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BioC 3.2: CHECK report for htSeqTools on zin1

This page was generated on 2016-04-23 10:11:53 -0700 (Sat, 23 Apr 2016).

Package 504/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.16.0
Oscar Reina
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/htSeqTools
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: htSeqTools
Version: 1.16.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.16.0.tar.gz
StartedAt: 2016-04-23 01:53:53 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:56:32 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 159.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: htSeqTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/htSeqTools.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’

Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘MASS’ ‘BSgenome’ ‘GenomeInfoDb’
  ‘GenomicRanges’
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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘htSeqTools’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Biobase’
  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
corRle: no visible global function definition for ‘Rle’
fillRleList: no visible global function definition for ‘Rle’
countHitsWindow,GRanges: possible error in countHitsWindow(x,
  chrLengths = chrLengths, windowSize = windowSize): unused argument
  (chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
  ‘chrLengths’
countRepeats,IRanges : .local: no visible global function definition
  for ‘Rle’
enrichedPeaks,RangedData-IRangesList-IRangesList: no visible global
  function definition for ‘pvec’
enrichedPeaks,RangedData-IRangesList-missing: no visible global
  function definition for ‘pvec’
enrichedRegions,missing-missing-RangedData-ANY-numeric: no visible
  global function definition for ‘DataFrame’
extendRanges,GRanges: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRanges: no visible binding for global variable
  ‘chrLength’
extendRanges,GRangesList: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRangesList: no visible binding for global variable
  ‘chrLength’
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
  function definition for ‘pvec’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : sortFun: no
  visible global function definition for ‘runValue’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : sortFun: no
  visible global function definition for ‘Rle’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : tableFun: no
  visible global function definition for ‘nrun’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : tableFun: no
  visible global function definition for ‘runValue’
regionsCoverage,ANY-ANY-ANY-RleList: no visible binding for global
  variable ‘DataFrame’
tabDuplReads,GRangesList: possible error in tabDuplReads(x, ,
  minRepeats = minRepeats, mc.cores = mc.cores): unused argument ()
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'gridCover,ANY,ANY'
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 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 ... [14s/14s] OK
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.


htSeqTools.Rcheck/00install.out:

* installing *source* package ‘htSeqTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘htSeqTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htSeqTools)

htSeqTools.Rcheck/htSeqTools-Ex.timings:

nameusersystemelapsed
alignPeaks0.1380.0000.138
cmds1.8300.0201.853
cmdsFit-class0.0010.0000.001
cmdsFit0.0010.0000.000
countHitsWindow0.0430.0000.043
coverageDiff0.1130.0000.113
enrichedChrRegions1.3350.0121.349
enrichedPeaks0.6220.0040.634
enrichedRegions0.2070.0040.211
extendRanges0.1320.0000.132
fdrEnrichedCounts0.1460.0000.146
filterDuplReads0.2530.0000.253
findPeakHeight0.8680.0040.871
giniCoverage0.7460.0040.750
gridCover-class0.0000.0000.001
htSample0.2370.0000.237
islandCounts0.2320.0000.231
listOverlap0.0060.0000.006
mergeRegions0.0450.0000.044
plot-methods0.0010.0000.001
plotChrRegions0.0120.0000.012
regionsCoverage0.0010.0000.001
rowLogRegLRT0.0020.0000.002
ssdCoverage0.2550.0040.259
stdPeakLocation0.0710.0000.071