[R-SIG-Mac] Missing pkg-config and glib

[David Winsemius]

On Sep 18, 2009, at 5:46 PM, Simon Urbanek wrote:

> David,
>
> 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
> PATH=/Library/Frameworks/GTK+.framework/Resources/bin:$PATH
> 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.

$ PATH=/Library/Frameworks/GTK+.framework/Resources/bin:$PATH
$ echo $PATH

/Library/Frameworks/GTK+.framework/Resources/dev/bin:/sw/bin:/sw/sbin:/ 
usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/ 
usr/X11R6/bin

(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:
[1] "Ruuid"
Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =  
dependencies,  :
   argument 'lib' is missing: using '/Users/davidwinsemius/Library/R/ 
2.9/library'
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/Ruuid’

The downloaded packages are in
	‘/private/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-/RtmpzkRkjs/ 
downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =  
dependencies,  :
   installation of package 'Ruuid' had non-zero exit status


>
> Cheers,
> Simon
>
>
>> ... 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:
>> [1] "Ruuid"
>> Please wait...
>>
>> Warning in install.packages(pkgs = pkgs, repos = repos,  
>> dependencies = dependencies,  :
>> argument 'lib' is missing: using '/Users/davidwinsemius/Library/R/ 
>> 2.9/library'
>> 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/ 
>> Ruuid’
>>
>> (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
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT