Rgraphviz installation fails
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Entering edit mode
@giovanni-calice-6415
Last seen 9 months ago
Italy

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
 
 
rgraphviz • 3.6k views
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Entering edit mode

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

 

 

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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 REPLY •
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Entering edit mode

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
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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
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checking for stddef.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for stdint.h... (cached) yes
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checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
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checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
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checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
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
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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
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checking for ld used by g++... /usr/bin/ld -m elf_x86_64
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checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/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
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checking tcl.h usability... yes
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Entering edit mode
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
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Entering edit mode
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

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Entering edit mode

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 REPLY •
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Entering edit mode

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

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Entering edit mode

Sorry,

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

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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 REPLY •
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Entering edit mode

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

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Entering edit mode

Hi Kasper,

as I announced I have updated R to the latest version and lightly readjusted

my configure command call removing very little for other stuff and anyway

linking the rest to have all in capabilities() TRUE/Ok.

So Rgraphviz is intalled correctly to the latest version 2.22.0 .

Best,

Giovanni

 

 

ADD REPLY •
0
Entering edit mode
I have a hard time fully understanding your message, but it seems to me that you're saying everything works now? Best, Kasper On Wed, Jan 10, 2018 at 7:05 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="" #104754="">: > > Hi Kasper, > > as I announced I have updated R to the latest version and lightly > readjusted > > my configure command call removing very little for other stuff and anyway > > linking the rest to have all in capabilities() TRUE/Ok. > > So Rgraphviz is intalled correctly to the latest version 2.22.0 . > > Best, > > Giovanni > > > > > > ------------------------------ > > Post tags: rgraphviz > > You may reply via email or visit https://support.bioconductor. > org/p/99060/#104754 >
ADD REPLY •
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Entering edit mode

I'm sorry if I did not describe better in the previous message.

Yes, everything works after updating and readjusting the configuration.

 

Best,

Giovanni

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