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BioC 2.13: CHECK report for htSeqTools on zin1

This page was generated on 2014-04-05 09:48:06 -0700 (Sat, 05 Apr 2014).

Package 353/750HostnameOS / ArchBUILDCHECKBUILD BIN
htSeqTools 1.8.0
Oscar Reina
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/htSeqTools
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: htSeqTools
Version: 1.8.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.8.0.tar.gz
StartedAt: 2014-04-05 01:53:00 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:55:16 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 136.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: htSeqTools.Rcheck
Warnings: 2

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/htSeqTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.8.0’
* 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 ‘htSeqTools’ can be installed ... [12s/12s] 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 dependencies in R code ... WARNING
‘library’ or ‘require’ call not declared from: ‘species’
‘library’ or ‘require’ call to ‘BSgenome’ which was already attached by Depends.
  Please remove these calls from your code.
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
countHitsWindow,GRanges: possible error in countHitsWindow(x,
  chrLengths = chrLengths, windowSize = windowSize): unused argument
  (chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
  ‘chrLengths’
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’
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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘htSeqTools.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [18s/18s] WARNING
Found the following significant warnings:

  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
  Warning: seqselect() is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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 ‘plot’ from package ‘graphics’ in package ‘htSeqTools’
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
alignPeaks0.5200.0040.524
cmds3.1560.0123.177
cmdsFit-class0.0000.0000.003
cmdsFit0.0000.0000.001
countHitsWindow0.0720.0000.074
coverageDiff0.1560.0080.163
enrichedChrRegions2.1800.0002.185
enrichedPeaks1.1480.0041.156
enrichedRegions0.4160.0000.415
extendRanges0.1640.0000.163
fdrEnrichedCounts0.1240.0040.127
filterDuplReads0.3040.0000.306
findPeakHeight2.4440.0042.451
giniCoverage0.4330.0000.432
gridCover-class0.0040.0000.000
htSample0.2880.0040.294
islandCounts0.3880.0000.389
listOverlap0.0160.0000.014
mergeRegions0.0840.0000.082
plot-methods0.0040.0000.004
plotChrRegions0.0360.0000.036
regionsCoverage0.0040.0000.004
rowLogRegLRT0.0040.0040.008
ssdCoverage0.3600.0000.362
stdPeakLocation0.1160.0000.116