SNPlocs.Hsapiens.dbSNP.20110815

Package: SNPlocs.Hsapiens.dbSNP.20110815
Title: SNP locations for Homo sapiens (dbSNP Build 134)
Description: SNP locations and alleles for Homo sapiens extracted from
NCBI dbSNP Build 134. The source data files used for this
package were created by NCBI on Aug 15, 2011, and contain SNPs
mapped to reference genome GRCh37.p2.
WARNING: Note that the GRCh37.p2 genome is a patched version of
GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT.
GRCh37 itself is the same as the hg19 genome from UCSC *except*
for the mitochondrion chromosome. Therefore, the SNPs in this
package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they
will land at the correct location but this injection will exclude
chrM (i.e. nothing will be injected in that sequence).
Version: 0.99.7
Author: Herve Pages
Maintainer: H. Pages <hpages@fhcrc.org>
Depends: R (>= 2.10), IRanges, GenomicRanges
Imports: methods, S4Vectors, IRanges, GenomicRanges
Suggests: Biostrings, BSgenome (>= 1.16.1), BSgenome.Hsapiens.UCSC.hg19
License: Artistic-2.0
organism: Homo sapiens
species: Human
provider: NCBI
provider_version: 20110815
source_url: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat
biocViews: AnnotationData, Genetics, Homo_sapiens
Collate: 00datacache.R getSNPlocs.R COMPATIBLE_BSGENOMES.R zzz.R
NeedsCompilation: no
Packaged: 2015-08-10 18:45:50 UTC; hpages

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SNPlocs.Hsapiens.dbSNP.20110815' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPlocs.Hsapiens.dbSNP.20110815'
    finding HTML links ... done
    getSNPlocs                              html  
Rd warning: /tmp/Rtmplhnhn7/R.INSTALL6f9323de1130/SNPlocs.Hsapiens.dbSNP.20110815/man/getSNPlocs.Rd:100: missing file link 'GRanges'
Rd warning: /tmp/Rtmplhnhn7/R.INSTALL6f9323de1130/SNPlocs.Hsapiens.dbSNP.20110815/man/getSNPlocs.Rd:155: missing file link 'GRanges'
Rd warning: /tmp/Rtmplhnhn7/R.INSTALL6f9323de1130/SNPlocs.Hsapiens.dbSNP.20110815/man/getSNPlocs.Rd:158: missing file link 'GRanges'
Rd warning: /tmp/Rtmplhnhn7/R.INSTALL6f9323de1130/SNPlocs.Hsapiens.dbSNP.20110815/man/getSNPlocs.Rd:169: missing file link 'GRanges'
Rd warning: /tmp/Rtmplhnhn7/R.INSTALL6f9323de1130/SNPlocs.Hsapiens.dbSNP.20110815/man/getSNPlocs.Rd:183: missing file link 'findOverlaps'
    package                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (SNPlocs.Hsapiens.dbSNP.20110815)
Making 'packages.html' ... done