Package: waveTiling

Version: 1.20.0

Command: rm -rf waveTiling.buildbin-libdir waveTiling.Rcheck && mkdir waveTiling.buildbin-libdir waveTiling.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=waveTiling.buildbin-libdir waveTiling_1.20.0.tar.gz >waveTiling.Rcheck\00install.out 2>&1 && cp waveTiling.Rcheck\00install.out waveTiling-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=waveTiling.buildbin-libdir --install="check:waveTiling-install.out" --force-multiarch --no-vignettes --timings waveTiling_1.20.0.tar.gz

StartedAt: 2018-04-12 03:49:57 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:58:48 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 530.9 seconds

RetCode: 0

Status:  OK

CheckDir: waveTiling.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf waveTiling.buildbin-libdir waveTiling.Rcheck && mkdir waveTiling.buildbin-libdir waveTiling.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=waveTiling.buildbin-libdir waveTiling_1.20.0.tar.gz >waveTiling.Rcheck\00install.out 2>&1 && cp waveTiling.Rcheck\00install.out waveTiling-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=waveTiling.buildbin-libdir --install="check:waveTiling-install.out" --force-multiarch --no-vignettes --timings waveTiling_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/waveTiling.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.20.0'
* 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: 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-3.6-bioc/meat/waveTiling.buildbin-libdir/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
wfm.fit                       33.55   1.08   36.41
WaveTilingFeatureSet-class    32.61   1.33   35.19
MapFilterProbe-class          11.09   0.10   11.75
selectProbesFromFilterOverlap 10.25   0.39   10.64
getNonAnnotatedRegions         6.55   0.80   61.88
getSigGenes                    4.35   0.11   15.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
wfm.fit                       26.42   0.92   27.46
WaveTilingFeatureSet-class    26.34   0.66   27.00
MapFilterProbe-class           9.66   0.15    9.81
selectProbesFromFilterOverlap  8.23   0.25    8.48
getNonAnnotatedRegions         5.12   0.41    5.53
* 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-3.6-bioc/meat/waveTiling.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'waveTiling' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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/g++ -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/i386
** R
** inst
** preparing 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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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/g++ -shared -s -static-libgcc -o waveTiling.dll tmp.def waveTiling.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/waveTiling.buildbin-libdir/waveTiling/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'waveTiling' as waveTiling_1.20.0.zip
* DONE (waveTiling)
In R CMD INSTALL
In R CMD INSTALL