[BioC] installation of affycoretools

James W. MacDonald jmacdon at med.umich.edu
Thu Dec 20 16:51:47 CET 2007 

Hi Sean and James,

I just wanted to note that biocLite() _will_ install dependencies of 
dependencies (and on down the dependency tree), otherwise it would be a 
pretty worthless install script for the BioC packages.

To ensure that what I state above is true, I downloaded and built a 
brand new R-devel, and the first and only thing I did upon starting it 
was to run biocLite("affycoretools").

OK. I lied -- I ran install.packages("rcompgen") first, because my 
Rprofile file loads that package and doesn't like it if it is missing, 
but that is peripheral to this discussion.

The result:

 > library(affycoretools)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

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: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: xtable
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: biomaRt
Loading required package: RCurl

Attaching package: 'biomaRt'


	The following object(s) are masked from package:annotate :

	 getGO

Loading required package: gcrma
Loading required package: matchprobes
Loading required package: annaffy
Loading required package: GO

Attaching package: 'GO'


	The following object(s) are masked from package:GO.db :

	 GOBPANCESTOR,
	 GOBPCHILDREN,
	 GOBPOFFSPRING,
	 GOBPPARENTS,
	 GOCCANCESTOR,
	 GOCCCHILDREN,
	 GOCCOFFSPRING,
	 GOCCPARENTS,
	 GOMAPCOUNTS,
	 GOMFANCESTOR,
	 GOMFCHILDREN,
	 GOMFOFFSPRING,
	 GOMFPARENTS,
	 GOOBSOLETE,
	 GOSYNONYM,
	 GOTERM

Loading required package: KEGG

Attaching package: 'annaffy'


	The following object(s) are masked from package:RCurl :

	 getURL

 > sessionInfo()
R version 2.7.0 Under development (unstable) (2007-12-20 r43739)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices datasets  utils
[8] methods   base

other attached packages:
  [1] affycoretools_1.11.2 annaffy_1.11.1       KEGG_2.0.1
  [4] GO_2.0.1             gcrma_2.11.1         matchprobes_1.11.0
  [7] biomaRt_1.13.6       RCurl_0.8-1          GOstats_2.5.0
[10] Category_2.5.0       genefilter_1.17.7    survival_2.34
[13] RBGL_1.15.6          annotate_1.17.3      xtable_1.5-2
[16] GO.db_2.0.2          AnnotationDbi_1.1.6  RSQLite_0.6-4
[19] DBI_0.2-4            graph_1.17.14        limma_2.13.1
[22] affy_1.17.3          preprocessCore_1.1.5 affyio_1.7.6
[25] Biobase_1.17.7       rcompgen_0.1-17

loaded via a namespace (and not attached):
[1] cluster_1.11.9 XML_1.9-0

So all you should ever have to do is run biocLite() to install things. 
However, it may come to pass that certain packages for whatever reason 
don't get installed correctly (or at all, although barring the 
occasional missing package on BioC, I have never personally seen such a 
thing), in which case you may need an additional 
biocLite("TheMissingPackage").

Best,

Jim



Sean Davis wrote:
> On Dec 19, 2007 5:06 PM, James Anderson <janderson_net at yahoo.com> wrote:
> 
>> Sean,
>>
>> Thanks for your advice. I followed your suggestion and typed
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
>> biocLite("affycoretools")
>>
>> and there is nothing abnormal. However, when I type
>> library(affycoretools), it pops up the following lines:
>>
>> Loading required package: affy
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> 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: affyio
>> Loading required package: preprocessCore
>> Loading required package: limma
>> Loading required package: GOstats
>> Loading required package: graph
>> Loading required package: GO.db
>> Loading required package: AnnotationDbi
>> Loading required package: DBI
>> Loading required package: RSQLite
>> Loading required package: annotate
>> Loading required package: xtable
>> Loading required package: RBGL
>> Loading required package: Category
>> Loading required package: genefilter
>> Loading required package: survival
>> Loading required package: splines
>> Loading required package: biomaRt
>> Loading required package: RCurl
>> Error: package 'RCurl' could not be loaded
>> In addition: Warning message:
>> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
>> lib.loc) :
>>   there is no package called 'RCurl'
>>
>> Below is what I got from using sessionInfo() for diagnose
>>
>> R version 2.6.1 (2007-11-26)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] GOstats_2.4.0        Category_2.4.0       genefilter_1.16.0
>>  [4] survival_2.34        RBGL_1.14.0          annotate_1.16.1
>>  [7] xtable_1.5-2         GO.db_2.0.2          AnnotationDbi_1.0.6
>> [10] RSQLite_0.6-4        DBI_0.2-4            graph_1.16.1
>> [13] limma_2.12.0         affy_1.16.0          preprocessCore_1.0.0
>> [16] affyio_1.6.1         Biobase_1.16.2
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.9
>>
>> Seems that it still can not find the package Rcurl.
>>
> 
> Unfortunately, biocLite() does not find dependencies of dependencies (and I
> believe RCurl is a dependency of biomaRt).  My guess is that you have
> installed other packages without using biocLite() in the past and have
> missed installing the RCurl dependency for one of them.  Therefore, I would
> suggest using biocLite() to install ALL PACKAGES ALL THE TIME so that this
> doesn't occur in the future.  However, in the short term, you might try:
> 
> biocLite('RCurl')
> library(affycoretools)
> 
> Hope that helps.
> 
> Sean
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

More information about the Bioconductor mailing list