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BioC experimental data: CHECK report for leeBamViews on malbec1

This page was generated on 2017-04-15 16:49:30 -0400 (Sat, 15 Apr 2017).

Package 167/310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
leeBamViews 1.10.0
VJ Carey
Snapshot Date: 2017-04-15 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/leeBamViews
Last Changed Rev: 3958 / Revision: 4141
Last Changed Date: 2016-10-17 14:47:53 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: leeBamViews
Version: 1.10.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings leeBamViews_1.10.0.tar.gz
StartedAt: 2017-04-15 11:02:27 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 11:04:58 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 150.3 seconds
RetCode: 0
Status:  OK 
CheckDir: leeBamViews.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings leeBamViews_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/leeBamViews.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘1.10.0’
* 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 ... 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
Malformed Description field: should contain one or more complete sentences.
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:
  ‘BSgenome’ ‘Biobase’ ‘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 : <anonymous>: no visible global function definition for
  ‘as’
.tabulateReads: no visible global function definition for ‘start’
.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’
Undefined global functions or variables:
  DataFrame GRanges IRanges ScanBamParam as bamPaths bamRanges
  bamSamples elementMetadata mclapply scanBam seqnames start values
  values<-
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘lbvtest.R’
 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

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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
bs10.6120.0680.679
leeRPKM0.0360.0000.035
leeUnn0.0640.0040.068
tabulateReads4.1000.0284.128
totalReadCounts0.8000.0080.808