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Question: Rgraphviz installation fails
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gravatar for Giovanni Calice
3 months ago by
Italy
Giovanni Calice150 wrote:

Hi all,

 

I'm trying to install Rgraphviz package but I get the following error message:

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

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 (QtCore not available)

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

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

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

  tcldot:        No (tcl not available)
  tclpathplan:   No (tcl not available)
  gdtclft:       No (tcl not available)
  tkspline:      No (tk not available)
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make  install-recursive
make[1]: Entering directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz/libltdl'
make  install-am
make[3]: Entering directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz/libltdl'
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl   -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile:  gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c  -fPIC -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/bash ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -module -avoid-version -L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl -o dlopen.la  dlopen.lo -ldl -ldl
./libtool: line 4984: cd: -/: invalid option
cd: usage: cd [-L|[-P [-e]] [-@]] [dir]
libtool: link: cannot determine absolute directory name of `-L/usr/lib/'
make[3]: *** [dlopen.la] Error 1
make[3]: Leaving directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz/libltdl'
make[2]: *** [install] Error 2
make[2]: Leaving directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz/libltdl'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz'
make: *** [install] Error 2
cp: cannot stat '/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/libunix/lib/*': No such file or directory
cp: cannot stat '/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/libunix/lib/graphviz/*': No such file or directory
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for deflateBound in -lz... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CFLAGS= -I/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2  -c LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:0:
common.h:16:17: fatal error: gvc.h: File o directory non esistente
 #include <gvc.h>
                 ^
compilation terminated.
make: *** [LL_funcs.o] Errore 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/usr/local/lib64/R/library_Bioc_3_3/Rgraphviz’

I cut off the beginning of the output; I also installed the graphviz specific version 2.28.0 before to run Rgraphviz installation and check the include header and the compiler

/usr/local/graphviz-2.28.0/lib/gvc/gvc.h
/usr/local/include/graphviz/gvc.h

R CMD config CC
gcc -std=gnu99

 `R CMD config CC` --version
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

but I get the same error.

What's wrong?

Thanks in advance, Regards

 

Giovanni

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=it_IT.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1
 
 
ADD COMMENTlink written 3 months ago by Giovanni Calice150

Hi all,

 

does anyone find the same error?

I do not know if it might be useful to add the other lines of the installation output.

Thank you in advance for possible suggestions, Best Regards

 

Giovanni

 

 

ADD REPLYlink written 3 months ago by Giovanni Calice150

You don't need to install Graphviz yourself, it is bundled with Rgraphviz. What is the beginning of the Rgraphviz installation output and what command (exactly) do you use to install it?

ADD REPLYlink written 3 months ago by Kasper Daniel Hansen6.3k

Hi Kasper,

It was a subsequent test to install the exact graphviz version (2.28.0) before.

This is the command and the output (I cut off the final part I attached in the previous message):

biocLite("Rgraphviz")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘Rgraphviz’
provo con l'URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Rgraphviz_2.16.0.tar.gz'
Content type 'unknown' length 7453514 bytes (7.1 MB)
==================================================
downloaded 7.1 MB

* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu99... gcc3
checking for library containing strerror... none required
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for sed... /bin/sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/bin/tclsh8.6
checking whether gcc -std=gnu99 and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... 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... gcc -std=gnu99 -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
ADD REPLYlink written 3 months ago by Giovanni Calice150
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/inotify.h usability... yes
checking sys/inotify.h presence... yes
checking for sys/inotify.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for socklen_t... yes
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... yes
checking for fesetenv... yes
checking libgen.h usability... yes
checking libgen.h presence... yes
checking for libgen.h... yes
checking for basename in -lgen... no
checking for working alloca.h... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... no
checking for setenv... yes
checking for getenv... yes
checking for __freadable... yes
ADD REPLYlink written 3 months ago by Giovanni Calice150
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... yes
checking for memset... yes
checking for nl_langinfo... yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for _NSGetEnviron... no
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
ADD REPLYlink written 3 months ago by Giovanni Calice150
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /lib/i386-linux-gnu /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/nvidia-375 /usr/lib32/nvidia-375 /usr/lib/nvidia-375 /usr/lib32/nvidia-375 /lib64 /usr/lib64 /lib32 /usr/lib32 /libx32 /usr/libx32
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for ltdl.h... yes
checking whether lt_dlinterface_register is declared... yes
checking for lt_dladvise_preload in -lltdl... yes
checking where to find libltdl headers...
checking where to find libltdl library... -lltdl
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/usr/include/tcl8.6 -I/usr/include/tcl8.6/generic
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
configure: WARNING: Unable to find tclConfig.sh. The Tcl packages will not be built
configure: WARNING: No Tcl. The Tk packages will not be built either
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for X11/Xaw/Text.h... no
configure: WARNING: Optional Xaw library not available - missing headers
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... no
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... qmake
checking for QTCORE... no
checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... yes
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
ADD REPLYlink written 3 months ago by Giovanni Calice150
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 (/tmp/RtmpAkiXyI/R.INSTALL232b743b6fa8/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/tmp/RtmpAkiXyI/R.INSTALL232b743b6fa8/Rgraphviz/src/libunix'  'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'LDFLAGS=-L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl' '--libdir=/tmp/RtmpAkiXyI/R.INSTALL232b743b6fa8/Rgraphviz/src/libunix/lib' '--includedir=/tmp/RtmpAkiXyI/R.INSTALL232b743b6fa8/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'R_LIBS=/usr/local/lib64/R/library_Bioc_3_3:/usr/local/lib64/R/library_Bioc_3_3' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu99... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
ADD REPLYlink written 3 months ago by Giovanni Calice150
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /lib/i386-linux-gnu /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/nvidia-375 /usr/lib32/nvidia-375 /usr/lib/nvidia-375 /usr/lib32/nvidia-375 /lib64 /usr/lib64 /lib32 /usr/lib32 /libx32 /usr/libx32
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

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

graphviz-2.28.0 will be compiled with the following:
...
...

 

Thank you, Best

Giovanni

ADD REPLYlink written 3 months ago by Giovanni Calice150

You're using the bundled Graphviz, so the fact you have it installed in your system shouldn't matter.

This looks weird:

/bin/bash ./libtool --tag=CC   --mode=link gcc -std=gnu99  -g -O2 -module -avoid-version -L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl -o dlopen.la  dlopen.lo -ldl -ldl
./libtool: line 4984: cd: -/: invalid option
cd: usage: cd [-L|[-P [-e]] [-@]] [dir]
libtool: link: cannot determine absolute directory name of `-L/usr/lib/'
make[3]: *** [dlopen.la] Error 1
make[3]: Leaving directory `/tmp/RtmpgGl9fq/R.INSTALL169842734085/Rgraphviz/src/graphviz/libltdl'

Note the 

-L-L/usr/lib/

which is weird, also the trailing / on the /usr/lib.  Does this come from something like .R/Makevars or from environment variables? You can check the later by using "env" in bash.

ADD REPLYlink written 3 months ago by Kasper Daniel Hansen6.3k

Yes, I disinstalled the graphviz version 2.28.0; this was just another test to verify if the Rgraphviz installation was successful.

Anyway there isn't any configuration file (like .R/Makevars) and the only env var set, which concerns R, is

R_LIBS_USER=/usr/local/lib64/R/library_Bioc

that I set for Bioc release packages and has always worked great.

Thank you, Best

Giovanni

ADD REPLYlink written 3 months ago by Giovanni Calice150

Sorry,

How can I fix/force the lib path before run Rgraphviz installation?

ADD REPLYlink written 3 months ago by Giovanni Calice150
You should do # env | grep usr/lib to see what is being set. You could also try to have a look at # R CMD config CFLAGS # R CMD config LDFLAGS Comparing to the build report, which has the following invocation: /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo -ldl -ldl You are linking to tcltk and other stuff. /bin/bash ./libtool --tag=CC --mode=link gcc -std=gnu99 -g -O2 -module -avoid-version -L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl -o dlopen.la dlopen.lo -ldl -ldl Why? That is probably the answer How did you install R? On Wed, Aug 23, 2017 at 10:55 AM, Giovanni Calice [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Giovanni Calice <https: support.bioconductor.org="" u="" 6415=""/> wrote Comment: > Rgraphviz installation fails > <https: support.bioconductor.org="" p="" 99060="" #99618="">: > > Yes, I disinstalled the graphviz version 2.28.0; this was just another > test to verify if the Rgraphviz installation was successful. > > Anyway there isn't any configuration file (like .R/Makevars) and the only > env var set, which concerns R, is > > R_LIBS_USER=/usr/local/lib64/R/library_Bioc > > that I set for Bioc release packages and has always worked great. > > Thank you, Best > > Giovanni > > ------------------------------ > > Post tags: rgraphviz > > You may reply via email or visit https://support.bioconductor. > org/p/99060/#99618 >
ADD REPLYlink written 3 months ago by Kasper Daniel Hansen6.3k

Hi Kasper,

Ok I've already checked my env and mentioned the only env var that refers to R.

There's something to reset in configure command when I installed R; what I was wondering is why the compilation is successfull for all other packages .

Anyway I'll reset/reinstall R (also because I want to update it to the latest version released) ASAP and update the tag soon too.

Thanks a lot for all suggestions, Best

Giovanni

ADD REPLYlink written 3 months ago by Giovanni Calice150
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