Package: BSgenome

Version: 1.52.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BSgenome_1.52.0.tar.gz

StartedAt: 2019-10-16 00:11:57 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:19:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 455.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BSgenome.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BSgenome_1.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BSgenome.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.52.0’
* 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  7.6Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    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’
  ‘IRanges:::unlist_as_integer’ ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
XtraSNPlocs-class   94.230  2.547  97.889
SNPlocs-class       50.676  1.712  54.535
BSgenome-utils      24.445  0.224  25.043
BSgenomeViews-class 17.602  1.522  19.125
injectSNPs          10.934  1.676  13.207
BSgenome-class      11.080  0.721  12.958
export-methods       6.498  0.324   6.822
getSeq-methods       6.390  0.020   6.414
bsapply              5.862  0.223   7.048
* 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 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BSgenome.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BSgenome
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BSgenome’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	11.080	0.721	12.958
BSgenome-utils	24.445	0.224	25.043
BSgenomeForge	4.792	0.060	4.885
BSgenomeViews-class	17.602	1.522	19.125
SNPlocs-class	50.676	1.712	54.535
XtraSNPlocs-class	94.230	2.547	97.889
available.genomes	3.457	0.196	4.294
bsapply	5.862	0.223	7.048
export-methods	6.498	0.324	6.822
getSeq-methods	6.390	0.020	6.414
injectSNPs	10.934	1.676	13.207