[BioC] GGtools and GGBase installation problems

Neel Aluru naluru at whoi.edu
Thu Mar 3 15:11:11 CET 2011 

Thank you, Vincent. It installed Ruuid from the command line. Earlier, I was trying to install Ruuid using R Gui and it doesn't work. 

Thanks a lot.

Neel

On Mar 3, 2011, at 6:40 AM, Vincent Carey wrote:

> 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
>> 
>> 
> 

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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