waveTiling 1.13.0
Kristof De Beuf
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/waveTiling | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | 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 waveTiling_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/waveTiling.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘waveTiling’ can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Package in Depends field not imported from: ‘GenomeGraphs’
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 ... NOTE
Foreign function calls to a different package:
.C("dwt", ..., PACKAGE = "waveslim")
.C("idwt", ..., PACKAGE = "waveslim")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[1]]), end(regions[[1]]))),
location = Gloc, start = sta, end = end, region = c(trackCount,
trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[2]]), end(regions[[2]]))),
location = Gloc, start = sta, end = end, region = c(trackCount,
trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[effectId[effectNo] + 1]]),
end(regions[[effectId[effectNo] + 1]]))), location = Gloc, start =
sta, end = end, region = c(trackCount, trackCount), dp =
DisplayPars(color = "darkgrey", alpha = 0.1)): partial argument match
of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[effectId[length(effectsToPlot) -
2] + 2]]), end(regions[[effectId[length(effectsToPlot) - 2] + 2]]))),
location = Gloc, start = sta, end = end, region = c(trackCount,
trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[i + 1]]), end(regions[[i +
1]]))), location = Gloc, start = sta, end = end, region =
c(trackCount, trackCount), dp = DisplayPars(color = "darkgrey", alpha
= 0.1)): partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
makeNewTranscriptRectangleOverlay(sigRegions =
as.matrix(data.frame(start(regions[[i]]), end(regions[[i]]))),
location = Gloc, start = sta, end = end, region = c(trackCount,
trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
partial argument match of 'location' to 'locations'
makeNewAnnotationTextOverlay: no visible global function definition for
‘DisplayPars’
makeNewAnnotationTextOverlay: no visible global function definition for
‘transcripts’
makeNewAnnotationTextOverlay: no visible global function definition for
‘elementMetadata’
makeNewAnnotationTextOverlay: no visible global function definition for
‘makeTextOverlay’
makeNewAnnotationTrack: no visible global function definition for
‘DisplayPars’
makeNewAnnotationTrack: no visible global function definition for
‘exons’
makeNewAnnotationTrack: no visible global function definition for
‘elementMetadata’
makeNewAnnotationTrack: no visible global function definition for
‘makeAnnotationTrack’
makeNewTranscriptRectangleOverlay: no visible global function
definition for ‘DisplayPars’
makeNewTranscriptRectangleOverlay: no visible global function
definition for ‘makeRectangleOverlay’
pm2mm: no visible global function definition for ‘subseq’
filterOverlap,WaveTilingFeatureSet: no visible global function
definition for ‘ac.character’
filterOverlap,WaveTilingFeatureSet: no visible binding for global
variable ‘dataMMSegRevComp’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
definition for ‘exons’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
definition for ‘Rle’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
‘transcripts’
plotWfm,WfmFit-WfmInf: no visible global function definition for
‘makeGenericArray’
plotWfm,WfmFit-WfmInf: no visible global function definition for
‘DisplayPars’
plotWfm,WfmFit-WfmInf: no visible global function definition for
‘makeGenomeAxis’
plotWfm,WfmFit-WfmInf: no visible global function definition for
‘gdPlot’
Undefined global functions or variables:
DisplayPars Rle ac.character dataMMSegRevComp elementMetadata exons
gdPlot makeAnnotationTrack makeGenericArray makeGenomeAxis
makeRectangleOverlay makeTextOverlay subseq transcripts
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [97s/98s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
WaveTilingFeatureSet-class 28.592 0.419 29.038
wfm.fit 27.899 0.488 28.420
MapFilterProbe-class 10.122 0.079 10.216
selectProbesFromFilterOverlap 9.392 0.132 9.527
getNonAnnotatedRegions 4.937 0.249 5.670
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/waveTiling.Rcheck/00check.log’
for details.