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CHECK report for waveTiling on tokay1

This page was generated on 2019-04-13 11:22:17 -0400 (Sat, 13 Apr 2019).

Package 1630/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: waveTiling
Version: 1.24.0
Command: 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
StartedAt: 2019-04-13 06:11:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:20:18 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 515.9 seconds
RetCode: 0
Status:  OK  
CheckDir: waveTiling.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/waveTiling_1.24.0.tar.gz && rm -rf waveTiling.buildbin-libdir && mkdir waveTiling.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=waveTiling.buildbin-libdir waveTiling_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL waveTiling_1.24.0.zip && rm waveTiling_1.24.0.tar.gz waveTiling_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 32334  100 32334    0     0   821k      0 --:--:-- --:--:-- --:--:--  902k

install for i386

* installing *source* package 'waveTiling' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c waveTiling.c -o waveTiling.o
waveTiling.c: In function 'MAPMARG':
waveTiling.c:10:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGEQSMOOTH':
waveTiling.c:43:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGIMP':
waveTiling.c:81:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGIMPEQSMOOTH':
waveTiling.c:114:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'waveTiling'
    finding HTML links ... done
    GenomeInfo-class                        html  
    MapFilterProbe-class                    html  
    WaveTilingFeatureSet-class              html  
    finding level-2 HTML links ... done

    WfmFit-class                            html  
    WfmFitCircadian-class                   html  
    WfmFitCustom-class                      html  
    WfmFitFactor-class                      html  
    WfmFitTime-class                        html  
    WfmInf-class                            html  
    WfmInfCompare-class                     html  
    WfmInfCustom-class                      html  
    WfmInfEffects-class                     html  
    WfmInfMeans-class                       html  
    WfmInfOverallMean-class                 html  
    addPheno                                html  
    bgCorrQn                                html  
    cel2TilingFeatureSet                    html  
    filterOverlap                           html  
    getNonAnnotatedRegions                  html  
    getSigGenes                             html  
    makeContrasts                           html  
    makeDesign                              html  
    plotWfm                                 html  
    selectProbesFromFilterOverlap           html  
    selectProbesFromTilingFeatureSet        html  
    wfm.fit                                 html  
    wfm.inference                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'waveTiling' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c waveTiling.c -o waveTiling.o
waveTiling.c: In function 'MAPMARG':
waveTiling.c:10:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGEQSMOOTH':
waveTiling.c:43:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGIMP':
waveTiling.c:81:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function 'MAPMARGIMPEQSMOOTH':
waveTiling.c:114:11: warning: unused variable 'n' [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'waveTiling' as waveTiling_1.24.0.zip
* DONE (waveTiling)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'waveTiling' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

waveTiling.Rcheck/examples_i386/waveTiling-Ex.timings

nameusersystemelapsed
GenomeInfo-class000
MapFilterProbe-class13.10 0.1713.42
WaveTilingFeatureSet-class37.83 3.9042.58
WfmFit-class1.340.061.92
WfmFitCircadian-class000
WfmFitCustom-class000
WfmFitFactor-class000
WfmFitTime-class000
WfmInf-class1.190.031.50
WfmInfCompare-class000
WfmInfCustom-class000
WfmInfEffects-class000
WfmInfMeans-class000
WfmInfOverallMean-class000
addPheno000
bgCorrQn000
cel2TilingFeatureSet000
filterOverlap000
getNonAnnotatedRegions 6.86 1.3314.45
getSigGenes4.980.176.02
makeContrasts000
makeDesign0.020.000.01
plotWfm4.840.425.27
selectProbesFromFilterOverlap14.29 0.1714.47
selectProbesFromTilingFeatureSet000
wfm.fit34.86 1.0537.53
wfm.inference1.940.252.19

waveTiling.Rcheck/examples_x64/waveTiling-Ex.timings

nameusersystemelapsed
GenomeInfo-class000
MapFilterProbe-class9.040.169.20
WaveTilingFeatureSet-class23.47 0.6424.11
WfmFit-class0.830.000.83
WfmFitCircadian-class000
WfmFitCustom-class000
WfmFitFactor-class000
WfmFitTime-class000
WfmInf-class0.790.030.82
WfmInfCompare-class000
WfmInfCustom-class000
WfmInfEffects-class000
WfmInfMeans-class000
WfmInfOverallMean-class000
addPheno000
bgCorrQn000
cel2TilingFeatureSet000
filterOverlap000
getNonAnnotatedRegions4.420.294.72
getSigGenes5.230.305.54
makeContrasts000
makeDesign0.020.000.01
plotWfm2.750.142.89
selectProbesFromFilterOverlap7.900.208.11
selectProbesFromTilingFeatureSet000
wfm.fit25.17 1.0526.24
wfm.inference1.570.111.67