Question: Rgraphviz installation problem
0
gravatar for Janet Young
4.6 years ago by
Janet Young730
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young730 wrote:

Hi there,

I'm having a little trouble installing the devel version of Rgraphviz (release version installs fine for me).  I've seen posts from this spring reporting a similar error (common.h:16:17: fatal error: gvc.h: No such file or directory), but it looked like that issue had been solved.  

It's possible there's something unusual about my R installation that's causing problems (I installed b it myself in my user directory, not system-wide, and I confess I'm an ignorant sysadmin.  I've also got parallel R installations to let me use the release or devel packages, but this hasn't caused me any trouble in the past). 

I've tried biocLite, as well as trying to install from command line via R CMD INSTALL, using a tar.gz of Rgraphviz I downloaded from github - same issue with that.

I did this:

source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")

Here's the end of the output (session info and uname output are also below):

configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CFLAGS= -I/tmp/Rtmp0neKAH/R.INSTALL3b204df0edc8/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/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/Rtmp0neKAH/R.INSTALL3b204df0edc8/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: No such file or directory
compilation terminated.
make: *** [LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’

sessionInfo()
R version 3.1.1 Patched (2014-08-07 r66321)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.15.5

loaded via a namespace (and not attached):
[1] tools_3.1.1

system("uname -a")
Linux gizmod17 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

Hmm - any clues?  Not sure if this is a bug, or something wrong with my R installation, or maybe LIBRARY or INCLUDE settings.  But I thought Rgraphviz was a bundled graphviz library files, so hopefully whatever other libraries I do or don't have installed won't interfere with this installation.

thanks in advance for any help,

Janet Young

 

rgraphviz • 1.6k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Janet Young730

Hi there,

Thanks, Kasper - the full output is below.

thanks,

Janet

> biocLite('Rgraphviz')

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'Rgraphviz'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/Rgraphviz_2.9.1.tar.gz'
Content type 'application/x-gzip' length 7452931 bytes (7.1 Mb)
opened URL
==================================================
downloaded 7.1 Mb

* installing *source* package ‘Rgraphviz’ ...
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/Rcmd: 62: exec: config: not found
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for g++... g++
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.
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checking whether the shell understands some XSI constructs... yes
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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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 /opt/fhgfs/lib /usr/lib/i386-linux-gnu/mesa /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/x86_64-linux-gnu/mesa /lib32 /usr/lib32 
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configure: WARNING: X11 not available.
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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
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configure: WARNING: Optional Xpm library not available
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configure: WARNING: Optional Xaw library not available - missing headers
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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
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config.status: creating lib/xdot/Makefile
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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/RtmpN4TgGl/R.INSTALL763070d44722/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/tmp/RtmpN4TgGl/R.INSTALL763070d44722/Rgraphviz/src/libunix'  'CC=gcc' 'CXX=g++' 'CFLAGS=' 'CXXFLAGS=' 'LDFLAGS=' '--libdir=/tmp/RtmpN4TgGl/R.INSTALL763070d44722/Rgraphviz/src/libunix/lib' '--includedir=/tmp/RtmpN4TgGl/R.INSTALL763070d44722/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=/home/jayoung/malik_lab_shared/linux_gizmo/lib/pkgconfig' 'R_LIBS=/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/library' --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  sets $(MAKE)... no
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 ... none
checking for gcc... gcc
checking whether the C compiler works... yes
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checking for suffix of object files... o
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checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
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checking if the linker (/usr/bin/ld) is GNU ld... yes
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checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
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checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc 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
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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 /opt/fhgfs/lib /usr/lib/i386-linux-gnu/mesa /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/x86_64-linux-gnu/mesa /lib32 /usr/lib32 
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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:

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:            Yes

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:        Yes

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)
install: missing file operand
Try `install --help' for more information.
cp: cannot stat `/tmp/RtmpN4TgGl/R.INSTALL763070d44722/Rgraphviz/src/libunix/lib/*': No such file or directory
cp: cannot stat `/tmp/RtmpN4TgGl/R.INSTALL763070d44722/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/RtmpN4TgGl/R.INSTALL763070d44722/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/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/include -DNDEBUG  -I/usr/local/include   -I/tmp/RtmpN4TgGl/R.INSTALL763070d44722/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: No such file or directory
compilation terminated.
make: *** [LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/library/Rgraphviz’

The downloaded source packages are in
    ‘/tmp/RtmpWdSLYY/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘Rgraphviz’ had non-zero exit status

 

ADD REPLYlink modified 4.6 years ago by Martin Morgan ♦♦ 23k • written 4.6 years ago by Janet Young730
Answer: Rgraphviz installation problem
2
gravatar for Laurent Gatto
4.6 years ago by
Laurent Gatto1.1k
United Kingdom
Laurent Gatto1.1k wrote:

Dear Janet,

The message common.h:16:17: fatal error: gvc.h: No such file or directory suggest that you are missing libgvc6. On your ubuntu box, the following should sort your error out

sudo apt-get install libgvc6

Hope this helps.

Laurent

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Laurent Gatto1.1k

Thanks, Laurent -  I hadn't tried your suggestion, as I don't have root access on the machine I'm using, and hadn't got around to asking my sysadmins about it yet. That was partly as I was also a bit confused about your suggestion, as I'd read somewhere that Rgraphviz is packaged along with the libraries it needs (I think - not sure).  Hopefully Kasper will be able to help me out.

ADD REPLYlink written 4.6 years ago by Janet Young730
Answer: Rgraphviz installation problem
1
gravatar for Kasper Daniel Hansen
4.6 years ago by
United States
Kasper Daniel Hansen6.4k wrote:

Thanks Janet, this is very informative.  But we are not done yet.  Basically, as part of the configure script I execute

CC=`"${R_HOME}/bin/R" CMD config CC`

which basically should run "R CMD config CC".  The error message you get is the same I get if I run "/usr/local/R/R-3.1.x/lib/R/bin/Rcmd config" (this is with RHOME set to "/usr/local/R/R-3.1.x/lib/R") - note the subtle different between "R CMD config" and "Rcmd config".  It is a bit worrisome that this fails, but we should be able to track it down.

Could you first try to find out the following: how was R actually installed, was it from an RPM, or did someone compile it.  If someone compiled it themselves, did they also run "make install" or do you just run it from the compilation directory?  If you cannot figure it out, just answer the questions below.

Try the following and report the full output

R RHOME
R CMD config CC
ls `R RHOME`
ls `R RHOME`/bin

These commands are assuming that "R" is the command you write at the terminal to start R.  If you have something else (for example "R-3.0") substitute that for R above.  As a comparison, this is what I get when I execute these commands

$ R RHOME
/usr/local/R/R-3.1.x/lib/R
$ R CMD config CC
/usr/bin/clang -mtune=native
$ ls `R RHOME`
COPYING      SVN-REVISION bin          doc          etc          include      library      modules      share        site-library
$ ls `R RHOME`/bin
BATCH         LINK          Rcmd          Rdiff         SHLIB         build         exec          libtool       rtags
COMPILE       R             Rd2pdf        Rprof         Stangle       check         f77_f2c       mkinstalldirs
INSTALL       REMOVE        Rdconv        Rscript       Sweave        config        javareconf    pager

 

ADD COMMENTlink written 4.6 years ago by Kasper Daniel Hansen6.4k
Answer: Rgraphviz installation problem
0
gravatar for Kasper Daniel Hansen
4.6 years ago by
United States
Kasper Daniel Hansen6.4k wrote:

Actually, you should not have to install libgvc.

But you need to provide the full output of the installation, not just the small snippet you have provided.

Best,
Kasper

ADD COMMENTlink written 4.6 years ago by Kasper Daniel Hansen6.4k
Answer: Rgraphviz installation problem
0
gravatar for Janet Young
4.6 years ago by
Janet Young730
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young730 wrote:

Thanks, Kasper - those were very helpful questions to ask.  I must have messed up my R installation, and re-installing R a different way now allows me to install Rgraphviz with no problems. Sorry to bother you about something that's not your problem!

I had compiled and installed R myself, and I have two parallel installations going, as suggested here (I've called them Rdevel and R - one so I can use bioc dev versions, and one for release versions). Somehow although config was present in my RHOME/bin dir, the permissions were not set right on config (and various other things) for my Rdevel installation so that I did not have execute permission on config and some but not all of the other executables.  Strangely, execute permissions on config were fine for my regular R installation (but not my Rdevel installation).

jayoung@gizmod33:~$ Rdevel RHOME

WARNING: ignoring environment value of R_HOME

/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R

 

jayoung@gizmod33:~$ ls -l /home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/config

-rw-r-x---+ 1 jayoung g_jayoung 9459 May 28 12:39 /home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/bin/config

 

Turns out I was installing R in a slightly screwy way - I did use "make install", but when I did configure, instead of setting prefix, I set various things individually (bindir, mandir, libdir), dispersing various useful R things over various disconnected dirs, which doesn't make a lot of sense. Not sure where the permissions issue came from (perhaps inherited from parent directories?), but when I reinstall in a more rational way, config now has execute permissions for me, and Rgraphviz installs fine. Argh.

thanks again - that was very helpful,

Janet

 

 

ADD COMMENTlink written 4.6 years ago by Janet Young730
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