[R-SIG-Mac] Missing pkg-config and glib
dwinsemius at comcast.net
Sat Sep 19 00:28:41 CEST 2009
On Sep 18, 2009, at 5:46 PM, Simon Urbanek wrote:
> On Sep 18, 2009, at 17:40 , David Winsemius wrote:
>> I seem to have some missing or broken parts to my Leopard
>> installation. After again attempting to install the Gtk+ dmg inked
>> from the http://r.research.att.com/#other page I get no error. But
>> attempting to build from source a bioconductor package, Ruuid, I am
>> again seeing an error
>> checking for pkg-config... no
> You have to set
> if you want to compile GTK+ packages from sources (although that
> should not be necessary because BioC provides binaries ...). Also
> the choice of compilers can be tricky with GTK+...
There is no binary Ruuid that shows up in the BioConductor repository
with the 64bit GUI Package Installer, although there is a version that
is downloadable with the 32 bit version.
$ echo $PATH
(There is no /bin folder in the /Resources/ sub-directory when I look
with Finder.app. Should it have been /Library/Frameworks/GTK
+.framework/Resources/dev/bin ? Nope. Tried changing first entry in
PATH to that and no joy.)
So am still getting same error:
(I am wondering if there is a better way to test the Gtk+ installation
that compiling a bioc pkg?)
> biocLite("Ruuid", type="source", dependencies=TRUE)
Using R version 2.9.2, biocinstall version 2.4.12.
Installing Bioconductor version 2.4 packages:
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
argument 'lib' is missing: using '/Users/davidwinsemius/Library/R/
trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Ruuid_1.22.0.tar.gz'
Content type 'application/x-gzip' length 71857 bytes (70 Kb)
downloaded 70 Kb
* Installing *source* package ‘Ruuid’ ...
checking for pkg-config... no
checking for glib-config... no
configure: error: No glib package information found
ERROR: configuration failed for package ‘Ruuid’
* Removing ‘/Users/davidwinsemius/Library/R/2.9/library/Ruuid’
* Restoring previous ‘/Users/davidwinsemius/Library/R/2.9/library/Ruuid’
The downloaded packages are in
In install.packages(pkgs = pkgs, repos = repos, dependencies =
installation of package 'Ruuid' had non-zero exit status
>> ... that I have seen several times before, as well as one which
>> Mark Morgan on r-help says is due to a missing Gtk+ library.
>> > source("http://bioconductor.org/biocLite.R")
>> > biocLite("Ruuid", type="source")
>> Using R version 2.9.2, biocinstall version 2.4.12.
>> Installing Bioconductor version 2.4 packages:
>>  "Ruuid"
>> Please wait...
>> Warning in install.packages(pkgs = pkgs, repos = repos,
>> dependencies = dependencies, :
>> argument 'lib' is missing: using '/Users/davidwinsemius/Library/R/
>> trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Ruuid_1.22.0.tar.gz'
>> Content type 'application/x-gzip' length 71857 bytes (70 Kb)
>> opened URL
>> downloaded 70 Kb
>> * Installing *source* package ‘Ruuid’ ...
>> checking for pkg-config... no
>> checking for glib-config... no
>> configure: error: No glib package information found
>> ERROR: configuration failed for package ‘Ruuid’
>> * Removing ‘/Users/davidwinsemius/Library/R/2.9/library/Ruuid’
>> * Restoring previous ‘/Users/davidwinsemius/Library/R/2.9/library/
>> (I had been able to install the Ruuid package within the 32 bit R
>> GUI. And I can also build biocLite from source from the 64 bit GUI
>> without any reported errors.)
>> What should I be looking for to understand and restore my defective
>> pkg-config capabilities?
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
David Winsemius, MD
West Hartford, CT
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