Question: Problem installing Rgraphviz in R
0
gravatar for cristian
15 months ago by
cristian180
cristian180 wrote:

Hi,

I am having trouble installing Rgraphviz in R. Any kind soul to help me?

biocLite('Rgraphviz')

...

Libraries have been installed in:
   /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz

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

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in dot_layout
  CC       gvplugin_dot_layout.lo
  CC       gvlayout_dot_layout.lo
gvlayout_dot_layout.c:45:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma comment( lib, "graph.lib" )
            ^
gvlayout_dot_layout.c:46:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma comment( lib, "dotgen.lib" )
            ^
2 warnings generated.
  CCLD     libgvplugin_dot_layout_C.la
  CCLD     libgvplugin_dot_layout.la
 ../../config/install-sh -c -d '/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_dot_layout.la '/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
----------------------------------------------------------------------
Libraries have been installed in:
   /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz

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

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
Making install in neato_layout
  CC       gvplugin_neato_layout.lo
  CC       gvlayout_neato_layout.lo
  CCLD     libgvplugin_neato_layout_C.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout_C.a(dbg.o) has no symbols
  CCLD     libgvplugin_neato_layout.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libgvplugin_neato_layout.a(dbg.o) has no symbols
 ../../config/install-sh -c -d '/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz'
 /bin/sh ../../libtool   --mode=install /usr/bin/install -c   libgvplugin_neato_layout.la '/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a(dbg.o) has no symbols
----------------------------------------------------------------------
Libraries have been installed in:
   /private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpXu5l21/R.INSTALL1127235532a82/Rgraphviz/src/libunix/lib/graphviz

If you ever happen to want to link against installed libraries

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rgraphviz)

The downloaded source packages are in
    '/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpxvhXU2/downloaded_packages'
> library(Rgraphviz)
Error: package or namespace load failed for 'Rgraphviz':
 .onLoad failed in loadNamespace() for 'Rgraphviz', details:
  call: value[[3L]](cond)
  error: unable to load shared object '/usr/local/lib/R/3.4/site-library/Rgraphviz/libs/Rgraphviz.so':
  `maximal number of DLLs reached...

  Rgraphviz is unable to be loaded.  This typically is a symptom of an
  installation problem.  From 2.x.x onwards, Graphviz ought to come bundled with
  Rgraphviz.

  If you are trying to use an external Graphviz, see additional instructions in
  the 'README' file of the Rgraphviz 'source' distribution, available at

  http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html

  Ask further questions on the Bioconductor mailing list

  http://bioconductor.org/docs/mailList.html


  Rgraphviz is unable to be loaded.  This typically is a symptom of an
  installation problem.  From 2.x.x onwards, Graphviz ought to come bundled with
  Rgraphviz.

  If you are trying to use an external Graphviz, see a

Thanks. Best, C.

ADD COMMENTlink modified 15 months ago by h.mon21k • written 15 months ago by cristian180
1

Could you post the output of sessionInfo()?

ADD REPLYlink written 15 months ago by h.mon21k
sessionInfo()
Error in La_library() : LAPACK routines cannot be loaded
In addition: Warning message:
In La_library() :
  unable to load shared object '/usr/local/Cellar/r/3.4.0_1/R.framework/Resources/modules//lapack.so':
  `maximal number of DLLs reached...

Interesting...

usually gives a list of installed packages. I wonder what these DLLs are...? dynamic-linked library?

C.

ADD REPLYlink modified 15 months ago • written 15 months ago by cristian180
4
gravatar for h.mon
15 months ago by
h.mon21k
Brazil
h.mon21k wrote:

The key here is maximal number of DLLs reached, which you got both when trying library(Rgraphviz) and sessionInfo(). R has a hard limit on the number of shared libraries which can be loaded (apparently 100, see here and here). Close your session and try again. Are you loading a lot of packages at start-up?

ADD COMMENTlink written 15 months ago by h.mon21k
3

Not a hard limit. Number of max number of DLLs can be increased by tweaking .Renviron. Default seems to be 100 as you mentioned.

ADD REPLYlink modified 15 months ago • written 15 months ago by cpad011210k

Hi,

Thanks, I have increased the maximum number of DLLs in .Renviron and it works now. Do you know what these DLLs are?

C.

ADD REPLYlink written 15 months ago by cristian180

Hi,

I am using loads of packages even though I am not 'loading' them with the 'library()' function. I use the functions inside the packages with the syntax packageName::functionName.

ADD REPLYlink written 15 months ago by cristian180

What is a 'library'? and what is a 'shared library'?

C.

ADD REPLYlink written 15 months ago by cristian180
1

library() is a R command to load packages.

A shared library (or dynamic-link library in windows) are, well, libraries of functions that can be used (shared) by many executables.

ADD REPLYlink written 15 months ago by h.mon21k
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