[BioC] package built under R version 3.1.0 warning

Diego Diez diez at ifrec.osaka-u.ac.jp
Thu Nov 7 07:17:55 CET 2013

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,

> 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
> 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’:


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,

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)

[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

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