[BioC] GGtools and GGBase installation problems

Vincent Carey stvjc at channing.harvard.edu
Thu Mar 3 12:40:43 CET 2011 

if you used fink, glib-config should be in /sw/bin -- check.  then
make sure /sw/bin is in your PATH

in a terminal

echo $PATH

if you do not see :/sw/bin: somewhere in the result, you must do

export PATH=$PATH:/sw/bin

then

which glib-config

should have a response /sw/bin/glib-config

in the same session, attempt the Ruuid installation from source

you can change your shell initialization to include the export PATH
above, typically $HOME/.bashrc is where that will be stored

On Thu, Mar 3, 2011 at 12:45 AM, Neel Aluru <naluru at whoi.edu> wrote:
> Hi Vincent,
>
> Thanks for the following guidelines. I followed the instructions and I still have the problem. I restarted the computer after installing Fink.
>
> Any help is appreciated.
>
> Thank you,
>
> Neel
>
> Here is what I get:
>
>> source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>> biocLite("Ruuid", type="source")
> Using R version 2.12.1, biocinstall version 2.7.4.
> Installing Bioconductor version 2.7 packages:
> [1] "Ruuid"
> Please wait...
>
> Installing package(s) into ‘/Users/naluru/Library/R/2.12/library’
> (as ‘lib’ is unspecified)
> trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/Ruuid_1.28.0.tar.gz'
> Content type 'application/x-gzip' length 71906 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/naluru/Library/R/2.12/library/Ruuid’
>
> The downloaded packages are in
>        ‘/private/var/folders/DF/DFRfPr1YEfih-Ckx-GdJAk+++TI/-Tmp-/Rtmp7PzZPu/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'Ruuid' had non-zero exit status
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
> I checked if I have the glib package is installed in my computer and here are the different glib packages installed from Fink.
>
>
> naluru$ fink list
>
> i   glib             1.2.10-51    Common C routines used by Gtk+ and other ...
>     glib-pm5100      1.222-1      Glib:: perl module (bindings for glib2)
>     glib-pm588       1.222-1      Glib:: perl module (bindings for glib2)
>  i   glib-shlibs      1.2.10-51    Common C routines used by Gtk+ and other ...
>  i   glib2-dev        2.22.4-4     Handy library of utility functions
>  i   glib2-shlibs     2.22.4-4     Handy library of utility functions
>     glibmm2.4        2.22.2-1     C++ interface for the glib2 library
>     glibmm2.4-dev    2.22.2-1     C++ interface for the glib2 library
>     glibmm2.4-shlib  2.22.2-1     C++ interface for the glib2 library
>
> On Feb 26, 2011, at 7:10 AM, Vincent Carey wrote:
>
>> This problem was addressed on Feb 7.  Let us know if the solution does
>> not work for you.  The problem concerns a dependency of Ruuid
>> infrastructure on glib2, which is not uniformly available on MacOSX
>> machines.  Quoting below from the Feb 7 exchange
>>
>> Dear Vincent,
>>
>> Thanks a lot. I have got GGtools installed in my Mac book pro (with
>> updated Mac OS and Xcode).
>>
>> What I have done:
>> (1). install fink in order to let all unix program run in Mac,
>> following the manual in fink website (http://www.finkproject.org/).
>>
>> (2). then, run "sudo fink install glib glib2-dev".
>>
>> (3). next, log in R, and
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Ruuid", type="source") # you must install Ruuid from source.
>> biocLite("GGtools")
>>
>> (4). invoke GGtools
>> library(GGtools)
>>
>> I need to mention that all my progresses were got under helps of Mr.
>> Vincent and Martin, especially Vincent has given me much.
>>
>> Thanks a lot.
>>
>> Best,
>>
>> On Sat, Feb 26, 2011 at 6:42 AM, Neel Aluru <naluru at whoi.edu> wrote:
>>> Hello,
>>>
>>> I have installed GGtools and GGBase and when I try to load them, I keep getting the following error messages. I really appreciate if someone can help me in sorting this problem.
>>>
>>> Thank you,
>>> Neel
>>>
>>>
>>> [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0]
>>>
>>> [Workspace restored from /Users/naluru/.RData]
>>> [History restored from /Users/naluru/.Rapp.history]
>>>
>>> Loading required package: Biobase
>>>
>>> Welcome to Bioconductor
>>>
>>>  Vignettes contain introductory material. To view, type
>>>  'openVignette()'. To cite Bioconductor, see
>>>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>
>>> Loading required package: snpMatrix
>>> Loading required package: survival
>>> Loading required package: splines
>>> Loading required package: RSQLite
>>> Loading required package: DBI
>>> Error in as.environment(pos) :
>>>  no item called "newtable" on the search list
>>> In addition: Warning message:
>>> In objects(newtable, all.names = TRUE) :
>>>  ‘newtable’ converted to character string
>>> Error: package/namespace load failed for 'GGBase'
>>> Loading required package: GGBase
>>> Error in as.environment(pos) :
>>>  no item called "newtable" on the search list
>>> In addition: Warning message:
>>> In objects(newtable, all.names = TRUE) :
>>>  ‘newtable’ converted to character string
>>> Error: package 'GGBase' could not be loaded
>>>
>>>> sessionInfo()
>>> R version 2.12.1 (2010-12-16)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] RSQLite_0.9-4    DBI_0.2-5        snpMatrix_1.14.1 survival_2.36-2  Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] annotate_1.28.0      AnnotationDbi_1.12.0 graph_1.28.0         GSEABase_1.12.2      tools_2.12.1
>>> [6] XML_3.2-0            xtable_1.5-6
>>>>
>>>
>>>
>>> Neel Aluru
>>> Visiting Investigator
>>> Biology Department
>>> Redfield Building 3-04
>>> Woods Hole Oceanographic Institution
>>> 45, Water Street
>>> Woods Hole, MA
>>>
>>> naluru at whoi.edu
>>> 508-289-3607
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>
> Neel Aluru
> Visiting Investigator
> Biology Department
> Redfield Building 3-04
> Woods Hole Oceanographic Institution
> 45, Water Street
> Woods Hole, MA
>
> naluru at whoi.edu
> 508-289-3607
>
>

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