BSgenome 1.45.1
H. Pagès
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome | | Last Changed Rev: 129205 / Revision: 131943 | | Last Changed Date: 2017-04-26 20:02:21 -0400 (Wed, 26 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BSgenome_1.45.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BSgenome.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.45.1’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
extdata 5.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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:
‘GenomeInfoDb:::compactPrintNamedAtomicVector’
‘GenomeInfoDb:::showGenomeDescription’ ‘IRanges:::.normargSEW’
‘S4Vectors:::anyMissing’ ‘S4Vectors:::anyMissingOrOutside’
‘S4Vectors:::decodeRle’ ‘S4Vectors:::diffWithInitialZero’
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
‘S4Vectors:::make_zero_col_DataFrame’ ‘S4Vectors:::quick_unlist’
‘S4Vectors:::quick_unsplit’ ‘S4Vectors:::recycleVector’
‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’
‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’
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:
‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’
‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’
‘forgeMaskedBSgenomeDataPkg’
‘getBatchesByOverlapsFromOnDiskLongTable’
‘getBatchesBySeqnameFromOnDiskLongTable’
‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIdFromOnDiskLongTable_old’
‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
‘rowids’ ‘saveAsOnDiskLongTable_old’
‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’
‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’
Undocumented S4 classes:
‘OnDiskLongTable_old’ ‘OnDiskLongTable’ ‘MaskedBSgenome’
‘GRanges_OR_NULL’
Undocumented S4 methods:
generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
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 'batchsizes' and siglist 'OnDiskLongTable'
generic 'blocksizes' and siglist 'OnDiskLongTable_old'
generic 'breakpoints' and siglist 'OnDiskLongTable'
generic 'breakpoints' and siglist 'OnDiskLongTable_old'
generic 'dim' and siglist 'OnDiskLongTable'
generic 'dim' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'OnDiskLongTable'
generic 'dimnames' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'XtraSNPlocs'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'names' and siglist 'TwobitNamedSequences'
generic 'rowids' and siglist 'OnDiskLongTable'
generic 'rowids' and siglist 'OnDiskLongTable_old'
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 'OnDiskLongTable_old'
generic 'show' and siglist 'OnDiskNamedSequences'
generic 'spatialIndex' and siglist 'OnDiskLongTable'
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 ... 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: SNPlocs-class
> ### Title: SNPlocs objects
> ### Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs
> ### ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs
> ### OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method
> ### providerVersion,SNPlocs-method releaseDate,SNPlocs-method
> ### releaseName,SNPlocs-method referenceGenome
> ### referenceGenome,SNPlocs-method compatibleGenomes
> ### compatibleGenomes,SNPlocs-method organism,SNPlocs-method
> ### commonName,SNPlocs-method seqinfo,SNPlocs-method
> ### seqnames,SNPlocs-method new_ODLT_SNPlocs newSNPlocs
> ### show,SNPlocs-method snpcount snpcount,SNPlocs-method
> ### snpcount,ODLT_SNPlocs-method snpcount,OldFashionSNPlocs-method
> ### snplocs snplocs,SNPlocs-method snplocs,ODLT_SNPlocs-method
> ### snplocs,OldFashionSNPlocs-method snpsBySeqname
> ### snpsBySeqname,SNPlocs-method snpsBySeqname,ODLT_SNPlocs-method
> ### snpsBySeqname,OldFashionSNPlocs-method snpsByOverlaps
> ### snpsByOverlaps,SNPlocs-method snpsByOverlaps,ODLT_SNPlocs-method
> ### snpsByOverlaps,OldFashionSNPlocs-method snpsById
> ### snpsById,SNPlocs-method snpsById,ODLT_SNPlocs-method
> ### snpsById,OldFashionSNPlocs-method snpid2loc snpid2loc,SNPlocs-method
> ### snpid2loc,OldFashionSNPlocs-method snpid2alleles
> ### snpid2alleles,SNPlocs-method snpid2alleles,OldFashionSNPlocs-method
> ### snpid2grange snpid2grange,SNPlocs-method
> ### snpid2grange,OldFashionSNPlocs-method
> ### Keywords: methods classes
>
> ### ** Examples
>
> library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
> snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38
> snpcount(snps)
1 2 3 4 5 6 7 8
10352408 11278817 9279095 8909116 8313890 7723096 7317091 7224402
9 10 11 12 13 14 15 16
5748221 6180295 6402437 6203669 4456153 4205104 3796823 4463462
17 18 19 20 21 22 X Y
3802080 3530777 3107971 2979767 1761244 1821463 3979053 192585
MT
1760
>
> ## ---------------------------------------------------------------------
> ## snpsBySeqname()
> ## ---------------------------------------------------------------------
>
> ## Get all SNPs located on chromosome 22 or MT:
> snpsBySeqname(snps, c("22", "MT"))
GPos object with 1823223 positions and 2 metadata columns:
seqnames pos strand | RefSNP_id alleles_as_ambig
<Rle> <integer> <Rle> | <character> <character>
[1] 22 10510770 * | rs71207739 M
[2] 22 10510928 * | rs71207740 R
[3] 22 10511116 * | rs4022986 R
[4] 22 10511641 * | rs71207745 R
[5] 22 10516682 * | rs4022528 S
... ... ... ... . ... ...
[1823219] MT 16512 * | rs373943637 Y
[1823220] MT 16519 * | rs3937033 Y
[1823221] MT 16528 * | rs386829315 Y
[1823222] MT 16529 * | rs370705831 Y
[1823223] MT 16529 * | rs386829316 Y
-------
seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome
>
> ## ---------------------------------------------------------------------
> ## snpsByOverlaps()
> ## ---------------------------------------------------------------------
>
> ## Get all SNPs overlapping some genomic region of interest:
> snpsByOverlaps(snps, "22:33.63e6-33.64e6")
GPos object with 510 positions and 2 metadata columns:
seqnames pos strand | RefSNP_id alleles_as_ambig
<Rle> <integer> <Rle> | <character> <character>
[1] 22 33630056 * | rs7287473 R
[2] 22 33630098 * | rs111817452 Y
[3] 22 33630112 * | rs369494860 W
[4] 22 33630115 * | rs373570932 Y
[5] 22 33630156 * | rs5749641 R
... ... ... ... . ... ...
[506] 22 33639944 * | rs556376727 Y
[507] 22 33639945 * | rs558589502 V
[508] 22 33639983 * | rs749782933 R
[509] 22 33639988 * | rs560390482 Y
[510] 22 33639992 * | rs182698410 Y
-------
seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome
>
> ## With the regions of interest being all the known CDS for hg38
> ## located on chromosome 22 or MT (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
> my_cds <- cds(txdb)
> seqlevels(my_cds, pruning.mode="coarse") <- c("chr22", "chrM")
> seqlevelsStyle(my_cds) # UCSC
[1] "UCSC"
> seqlevelsStyle(snps) # NCBI
[1] "NCBI" "Ensembl"
> seqlevelsStyle(my_cds) <- seqlevelsStyle(snps)
Warning in `seqlevelsStyle<-`(`*tmp*`, value = c("NCBI", "Ensembl")) :
more than one seqlevels style supplied, using the 1st one only
> genome(my_cds) <- genome(snps)
> my_snps <- snpsByOverlaps(snps, my_cds)
> my_snps
GPos object with 136176 positions and 2 metadata columns:
seqnames pos strand | RefSNP_id alleles_as_ambig
<Rle> <integer> <Rle> | <character> <character>
[1] 22 15528177 * | rs780256539 Y
[2] 22 15528179 * | rs200562384 K
[3] 22 15528187 * | rs549380368 R
[4] 22 15528188 * | rs750995283 Y
[5] 22 15528190 * | rs767866451 Y
... ... ... ... . ... ...
[136172] MT 15849 * | rs202225494 Y
[136173] MT 15851 * | rs3094281 R
[136174] MT 15860 * | rs201023973 R
[136175] MT 15863 * | rs386829263 R
[136176] MT 15884 * | rs527236195 R
-------
seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome
> table(my_snps %within% my_cds)
Error in recycleArg(arg, argname, length.out) :
'shift' is longer than 'x'
Calls: table ... eval -> shift -> shift -> recycleIntegerArg -> recycleArg
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, 1 WARNING, 5 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/BSgenome.Rcheck/00check.log’
for details.