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BioC 3.4: CHECK report for BSgenome on moscato1

This page was generated on 2016-09-21 03:41:48 -0700 (Wed, 21 Sep 2016).

Package 140/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.41.2
H. Pagès
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
Last Changed Rev: 120988 / Revision: 121152
Last Changed Date: 2016-09-15 15:14:12 -0700 (Thu, 15 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.41.2
Command: rm -rf BSgenome.buildbin-libdir BSgenome.Rcheck && mkdir BSgenome.buildbin-libdir BSgenome.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BSgenome.buildbin-libdir BSgenome_1.41.2.tar.gz >BSgenome.Rcheck\00install.out 2>&1 && cp BSgenome.Rcheck\00install.out BSgenome-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BSgenome.buildbin-libdir --install="check:BSgenome-install.out" --force-multiarch --no-vignettes --timings BSgenome_1.41.2.tar.gz
StartedAt: 2016-09-20 04:55:25 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:11:17 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 952.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BSgenome.buildbin-libdir BSgenome.Rcheck && mkdir BSgenome.buildbin-libdir BSgenome.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BSgenome.buildbin-libdir BSgenome_1.41.2.tar.gz >BSgenome.Rcheck\00install.out 2>&1 && cp BSgenome.Rcheck\00install.out BSgenome-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BSgenome.buildbin-libdir --install="check:BSgenome-install.out" --force-multiarch --no-vignettes --timings BSgenome_1.41.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BSgenome.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.41.2'
* 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 whether package 'BSgenome' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:::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' 'as.data.frame.BSgenomeViews'
  'blocksizes' 'breakpoints' 'forgeMaskedBSgenomeDataPkg'
  'getBatchesFromOnDiskLongTable' 'getRowsByIdFromOnDiskLongTable'
  'getRowsByIndexFromOnDiskLongTable' 'rowids' 'saveAsOnDiskLongTable'
  'saveRowidsForOnDiskLongTable'
Undocumented S4 classes:
  'OnDiskLongTable' 'MaskedBSgenome'
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 'blocksizes' and siglist 'OnDiskLongTable'
  generic 'breakpoints' and siglist 'OnDiskLongTable'
  generic 'colnames' and siglist 'OnDiskLongTable'
  generic 'dim' and siglist 'OnDiskLongTable'
  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 '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
XtraSNPlocs-class   64.16   0.89   88.62
SNPlocs-class       42.31   1.20   53.67
BSgenome-utils      35.00   0.26   36.45
injectSNPs          25.18   0.35   27.08
BSgenome-class      21.77   0.57   38.04
BSgenomeViews-class 15.05   0.99   42.81
bsapply             13.47   0.25   16.55
export-methods      10.73   0.46   12.93
available.genomes   10.34   0.71   43.79
getSeq-methods       9.12   0.07    9.21
BSgenomeForge        8.13   0.06    9.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
XtraSNPlocs-class   69.11   0.98   70.09
SNPlocs-class       42.51   1.09   43.60
injectSNPs          32.71   1.45   34.18
BSgenome-utils      33.82   0.30   34.22
BSgenome-class      23.39   0.43   23.82
bsapply             16.32   0.20   16.52
BSgenomeViews-class 15.37   0.94   16.33
export-methods      15.39   0.67   16.66
getSeq-methods      10.15   0.03   10.18
available.genomes    8.83   0.77   38.03
BSgenomeForge        6.69   0.03    6.81
* 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: 2 WARNINGs, 5 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/BSgenome.Rcheck/00check.log'
for details.


BSgenome.Rcheck/00install.out:


install for i386

* installing *source* package 'BSgenome' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BSgenome' as BSgenome_1.41.2.zip
* DONE (BSgenome)

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class21.77 0.5738.04
BSgenome-utils35.00 0.2636.45
BSgenomeForge8.130.069.16
BSgenomeViews-class15.05 0.9942.81
SNPlocs-class42.31 1.2053.67
XtraSNPlocs-class64.16 0.8988.62
available.genomes10.34 0.7143.79
bsapply13.47 0.2516.55
export-methods10.73 0.4612.93
getSeq-methods9.120.079.21
injectSNPs25.18 0.3527.08

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class23.39 0.4323.82
BSgenome-utils33.82 0.3034.22
BSgenomeForge6.690.036.81
BSgenomeViews-class15.37 0.9416.33
SNPlocs-class42.51 1.0943.60
XtraSNPlocs-class69.11 0.9870.09
available.genomes 8.83 0.7738.03
bsapply16.32 0.2016.52
export-methods15.39 0.6716.66
getSeq-methods10.15 0.0310.18
injectSNPs32.71 1.4534.18