Hi, I cannot update the annotationDbi package to its 1.30.1, when I try to donwload it from biocLite it retrieve the 1.28.2 version. I do not understand why since my R version is > 2.7.0.
That's the code I used:
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
> biocLite("AnnotationDbi")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.2.
Installing package(s) 'AnnotationDbi'
provo con l'URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/AnnotationDbi_1.28.2.tar.gz'
Content type 'application/x-gzip' length 4254362 bytes (4.1 Mb)
URL aperto
==================================================
downloaded 4.1 Mb
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a new generic function for ‘species’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for ‘species’
* DONE (AnnotationDbi)
The downloaded source packages are in
‘/tmp/Rtmp7bBzKv/downloaded_packages’
Old packages: 'Biostrings', 'gage', 'GenomicRanges', 'GSEABase', 'KEGGREST',
'Rsamtools'
>
> require(AnnotationDbi)
Carico il pacchetto richiesto: AnnotationDbi
Carico il pacchetto richiesto: stats4
Carico il pacchetto richiesto: BiocGenerics
Carico il pacchetto richiesto: 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
Carico il pacchetto richiesto: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Carico il pacchetto richiesto: GenomeInfoDb
Carico il pacchetto richiesto: S4Vectors
Carico il pacchetto richiesto: IRanges
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:GenomeInfoDb’:
species
The following object is masked from ‘package:BiocGenerics’:
species
Warning message:
multiple methods tables found for ‘species’
>
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] AnnotationDbi_1.28.2 GenomeInfoDb_1.4.1 IRanges_2.2.5
[4] S4Vectors_0.6.1 Biobase_2.26.0 BiocGenerics_0.14.0
[7] BiocInstaller_1.16.5
loaded via a namespace (and not attached):
[1] DBI_0.3.1 RSQLite_1.0.0 tools_3.1.2
>
> proc.time()
user system elapsed
14.336 0.308 18.370
