CHECK report for waveTiling on tokay1
This page was generated on 2019-04-13 11:22:17 -0400 (Sat, 13 Apr 2019).
waveTiling 1.24.0
Kristof De Beuf
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/waveTiling |
| Branch: RELEASE_3_8 |
| Last Commit: 9e16d0a |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:waveTiling.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings waveTiling_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/waveTiling.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'waveTiling/DESCRIPTION' ... OK
* this is package 'waveTiling' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'waveTiling' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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'
getSigGenes,WfmFit-WfmInf: no visible global function definition for
'queryHits'
getSigGenes,WfmFit-WfmInf: no visible global function definition for
'subjectHits'
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 queryHits subjectHits 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/waveTiling/libs/i386/waveTiling.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
WaveTilingFeatureSet-class 37.83 3.90 42.58
wfm.fit 34.86 1.05 37.53
selectProbesFromFilterOverlap 14.29 0.17 14.47
MapFilterProbe-class 13.10 0.17 13.42
getNonAnnotatedRegions 6.86 1.33 14.45
plotWfm 4.84 0.42 5.27
getSigGenes 4.98 0.17 6.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wfm.fit 25.17 1.05 26.24
WaveTilingFeatureSet-class 23.47 0.64 24.11
MapFilterProbe-class 9.04 0.16 9.20
selectProbesFromFilterOverlap 7.90 0.20 8.11
getSigGenes 5.23 0.30 5.54
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/waveTiling.Rcheck/00check.log'
for details.
Installation output
waveTiling.Rcheck/00install.out
Tests output
Example timings
|
waveTiling.Rcheck/examples_i386/waveTiling-Ex.timings
|
waveTiling.Rcheck/examples_x64/waveTiling-Ex.timings
|