[BioC] package built under R version 3.1.0 warning

Marc Carlson mcarlson at fhcrc.org
Thu Nov 7 22:33:27 CET 2013


Hi Diego,

It's perfectly OK to use that package.  You can completely ignore that 
warning.  But I will push a new version in a day or so that will not 
issue these unnecessary warnings.

  Marc



On 11/06/2013 10:17 PM, Diego Diez wrote:
> 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/downloaded_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
>
>



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