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BioC 3.1: CHECK report for waveTiling on moscato2

This page was generated on 2015-10-09 09:29:52 -0700 (Fri, 09 Oct 2015).

Package 1014/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
waveTiling 1.10.0
Kristof De Beuf
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/waveTiling
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: waveTiling
Version: 1.10.0
Command: rm -rf waveTiling.buildbin-libdir waveTiling.Rcheck && mkdir waveTiling.buildbin-libdir waveTiling.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=waveTiling.buildbin-libdir waveTiling_1.10.0.tar.gz >waveTiling.Rcheck\00install.out 2>&1 && cp waveTiling.Rcheck\00install.out waveTiling-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=waveTiling.buildbin-libdir --install="check:waveTiling-install.out" --force-multiarch --no-vignettes --timings waveTiling_1.10.0.tar.gz
StartedAt: 2015-10-09 07:07:09 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:15:18 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 489.6 seconds
RetCode: 0
Status:  OK  
CheckDir: waveTiling.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf waveTiling.buildbin-libdir waveTiling.Rcheck && mkdir waveTiling.buildbin-libdir waveTiling.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=waveTiling.buildbin-libdir waveTiling_1.10.0.tar.gz >waveTiling.Rcheck\00install.out 2>&1 && cp waveTiling.Rcheck\00install.out waveTiling-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=waveTiling.buildbin-libdir --install="check:waveTiling-install.out" --force-multiarch --no-vignettes --timings waveTiling_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/waveTiling.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.10.0'
* 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 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
** checking loading without being on the library search path ... 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 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 : .local: no visible global function
  definition for 'ac.character'
filterOverlap,WaveTilingFeatureSet : .local: 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'
* 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 'E:/biocbld/bbs-3.1-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/i386/waveTiling.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/x64/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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [138s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
wfm.fit                       39.39   0.82   41.65
WaveTilingFeatureSet-class    32.50   0.35   34.23
selectProbesFromFilterOverlap 12.61   0.15   12.77
MapFilterProbe-class          12.03   0.03   12.35
getNonAnnotatedRegions         5.59   0.28   16.43
** running examples for arch 'x64' ... [134s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
WaveTilingFeatureSet-class    40.97   0.60   41.56
wfm.fit                       39.28   0.95   40.25
MapFilterProbe-class          12.68   0.04   12.73
selectProbesFromFilterOverlap 11.39   0.16   11.54
getNonAnnotatedRegions         6.55   0.28    6.83
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/waveTiling.Rcheck/00check.log'
for details.


waveTiling.Rcheck/00install.out:


install for i386

* installing *source* package 'waveTiling' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c waveTiling.c -o waveTiling.o
waveTiling.c: In function 'MAPMARG':
waveTiling.c:10:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGEQSMOOTH':
waveTiling.c:43:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGIMP':
waveTiling.c:81:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGIMPEQSMOOTH':
waveTiling.c:114:11: warning: unused variable 'n' [-Wunused-variable]
gcc -m32 -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'waveTiling' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c waveTiling.c -o waveTiling.o
waveTiling.c: In function 'MAPMARG':
waveTiling.c:10:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGEQSMOOTH':
waveTiling.c:43:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGIMP':
waveTiling.c:81:11: warning: unused variable 'n' [-Wunused-variable]
waveTiling.c: In function 'MAPMARGIMPEQSMOOTH':
waveTiling.c:114:11: warning: unused variable 'n' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'waveTiling' as waveTiling_1.10.0.zip
* DONE (waveTiling)

waveTiling.Rcheck/examples_i386/waveTiling-Ex.timings:

nameusersystemelapsed
GenomeInfo-class0.010.000.02
MapFilterProbe-class12.03 0.0312.35
WaveTilingFeatureSet-class32.50 0.3534.23
WfmFit-class1.000.001.27
WfmFitCircadian-class000
WfmFitCustom-class000
WfmFitFactor-class000
WfmFitTime-class000
WfmInf-class0.980.011.02
WfmInfCompare-class000
WfmInfCustom-class000
WfmInfEffects-class000
WfmInfMeans-class000
WfmInfOverallMean-class000
addPheno000
bgCorrQn000
cel2TilingFeatureSet000
filterOverlap000
getNonAnnotatedRegions 5.59 0.2816.43
getSigGenes3.910.054.75
makeContrasts000
makeDesign0.020.000.02
plotWfm4.230.064.29
selectProbesFromFilterOverlap12.61 0.1512.77
selectProbesFromTilingFeatureSet000
wfm.fit39.39 0.8241.65
wfm.inference2.770.092.86

waveTiling.Rcheck/examples_x64/waveTiling-Ex.timings:

nameusersystemelapsed
GenomeInfo-class000
MapFilterProbe-class12.68 0.0412.73
WaveTilingFeatureSet-class40.97 0.6041.56
WfmFit-class0.900.010.92
WfmFitCircadian-class0.020.000.02
WfmFitCustom-class000
WfmFitFactor-class000
WfmFitTime-class000
WfmInf-class0.90.00.9
WfmInfCompare-class000
WfmInfCustom-class000
WfmInfEffects-class000
WfmInfMeans-class000
WfmInfOverallMean-class000
addPheno000
bgCorrQn000
cel2TilingFeatureSet000
filterOverlap000
getNonAnnotatedRegions6.550.286.83
getSigGenes4.010.114.12
makeContrasts000
makeDesign0.010.000.02
plotWfm4.140.144.27
selectProbesFromFilterOverlap11.39 0.1611.54
selectProbesFromTilingFeatureSet000
wfm.fit39.28 0.9540.25
wfm.inference2.480.202.68