[BioC] GGtools and GGBase installation problems
Neel Aluru
naluru at whoi.edu
Thu Mar 3 06:45:53 CET 2011
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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