Entering edit mode
Dear all,
I installed package Mus.musculus on my Bioc-2.13 install with R-3.0.2.
When loading the package it warns about it being built for R-3.1.0,
which is used for Bioc-devel. Anything wrong on my side?
Thank you,
Diego
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
3.0.2.
> biocLite("Mus.musculus")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
3.0.2.
Installing package(s) 'Mus.musculus'
trying URL 'http://bioconductor.org/packages/2.13/data/annotation/bin/
macosx/contrib/3.0/Mus.musculus_1.1.1.tgz'
Content type 'application/x-gzip' length 8014 bytes
opened URL
==================================================
downloaded 8014 bytes
The downloaded binary packages are in
/var/folders/jv/hhb2chw51w91mm401l2ns0jr0000gn/T//RtmpERLC5W/downloade
d_packages
> library(Mus.musculus)
Loading required package: AnnotationDbi
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?:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, duplicated, eval,
evalq,
get, intersect, is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: GO.db
Loading required package: DBI
Loading required package: org.Mm.eg.db
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Warning message:
package ?Mus.musculus? was built under R version 3.1.0
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] parallel graphics grDevices utils datasets stats
methods
[8] base
other attached packages:
[1] Mus.musculus_1.1.1
[2] TxDb.Mmusculus.UCSC.mm10.knownGene_2.10.1
[3] org.Mm.eg.db_2.10.1
[4] GO.db_2.10.1
[5] RSQLite_0.11.4
[6] DBI_0.2-7
[7] OrganismDbi_1.4.0
[8] GenomicFeatures_1.14.0
[9] GenomicRanges_1.14.3
[10] XVector_0.2.0
[11] IRanges_1.20.5
[12] AnnotationDbi_1.24.0
[13] Biobase_2.22.0
[14] BiocGenerics_0.8.0
[15] BiocInstaller_1.12.0
[16] ggplot2_0.9.3.1
[17] devtools_1.3
loaded via a namespace (and not attached):
[1] BSgenome_1.30.0 Biostrings_2.30.0 MASS_7.3-29
RBGL_1.38.0
[5] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.1
XML_3.95-0.2
[9] biomaRt_2.18.0 bitops_1.0-6 colorspace_1.2-4
dichromat_2.0-0
[13] digest_0.6.3 evaluate_0.5.1 graph_1.40.0
grid_3.0.2
[17] gtable_0.1.2 httr_0.2 labeling_0.2
memoise_0.1
[21] munsell_0.4.2 plyr_1.8 proto_0.3-10
reshape2_1.2.2
[25] rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2
stringr_0.6.2
[29] tools_3.0.2 whisker_0.3-2 zlibbioc_1.8.0
> biocValid()
[1] TRUE
--
Diego Diez, PhD
Assistant Professor
Quantitative Immunology Research Unit,
WPI Immunology Frontier Research Center (IFReC)
8F Integrated Life Science Building, Osaka University,
3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
Phone: +81-6-6879-4266
Fax: +81-6-6879-4272
diez at ifrec.osaka-u.ac.jp
Thank you Marc.