Entering edit mode
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
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
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?
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) yesThank you, Best
Giovanni
You're using the bundled Graphviz, so the fact you have it installed in your system shouldn't matter.
This looks weird:
Note the
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.
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
that I set for Bioc release packages and has always worked great.
Thank you, Best
Giovanni
Sorry,
How can I fix/force the lib path before run Rgraphviz installation?
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
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
I'm sorry if I did not describe better in the previous message.
Yes, everything works after updating and readjusting the configuration.
Best,
Giovanni