waveTiling 1.8.1
Kristof De Beuf
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/waveTiling | | Last Changed Rev: 96323 / Revision: 102249 | | Last Changed Date: 2014-11-01 11:53:19 -0700 (Sat, 01 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch waveTiling_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/waveTiling.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.8.1’
* 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 ... [31s/36s] 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
‘ranges’
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
‘ranges’
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’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
definition for ‘exons’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
definition for ‘ranges’
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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [183s/222s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
WaveTilingFeatureSet-class 61.509 2.040 66.285
wfm.fit 51.885 3.683 56.045
selectProbesFromFilterOverlap 12.234 0.815 13.199
MapFilterProbe-class 12.132 0.330 13.659
getNonAnnotatedRegions 7.486 1.193 33.804
getSigGenes 4.981 0.277 12.532
plotWfm 4.451 0.596 5.195
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/waveTiling.Rcheck/00check.log’
for details.
* installing *source* package ‘waveTiling’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c waveTiling.c -o waveTiling.o
waveTiling.c: In function ‘MAPMARG’:
waveTiling.c:10: warning: unused variable ‘n’
waveTiling.c: In function ‘MAPMARGEQSMOOTH’:
waveTiling.c:43: warning: unused variable ‘n’
waveTiling.c: In function ‘MAPMARGIMP’:
waveTiling.c:81: warning: unused variable ‘n’
waveTiling.c: In function ‘MAPMARGIMPEQSMOOTH’:
waveTiling.c:114: warning: unused variable ‘n’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o waveTiling.so waveTiling.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/waveTiling.Rcheck/waveTiling/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: ifelse, Map, paste, Reduce, Rle, sapply, subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: ifelse, Map, paste, Reduce, Rle, sapply, subseq
* DONE (waveTiling)