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BioC experimental data: CHECK report for leeBamViews on perceval

This page was generated on 2015-04-08 17:41:26 -0700 (Wed, 08 Apr 2015).

Package 128/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
leeBamViews 1.1.1
VJ Carey
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/leeBamViews
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: leeBamViews
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch leeBamViews_1.1.1.tar.gz
StartedAt: 2015-04-08 10:12:55 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 10:18:38 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 343.4 seconds
RetCode: 0
Status:  OK 
CheckDir: leeBamViews.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch leeBamViews_1.1.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/leeBamViews.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘1.1.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘leeBamViews’ can be installed ... [30s/31s] OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘BSgenome’ ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.tabulateReads: no visible global function definition for ‘bamRanges’
.tabulateReads: no visible global function definition for
  ‘elementMetadata’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘ScanBamParam’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘bamRanges’
.tabulateReads : alignByFirstRange: no visible global function
  definition for ‘bamPaths’
.tabulateReads: no visible global function definition for ‘bamSamples’
.tabulateReads: no visible global function definition for ‘IRanges’
.tabulateReads: no visible global function definition for ‘GRanges’
.tabulateReads: no visible global function definition for ‘seqnames’
.tabulateReads: no visible global function definition for ‘values’
.tabulateReads: no visible global function definition for ‘values<-’
.tabulateReads: no visible global function definition for ‘DataFrame’
tabulateReads,BamViews-characterORNULL-missing-missing: no visible
  binding for global variable ‘mclapply’
tabulateReads,BamViews-missing-missing-missing: no visible binding for
  global variable ‘mclapply’
totalReadCounts,BamViews: no visible global function definition for
  ‘bamPaths’
totalReadCounts,BamViews: no visible binding for global variable
  ‘scanBam’
totalReadCounts,BamViews: no visible global function definition for
  ‘ScanBamParam’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
tabulateReads 6.338  1.331   7.794
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘lbvtest.R’ [22s/26s]
 [23s/26s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘IRanges’
* 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

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/leeBamViews.Rcheck/00check.log’
for details.

leeBamViews.Rcheck/00install.out:

* installing *source* package ‘leeBamViews’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (leeBamViews)

leeBamViews.Rcheck/leeBamViews-Ex.timings:

nameusersystemelapsed
bs11.4470.1551.607
leeRPKM0.0600.0200.081
leeUnn0.0720.0260.099
tabulateReads6.3381.3317.794
totalReadCounts1.1270.1891.346