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

[Simon Urbanek]

On Sep 18, 2009, at 6:28 PM, David Winsemius wrote:

>
> 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.
>

Well, yes, we don't provide 64-bit version of GTK+ (the build is for  
Tiger which doesn't have sufficient 64-bit libraries), so that's why  
there is no 64-bit version of packages that require GTK+.


> $ 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.

.. then you have some other GTK+ framework (maybe the old runtime?).  
The current one is at
http://r.research.att.com/gtk2-framework.dmg
but, again, that one is not 64-bit. If it is of interest I could look  
into updating it, but it's usually a quite demanding endeavor so  
probably not before next week.

Cheers,
Simon


> 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
>
>