htSeqTools 1.18.0
Oscar Reina
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/htSeqTools | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/htSeqTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.18.0’
* 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’ ‘S4Vectors’ ‘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 ... 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.
Unexported object imported by a ':::' call: ‘S4Vectors:::decodeRle’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PeakLocationBase: no visible global function definition for
‘nclass.Sturges’
PeakLocationBase: no visible global function definition for ‘hist’
PeakLocationBase: no visible global function definition for ‘par’
PeakLocationBase: no visible global function definition for ‘segments’
PeakLocationBase: no visible global function definition for ‘text’
fdrEnrichedCounts : getNBinomParams : myLikelihood: no visible global
function definition for ‘dnbinom’
fdrEnrichedCounts : getNBinomParams : myLikelihood: no visible global
function definition for ‘dmultinom’
fdrEnrichedCounts : getNBinomParams : mynlminb: no visible global
function definition for ‘nlminb’
fdrEnrichedCounts: no visible global function definition for ‘isoreg’
fdrEnrichedCounts: no visible global function definition for ‘dnbinom’
getGrid: no visible global function definition for ‘approxfun’
plotChrRegions: no visible global function definition for ‘segments’
plotChrRegions: no visible global function definition for ‘text’
plotChrRegions: no visible global function definition for ‘rect’
plotminHeight: no visible global function definition for ‘isoreg’
plotminHeight: no visible global function definition for ‘approxfun’
plotminHeight: no visible global function definition for ‘abline’
plotminHeight: no visible global function definition for ‘par’
plotminHeight: no visible global function definition for ‘points’
plotminHeight: no visible global function definition for ‘axis’
plotminHeight: no visible global function definition for ‘legend’
randomHitsWindow: no visible global function definition for ‘rmultinom’
randomHitsWindow: no visible global function definition for ‘runif’
rowLogRegLRT: no visible global function definition for ‘pchisq’
rowLogRegLRT : <anonymous>: no visible global function definition for
‘chisq.test’
rowLogRegLRT: no visible global function definition for ‘p.adjust’
stdPeakLocationBase: no visible global function definition for ‘hist’
stdPeakLocationBase: no visible global function definition for ‘par’
stdPeakLocationBase: no visible global function definition for
‘segments’
stdPeakLocationBase: no visible global function definition for ‘text’
cmds,RangedDataList: no visible global function definition for
‘as.dist’
cmds,RangedDataList: no visible global function definition for
‘cmdscale’
cmds,RangedDataList: no visible global function definition for ‘dist’
cmdsFit,matrix: no visible global function definition for ‘cmdscale’
cmdsFit,matrix: no visible global function definition for ‘as.dist’
cmdsFit,matrix: no visible global function definition for ‘dist’
countHitsWindow,GRanges: possible error in countHitsWindow(x,
chrLengths = chrLengths, windowSize = windowSize): unused argument
(chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
‘chrLengths’
enrichedPeaks,RangedData-IRangesList-IRangesList: no visible global
function definition for ‘pvec’
enrichedPeaks,RangedData-IRangesList-missing: no visible global
function definition for ‘pvec’
enrichedRegions,RangedData-missing-missing-ANY-ANY: no visible global
function definition for ‘pbinom’
enrichedRegions,RangedData-missing-missing-ANY-ANY: no visible global
function definition for ‘p.adjust’
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’
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
function definition for ‘isoreg’
findPeakHeight,RangedData-IRangesList-IRangesList: no visible global
function definition for ‘approxfun’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : lorenzC :
plot.Lc: no visible global function definition for ‘abline’
giniCoverage,RangedData-ANY-ANY-ANY-missing-integer : plotRes: no
visible global function definition for ‘par’
listOverlap,character-character-character-character: no visible global
function definition for ‘glm’
listOverlap,character-character-character-character: no visible global
function definition for ‘anova’
listOverlap,character-character-missing-character: no visible global
function definition for ‘chisq.test’
listOverlap,factor-character-missing-missing: no visible global
function definition for ‘chisq.test’
plot,cmdsFit-ANY: no visible global function definition for ‘text’
plot,gridCover-ANY: no visible global function definition for ‘text’
plot,gridCover-ANY: no visible global function definition for ‘par’
plotMeanCoverage,RleList-RangedData: no visible global function
definition for ‘loess’
ssdCoverage,IRangesList: no visible global function definition for
‘weighted.mean’
tabDuplReads,GRangesList: possible error in tabDuplReads(x, ,
minRepeats = minRepeats, mc.cores = mc.cores): unused argument ()
Undefined global functions or variables:
abline anova approxfun as.dist axis chisq.test chrLength chrLengths
cmdscale dist dmultinom dnbinom glm hist isoreg legend loess
nclass.Sturges nlminb p.adjust par pbinom pchisq points pvec rect
rmultinom runif segments text weighted.mean
Consider adding
importFrom("grDevices", "nclass.Sturges")
importFrom("graphics", "abline", "axis", "hist", "legend", "par",
"points", "rect", "segments", "text")
importFrom("stats", "anova", "approxfun", "as.dist", "chisq.test",
"cmdscale", "dist", "dmultinom", "dnbinom", "glm", "isoreg",
"loess", "nlminb", "p.adjust", "pbinom", "pchisq",
"rmultinom", "runif", "weighted.mean")
to your NAMESPACE file.
* 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 ... 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-3.3-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.