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Question: Loading the necessary libraries in R
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gravatar for Angel
2.5 years ago by
Angel40
Berlin
Angel40 wrote:

 

Hello all,
after downloading my packages i went to load the libraries
> library(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

 

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

 

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Welcome to Bioconductor

 

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

 

Setting options('download.file.method.GEOquery'='auto')
Warning message:
package ‘BiocGenerics’ was built under R version 3.1.2 
> library(affy)
> library(gcrma)
> library(hugene10stv1cdf)

 

> library(hugene10stv1probe)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: IRanges

Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:GenomeInfoDb’:

    species

 

Warning messages:
1: package ‘AnnotationDbi’ was built under R version 3.1.3 
2: package ‘GenomeInfoDb’ was built under R version 3.1.3 
3: package ‘IRanges’ was built under R version 3.1.2 
> library(hugene10stprobeset.db)
Loading required package: org.Hs.eg.db
Loading required package: DBI

 

 
hugene10stprobeset.db is based on exon probesets. For a more
  gene-centric view, use the transcriptcluster version of this package.

 

Warning messages:
1: package ‘RSQLite’ was built under R version 3.1.3 
2: package ‘DBI’ was built under R version 3.1.3 
> library(hugene10sttranscriptcluster.db)
what does it mean? should i install  R version 3.1.3 ?? or libraries have been installed successfully?
ADD COMMENTlink written 2.5 years ago by Angel40
1

What version of R are you using, e.g., the output of

R.version.string

or 

sessionInfo()
ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 20k

 

hello
R version 3.1.1 (2014-07-10)
Platform: i386-w64-mingw32/i386 (32-bit)

 

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
ADD REPLYlink written 2.5 years ago by Angel40
2
gravatar for Martin Morgan
2.5 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

OK, the warning messages are probably ok to ignore. Ideally you would like to update your R, but internet connectivity seems to be a problem for you and it is probably better to try and get work done with your current configuration.

If you were to update your R, then you should update it to the most recent version (3.2.0) and then re-install Bioconductor packages with source("http://bioconductor.org/biocLite.R"); biocLite(c("GEOquery", "limma", "other pkgs")).

ADD COMMENTlink written 2.5 years ago by Martin Morgan ♦♦ 20k

thank you very much...

ADD REPLYlink written 2.5 years ago by Angel40
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