BSgenome 1.36.3
H. Pages
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BSgenome | | Last Changed Rev: 106752 / Revision: 109384 | | Last Changed Date: 2015-07-24 18:26:18 -0700 (Fri, 24 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BSgenome_1.36.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BSgenome.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.36.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
‘Biostrings’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
BSgenome/inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools/split_human_b36_female.sh
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome’ can be installed ... [23s/24s] OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
extdata 5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘Biostrings’ ‘rtracklayer’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::labeledLine’
‘GenomeInfoDb:::compactPrintNamedAtomicVector’
‘GenomeInfoDb:::showGenomeDescription’ ‘IRanges:::.normargSEW’
‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’
‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’
‘S4Vectors:::anyMissing’ ‘S4Vectors:::anyMissingOrOutside’
‘S4Vectors:::diffWithInitialZero’
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
‘S4Vectors:::quick_unlist’ ‘S4Vectors:::quick_unsplit’
‘S4Vectors:::recycleVector’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘as.data.frame.BSgenomeViews’ ‘blocksizes’ ‘breakpoints’
‘forgeMaskedBSgenomeDataPkg’ ‘getBatchesFromOnDiskLongTable’
‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIndexFromOnDiskLongTable’
‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘rowids’ ‘saveAsOnDiskLongTable’
‘saveRowidsForOnDiskLongTable’
Undocumented S4 classes:
‘MaskedBSgenome’ ‘OnDiskLongTable’
Undocumented S4 methods:
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
generic '[[' and siglist 'TwobitNamedSequences,ANY,ANY'
generic 'blocksizes' and siglist 'OnDiskLongTable'
generic 'breakpoints' and siglist 'OnDiskLongTable'
generic 'coerce' and siglist 'GenomeDataList,RangedDataList'
generic 'colnames' and siglist 'OnDiskLongTable'
generic 'dim' and siglist 'OnDiskLongTable'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'names' and siglist 'TwobitNamedSequences'
generic 'ncol' and siglist 'OnDiskLongTable'
generic 'ncol' and siglist 'XtraSNPlocs'
generic 'nrow' and siglist 'OnDiskLongTable'
generic 'nrow' and siglist 'XtraSNPlocs'
generic 'rowids' and siglist 'OnDiskLongTable'
generic 'seqinfo' and siglist 'FastaNamedSequences'
generic 'seqinfo' and siglist 'RdaNamedSequences'
generic 'seqinfo' and siglist 'TwobitNamedSequences'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'OnDiskLongTable'
generic 'show' and siglist 'OnDiskNamedSequences'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘BSgenome.Scerevisiae.UCSC.sacCer1’
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BSgenome-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: XtraSNPlocs-class
> ### Title: XtraSNPlocs objects
> ### Aliases: class:XtraSNPlocs XtraSNPlocs-class XtraSNPlocs
> ### colnames,XtraSNPlocs-method dim,XtraSNPlocs-method
> ### provider,XtraSNPlocs-method providerVersion,XtraSNPlocs-method
> ### releaseDate,XtraSNPlocs-method releaseName,XtraSNPlocs-method
> ### referenceGenome,XtraSNPlocs-method organism,XtraSNPlocs-method
> ### commonName,XtraSNPlocs-method species,XtraSNPlocs-method
> ### seqinfo,XtraSNPlocs-method seqnames,XtraSNPlocs-method newXtraSNPlocs
> ### show,XtraSNPlocs-method snpcount,XtraSNPlocs-method
> ### snpsBySeqname,XtraSNPlocs-method snpsByOverlaps,XtraSNPlocs-method
> ### snpsById,XtraSNPlocs-method
> ### Keywords: methods classes
>
> ### ** Examples
>
> library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
> snps <- XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
> snpcount(snps)
ch1 ch2 ch3 ch4 ch5 ch6 ch7 ch8 ch9 ch10 ch11
546378 584439 464593 456879 411943 471931 379787 332813 277342 327169 315134
ch12 ch13 ch14 ch15 ch16 ch17 ch18 ch19 ch20 ch21 ch22
327687 238349 215014 199033 199383 202858 184432 167132 153060 100948 94680
chX chY chMT
226135 10298 46
> colnames(snps)
[1] "seqnames" "start" "end" "width" "strand" "RefSNP_id"
[7] "alleles" "snpClass" "loctype"
>
> ## ---------------------------------------------------------------------
> ## snpsBySeqname()
> ## ---------------------------------------------------------------------
> ## Get the location, RefSNP id, and alleles for all "extra SNPs"
> ## located on chromosome 22 and MT:
> snpsBySeqname(snps, c("ch22", "chMT"), columns=c("RefSNP_id", "alleles"))
GRanges object with 94726 ranges and 2 metadata columns:
seqnames ranges strand | RefSNP_id alleles
<Rle> <IRanges> <Rle> | <character> <character>
[1] ch22 [10513380, 10513380] - | rs386831164 -/T
[2] ch22 [10519678, 10519677] + | rs71286731 -/TTT
[3] ch22 [10526387, 10526386] + | rs36149894 -/A
[4] ch22 [10547411, 10547413] + | rs4022899 -/TTA
[5] ch22 [10551396, 10551396] - | rs67003614 -/T
... ... ... ... ... ... ...
[94722] chMT [16180, 16181] + | rs371240719 -/AA
[94723] chMT [16187, 16189] + | rs386828865 CCT/TCC/TGC
[94724] chMT [16189, 16189] + | rs369574569 CC/T
[94725] chMT [16291, 16292] + | rs386828866 CC/TT
[94726] chMT [16293, 16294] + | rs386828867 AC/GT/TT
-------
seqinfo: 25 sequences (1 circular) from GRCh38 genome
>
> ## ---------------------------------------------------------------------
> ## snpsByOverlaps()
> ## ---------------------------------------------------------------------
> ## Get the location, RefSNP id, and alleles for all "extra SNPs"
> ## overlapping some regions of interest:
> snpsByOverlaps(snps, "ch22:33.63e6-33.64e6",
+ columns=c("RefSNP_id", "alleles"))
GRanges object with 32 ranges and 2 metadata columns:
seqnames ranges strand | RefSNP_id alleles
<Rle> <IRanges> <Rle> | <character> <character>
[1] ch22 [33630832, 33630832] + | rs11366195 -/A
[2] ch22 [33631155, 33631158] + | rs113414007 -/CTGT
[3] ch22 [33631157, 33631160] + | rs61016685 -/GTCT
[4] ch22 [33631157, 33631161] + | rs201902868 -/GTCTA
[5] ch22 [33631162, 33631162] + | rs376379301 -/T
... ... ... ... ... ... ...
[28] ch22 [33637609, 33637608] + | rs3831697 -/CC/CT
[29] ch22 [33638237, 33638241] + | rs375674091 -/AAGGT
[30] ch22 [33638460, 33638459] + | rs147043500 -/ATTA
[31] ch22 [33638463, 33638462] + | rs10689394 -/ATTA
[32] ch22 [33638464, 33638463] + | rs67593517 -/ATTA
-------
seqinfo: 25 sequences (1 circular) from GRCh38 genome
>
> ## With the regions of interest being all the known CDS for hg38
> ## (except for the chromosome naming convention, hg38 is the same
> ## as GRCh38):
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.
> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> hg38_cds <- cds(txdb)
> seqlevelsStyle(hg38_cds) # UCSC
[1] "UCSC"
> seqlevelsStyle(snps) # dbSNP
[1] "dbSNP"
> seqlevelsStyle(hg38_cds) <- seqlevelsStyle(snps)
> genome(hg38_cds) <- genome(snps)
> snpsByOverlaps(snps, hg38_cds, columns=c("RefSNP_id", "alleles"))
Error: embedded nul in string: '-/CCC\004\0'
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/BSgenome.Rcheck/00check.log’
for details.