Back to the "Multiple platform build/check report" A  B  C  D  E  F  G [H] I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for htSeqTools on zin1

This page was generated on 2015-08-24 10:48:02 -0700 (Mon, 24 Aug 2015).

Package 490/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.15.1
Oscar Reina
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/htSeqTools
Last Changed Rev: 103190 / Revision: 107696
Last Changed Date: 2015-04-28 04:31:40 -0700 (Tue, 28 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.15.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.15.1.tar.gz
StartedAt: 2015-08-24 00:48:02 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:50:44 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 161.5 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/htSeqTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.15.1’
* 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 ... [15s/15s] 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
alignPeaks0.1250.0000.125
cmds1.6600.0081.666
cmdsFit-class0.0010.0000.001
cmdsFit0.0000.0000.001
countHitsWindow0.0450.0000.045
coverageDiff0.1160.0000.117
enrichedChrRegions1.4900.0081.496
enrichedPeaks0.6610.0080.669
enrichedRegions0.2240.0000.224
extendRanges0.1410.0000.142
fdrEnrichedCounts0.1600.0000.159
filterDuplReads0.2920.0000.294
findPeakHeight0.9400.0040.955
giniCoverage0.4850.0040.488
gridCover-class0.0010.0000.001
htSample0.4960.0000.496
islandCounts0.2050.0000.205
listOverlap0.0060.0000.006
mergeRegions0.0360.0040.040
plot-methods000
plotChrRegions0.0100.0000.011
regionsCoverage0.0000.0000.001
rowLogRegLRT0.0020.0000.002
ssdCoverage0.2260.0000.226
stdPeakLocation0.0680.0000.068