~~~~~~~~~~~~~~
ltdl.c:1887:20: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
      if (!is_done && *sys_dlsearch_path)
                   ^  ~~~~~~~~~~~~~~~~~~
ltdl.c:1887:20: note: use '&' for a bitwise operation
      if (!is_done && *sys_dlsearch_path)
                   ^~
                   &
ltdl.c:1887:20: note: remove constant to silence this warning
      if (!is_done && *sys_dlsearch_path)
                  ~^~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/sh ./libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c  -fno-common -DPIC -o libltdlc_la-slist.o
mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo
/bin/sh ./libtool --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -Wall -g -O2 -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c -o argz.lo argz.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -Wall -g -O2 -MT argz.lo -MD -MP -MF .deps/argz.Tpo -c argz.c  -fno-common -DPIC -o argz.o
mv -f .deps/argz.Tpo .deps/argz.Plo
/bin/sh ./libtool --tag=CC   --mode=link clang -mmacosx-version-min=10.13  -Wall -g -O2 -no-undefined -dlpreopen dlopen.la  -L/usr/local/lib -o libltdlc.la  libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo argz.lo 
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && clang -mmacosx-version-min=10.13 -Wall -g -O2 -c -fno-builtin -fno-rtti -fno-exceptions  -fno-common -DPIC "libltdlcS.c")
libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT"
libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a")
libtool: link: ar cru .libs/libltdlc.a  libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o argz.o .libs/libltdlcS.o  .libs/libltdlc.lax/dlopen.a/dlopen.o 
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
Making install in lib
Making install in cdt
  CC       dtclose.lo
  CC       dtdisc.lo
  CC       dtextract.lo
  CC       dtflatten.lo
  CC       dthash.lo
  CC       dtlist.lo
  CC       dtmethod.lo
  CC       dtopen.lo
  CC       dtrenew.lo
  CC       dtrestore.lo
  CC       dtsize.lo
  CC       dtstat.lo
  CC       dtstrhash.lo
  CC       dttree.lo
  CC       dttreeset.lo
  CC       dtview.lo
  CC       dtwalk.lo
  CCLD     libcdt.la
  CCLD     libcdt_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libcdt.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 cdt.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 cdt.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libcdt.pc '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 cdt.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in graph
  CC       attribs.lo
attribs.c:240:7: warning: explicitly assigning value of variable of type 'Agraph_t *' (aka 'struct Agraph_t *') to itself [-Wself-assign]
    g = g;
    ~ ^ ~
1 warning generated.
  CC       agxbuf.lo
  CC       edge.lo
edge.c:271:10: warning: explicitly assigning value of variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
    dict = dict;
    ~~~~ ^ ~~~~
1 warning generated.
  CC       graph.lo
  CC       graphio.lo
  CC       lexer.lo
lexer.c:147:12: warning: returning 'unsigned char *' from a function with result type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
    return p;
           ^
lexer.c:435:26: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
            LexPtr = scan_token(LexPtr, tbuf);
                                ^~~~~~
lexer.c:136:40: note: passing argument to parameter 'p' here
static char *scan_token(unsigned char *p, unsigned char *token)
                                       ^
lexer.c:435:34: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
            LexPtr = scan_token(LexPtr, tbuf);
                                        ^~~~
lexer.c:136:58: note: passing argument to parameter 'token' here
static char *scan_token(unsigned char *p, unsigned char *token)
                                                         ^
3 warnings generated.
  CC       node.lo
node.c:138:10: warning: explicitly assigning value of variable of type 'Agdict_t *' (aka 'struct Agdict_t *') to itself [-Wself-assign]
    dict = dict;
    ~~~~ ^ ~~~~
1 warning generated.
  CC       parser.lo
  CC       refstr.lo
  CC       trie.lo
  CCLD     libgraph.la
  CCLD     libgraph_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgraph.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 graph.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 graph.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgraph.pc '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graph.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in pathplan
  CC       cvt.lo
cvt.c:276:13: warning: function 'append_bezier' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void append_bezier(Ppoint_t * bezier)
            ^
1 warning generated.
  CC       inpoly.lo
  CC       route.lo
  CC       shortest.lo
  CC       shortestpth.lo
  CC       solvers.lo
  CC       triang.lo
  CC       util.lo
  CC       visibility.lo
  CCLD     libpathplan.la
  CCLD     libpathplan_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libpathplan.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pathplan.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pathplan.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libpathplan.pc '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in vpsc
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in rbtree
  CC       misc.lo
  CC       red_black_tree.lo
  CC       stack.lo
  CCLD     librbtree_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in ortho
  CC       fPQ.lo
  CC       intset.lo
  CC       maze.lo
  CC       ortho.lo
ortho.c:474:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
             ^
ortho.c:474:7: note: use function 'fabs' instead
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
             ^~~
             fabs
ortho.c:474:28: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
                                  ^
ortho.c:474:28: note: use function 'fabs' instead
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
                                  ^~~
                                  fabs
ortho.c:504:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
             ^
ortho.c:504:7: note: use function 'fabs' instead
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
             ^~~
             fabs
ortho.c:504:28: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
                                  ^
ortho.c:504:28: note: use function 'fabs' instead
        wt = abs(p.x - midp.x) +  abs(p.y - midp.y);
                                  ^~~
                                  fabs
ortho.c:1422:14: warning: variable 'p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
    else if (cp->sides[M_RIGHT] == np) {
             ^~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:1426:12: note: uninitialized use occurs here
    return p;
           ^
ortho.c:1422:10: note: remove the 'if' if its condition is always true
    else if (cp->sides[M_RIGHT] == np) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:1409:5: note: variable 'p' is declared here
    point p;
    ^
5 warnings generated.
  CC       partition.lo
partition.c:656:14: warning: variable 'size' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
    else if (tr[tr_start].d0 > 0)
             ^~~~~~~~~~~~~~~~~~~
partition.c:665:10: note: uninitialized use occurs here
  return size;
         ^~~~
partition.c:656:10: note: remove the 'if' if its condition is always true
    else if (tr[tr_start].d0 > 0)
         ^~~~~~~~~~~~~~~~~~~~~~~~
partition.c:620:16: note: initialize the variable 'size' to silence this warning
    int i, size;
               ^
                = 0
1 warning generated.
  CC       rawgraph.lo
  CC       sgraph.lo
  CC       trapezoid.lo
  CCLD     libortho_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sparse
  CC       SparseMatrix.lo
  CC       general.lo
  CC       BinaryHeap.lo
  CC       IntStack.lo
  CCLD     libsparse_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in patchwork
  CC       patchwork.lo
  CC       patchworkinit.lo
  CC       tree_map.lo
  CCLD     libpatchwork_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in common
  CC       arrows.lo
  CC       colxlate.lo
  CC       fontmetrics.lo
  CC       args.lo
  CC       memory.lo
  CC       globals.lo
  CC       htmllex.lo
  CC       htmlparse.lo
  CC       htmltable.lo
  CC       input.lo
  CC       pointset.lo
  CC       postproc.lo
  CC       routespl.lo
  CC       splines.lo
  CC       psusershape.lo
  CC       timing.lo
  CC       labels.lo
  CC       ns.lo
  CC       shapes.lo
shapes.c:758:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^
shapes.c:758:15: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^~~
              fabs
./arith.h:87:27: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                          ^
shapes.c:758:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^
shapes.c:758:15: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^~~
              fabs
./arith.h:87:39: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                      ^
shapes.c:758:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^
shapes.c:758:15: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
              ^~~
              fabs
./arith.h:87:53: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                                    ^
shapes.c:758:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^
shapes.c:758:38: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^~~
                                     fabs
./arith.h:87:27: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                          ^
shapes.c:758:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^
shapes.c:758:38: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^~~
                                     fabs
./arith.h:87:39: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                      ^
shapes.c:758:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^
shapes.c:758:38: note: use function 'fabs' instead
    if (ROUND(abs(dimen.x)) || ROUND(abs(dimen.y))) {
                                     ^~~
                                     fabs
./arith.h:87:53: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                                    ^
shapes.c:1253:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
            angle = angle;
            ~~~~~ ^ ~~~~~
shapes.c:1261:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
            angle = angle;
            ~~~~~ ^ ~~~~~
8 warnings generated.
  CC       utils.lo
  CC       geom.lo
  CC       output.lo
  CC       emit.lo
  CCLD     libcommon_C.la
make[4]: Nothing to be done for `install-exec-am'.
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in pack
  CC       ccomps.lo
  CC       pack.lo
pack.c:936:9: warning: variable 'pts' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
    if (pinfo->mode == l_array) {
        ^~~~~~~~~~~~~~~~~~~~~~
pack.c:953:12: note: uninitialized use occurs here
    return pts;
           ^~~
pack.c:936:5: note: remove the 'if' if its condition is always true
    if (pinfo->mode == l_array) {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pack.c:920:15: note: initialize the variable 'pts' to silence this warning
    point* pts;
              ^
               = NULL
1 warning generated.
  CCLD     libpack_C.la
make[4]: Nothing to be done for `install-exec-am'.
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 pack.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 pack.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 pack.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in xdot
  CC       xdot.lo
  CCLD     libxdot.la
  CCLD     libxdot_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libxdot.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 xdot.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 xdot.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxdot.pc '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 xdot.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in gvc
  CC       gvrender.lo
  CC       gvlayout.lo
  CC       gvdevice.lo
  CC       gvloadimage.lo
  CC       gvcontext.lo
  CC       gvjobs.lo
  CC       gvevent.lo
gvevent.c:546:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (abs(dx) < EPSILON && abs(dy) < EPSILON)  /* ignore motion events with no motion */
        ^
gvevent.c:546:9: note: use function 'fabs' instead
    if (abs(dx) < EPSILON && abs(dy) < EPSILON)  /* ignore motion events with no motion */
        ^~~
        fabs
gvevent.c:546:30: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (abs(dx) < EPSILON && abs(dy) < EPSILON)  /* ignore motion events with no motion */
                             ^
gvevent.c:546:30: note: use function 'fabs' instead
    if (abs(dx) < EPSILON && abs(dy) < EPSILON)  /* ignore motion events with no motion */
                             ^~~
                             fabs
2 warnings generated.
  CC       gvplugin.lo
  CC       gvconfig.lo
  CC       gvtextlayout.lo
  CC       gvusershape.lo
  CC       gvc.lo
  CCLD     libgvc.la
  CCLD     libgvc_C.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvc.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 /usr/bin/install -c -m 644 gvc.3 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 /usr/bin/install -c -m 644 gvc.3.pdf '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 /usr/bin/install -c -m 644 libgvc.pc '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
Making install in 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
  CC       nodeset.lo
  CCLD     libcircogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in dotgen
  CC       acyclic.lo
  CC       class1.lo
  CC       class2.lo
class2.c:53:10: warning: explicitly assigning value of variable of type 'edge_t *' (aka 'struct Agedge_t *') to itself [-Wself-assign]
    orig = orig;
    ~~~~ ^ ~~~~
1 warning generated.
  CC       cluster.lo
  CC       compound.lo
  CC       conc.lo
  CC       decomp.lo
  CC       fastgr.lo
  CC       flat.lo
  CC       dotinit.lo
  CC       mincross.lo
  CC       position.lo
  CC       rank.lo
  CC       sameport.lo
  CC       dotsplines.lo
dotsplines.c:1604:25: warning: expression result unused [-Wunused-value]
        lp = ED_label(e)->pos, lp;
                               ^~
1 warning generated.
  CC       aspect.lo
  CCLD     libdotgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in fdpgen
  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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libfdpgen_C.a(dbg.o) has no symbols
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in neatogen
  CC       adjust.lo
adjust.c:674:30: warning: variable 'nedge_nodes' is uninitialized when used here [-Wuninitialized]
        if (elabels && IS_LNODE(n)) nedge_nodes++;
                                    ^~~~~~~~~~~
adjust.c:670:23: note: initialize the variable 'nedge_nodes' to silence this warning
    int i, nedge_nodes;
                      ^
                       = 0
adjust.c:1073:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PORTHO_YX:
             ^~~~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1074:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PORTHO:
             ^~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1075:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PORTHOXY:
             ^~~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1076:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PORTHOYX:
             ^~~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1077:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_ORTHO_YX:
             ^~~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1078:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_ORTHO:
             ^~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1079:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_ORTHOXY:
             ^~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1080:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_ORTHOYX:
             ^~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1070:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PUSHPULL:
             ^~~~~~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1067:7: warning: variable 'ret' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
        case AM_PUSH:
             ^~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1099:2: warning: variable 'ret' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
        default:                /* to silence warnings */
        ^~~~~~~
adjust.c:1105:9: note: uninitialized use occurs here
        return ret;
               ^~~
adjust.c:1045:12: note: initialize the variable 'ret' to silence this warning
    int ret;
           ^
            = 0
12 warnings generated.
  CC       circuit.lo
  CC       edges.lo
  CC       geometry.lo
  CC       heap.lo
  CC       hedges.lo
  CC       info.lo
  CC       neatoinit.lo
neatoinit.c:744:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^
neatoinit.c:744:45: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^~~
                                            fabs
../../lib/common/arith.h:87:27: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                          ^
neatoinit.c:744:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^
neatoinit.c:744:45: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^~~
                                            fabs
../../lib/common/arith.h:87:39: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                      ^
neatoinit.c:744:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^
neatoinit.c:744:45: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                            ^~~
                                            fabs
../../lib/common/arith.h:87:53: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                                    ^
neatoinit.c:744:74: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^
neatoinit.c:744:74: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^~~
                                                                         fabs
../../lib/common/arith.h:87:27: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                          ^
neatoinit.c:744:74: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^
neatoinit.c:744:74: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^~~
                                                                         fabs
../../lib/common/arith.h:87:39: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                      ^
neatoinit.c:744:74: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^
neatoinit.c:744:74: note: use function 'fabs' instead
    if (adjust && !haveBackground && (ROUND(abs(GD_bb(g).LL.x)) || ROUND(abs(GD_bb(g).LL.y))))
                                                                         ^~~
                                                                         fabs
../../lib/common/arith.h:87:53: note: expanded from macro 'ROUND'
#define ROUND(f)        ((f>=0)?(int)(f + .5):(int)(f - .5))
                                                    ^
6 warnings generated.
  CC       legal.lo
  CC       lu.lo
  CC       matinv.lo
  CC       memory.lo
  CC       poly.lo
  CC       printvis.lo
  CC       site.lo
  CC       solve.lo
  CC       neatosplines.lo
neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable]
    router_t* rtr = 0;
              ^
1 warning generated.
  CC       stuff.lo
  CC       voronoi.lo
  CC       stress.lo
stress.c:1383:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
            delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);
                     ^
stress.c:1383:15: note: use function 'fabsf' instead
            delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);
                     ^~~
                     fabsf
stress.c:1383:6: warning: variable 'delta' is uninitialized when used here [-Wuninitialized]
            delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]);
            ^~~~~
stress.c:1370:17: note: initialize the variable 'delta' to silence this warning
    double delta;
                ^
                 = 0.0
2 warnings generated.
  CC       kkutils.lo
  CC       matrix_ops.lo
  CC       embed_graph.lo
  CC       dijkstra.lo
  CC       conjgrad.lo
  CC       pca.lo
  CC       closest.lo
  CC       bfs.lo
  CC       constraint.lo
  CC       quad_prog_solve.lo
  CC       smart_ini_x.lo
  CC       constrained_majorization.lo
  CC       opt_arrangement.lo
  CC       overlap.lo
  CC       call_tri.lo
  CC       compute_hierarchy.lo
  CC       delaunay.lo
  CC       multispline.lo
  CCLD     libneatogen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in twopigen
  CC       twopiinit.lo
  CC       circle.lo
  CCLD     libtwopigen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in sfdpgen
  CC       sfdpinit.lo
  CC       spring_electrical.lo
spring_electrical.c:287:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
    step = step;
    ~~~~ ^ ~~~~
spring_electrical.c:1308:16: warning: use of unary operator that may be intended as compound assignment (-=)
    nsuper_avg =- 0;
               ^~
spring_electrical.c:1548:16: warning: use of unary operator that may be intended as compound assignment (-=)
    nsuper_avg =- 0;
               ^~
3 warnings generated.
  CC       LinkedList.lo
  CC       sparse_solve.lo
  CC       post_process.lo
  CC       stress_model.lo
  CC       uniform_stress.lo
  CC       QuadTree.lo
  CC       Multilevel.lo
  CC       PriorityQueue.lo
  CCLD     libsfdpgen_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in osage
  CC       osageinit.lo
  CCLD     libosage_C.la
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
Making install in plugin
Making install in core
  CC       gvplugin_core.lo
  CC       gvrender_core_dot.lo
  CC       gvrender_core_fig.lo
  CC       gvrender_core_map.lo
  CC       gvrender_core_ps.lo
  CC       gvrender_core_svg.lo
  CC       gvrender_core_tk.lo
  CC       gvrender_core_vml.lo
  CC       gvloadimage_core.lo
  CCLD     libgvplugin_core_C.la
  CCLD     libgvplugin_core.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_core.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in dot_layout
  CC       gvplugin_dot_layout.lo
  CC       gvlayout_dot_layout.lo
gvlayout_dot_layout.c:45:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma comment( lib, "graph.lib" )
            ^
gvlayout_dot_layout.c:46:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma comment( lib, "dotgen.lib" )
            ^
2 warnings generated.
  CCLD     libgvplugin_dot_layout_C.la
  CCLD     libgvplugin_dot_layout.la
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in neato_layout
  CC       gvplugin_neato_layout.lo
  CC       gvlayout_neato_layout.lo
  CCLD     libgvplugin_neato_layout_C.la
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
  CCLD     libgvplugin_neato_layout.la
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a(dbg.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
   /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[3]: Nothing to be done for `install-exec-am'.
 config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
 /usr/bin/install -c -m 644 graphviz.7 '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
 config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 /usr/bin/install -c -m 644 graphviz_version.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
 config/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
 /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
cp: /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/graphviz is a directory (not copied).
cp: /Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig is a directory (not copied).
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for deflateBound in -lz... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CFLAGS= -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c LL_funcs.c -o LL_funcs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c Rgraphviz.c -o Rgraphviz.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c RgraphvizInit.c -o RgraphvizInit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c agopen.c -o agopen.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c agread.c -o agread.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c agwrite.c -o agwrite.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c bezier.c -o bezier.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c buildEdgeList.c -o buildEdgeList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c buildNodeList.c -o buildNodeList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c doLayout.c -o doLayout.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c graphvizVersion.c -o graphvizVersion.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I/Users/biocbuild/bbs-3.13-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

Rgraphviz.Rcheck/tests/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.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 -- Sun Aug  1 22:44:10 2021 
*********************************************** 
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 
  2.236   0.167   2.387 

Example timings

Rgraphviz.Rcheck/Rgraphviz-Ex.timings

nameusersystemelapsed
AgEdge-class0.0630.0060.070
AgNode-class0.0070.0010.009
AgTextLabel-class0.0140.0020.016
BezierCurve-class0.0100.0020.012
GraphvizLayouts0.0050.0010.006
Ragraph-class0.0360.0120.048
agopen0.0140.0010.014
agopenSimple0.0880.0020.090
agwrite0.0100.0010.011
boundingBox-class0.0090.0000.009
buildNodeList0.0030.0000.004
clusterData-methods0.3020.0080.313
getDefaultAttrs0.0020.0010.003
graphLayout0.0100.0000.011
graphvizCapabilities0.0020.0010.003
graphvizVersion0.0010.0010.001
layoutGraph0.2700.0040.309
makeNodeAttrs0.0030.0010.004
pEdge-class0.0040.0010.005
pNode-class0.0030.0010.004
pieGlyph0.0090.0010.009
plot-methods0.0000.0000.001
removedEdges0.0040.0000.003
renderGraph0.0800.0020.082
toDot-methods0.0090.0000.010
toFile0.0330.0020.035
xyPoint-class0.0010.0010.001