[BioC] installation of affycoretools
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Thu Dec 20 18:08:36 CET 2007
I think what is more correct to say has to do with dependency
checking. Say we have a dependency tree like
A requires B requires C
and that someone install B without install C. When you then do
biocLite("A") it checks whether B is installed and if that is the
case, I believe it stops. It does not check whether C exists.
Kasper
On Dec 20, 2007, at 7:51 AM, James W. MacDonald wrote:
> 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]]
>>
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>
> --
> 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
>
> _______________________________________________
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> gmane.science.biology.informatics.conductor
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