waveTiling 1.0.0
Kristof De Beuf
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/waveTiling | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/waveTiling.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'waveTiling/DESCRIPTION' ... OK
* this is package 'waveTiling' version '1.0.0'
* 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 whether package 'waveTiling' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
.C("dwt", ..., PACKAGE = "waveslim")
.C("idwt", ..., PACKAGE = "waveslim")
See the chapter 'System and foreign language interfaces' of 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 gdPlot(trackInfo, minBase = minBase,
maxBase = maxBase, overlay = overlayInfoCorr[hlpIndex]): partial
argument match of 'overlay' to 'overlays'
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'
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
WaveTilingFeatureSet-class 61.280 2.325 64.393
wfm.fit 48.509 3.854 52.728
selectProbesFromFilterOverlap 14.541 0.866 15.466
MapFilterProbe-class 14.130 0.310 14.556
getNonAnnotatedRegions 7.575 1.182 9.853
getSigGenes 6.923 0.494 7.450
plotWfm 5.740 0.843 6.630
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/waveTiling.Rcheck/00check.log'
for details.