Package: Starr

Version: 1.39.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Starr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Starr_1.39.0.tar.gz

StartedAt: 2019-04-09 06:11:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:15:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 235.9 seconds

RetCode: 0

Status:  OK

CheckDir: Starr.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Starr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Starr_1.39.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Starr/DESCRIPTION' ... OK
* this is package 'Starr' version '1.39.0'
* 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 'Starr' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RGlist2ExpresionSet: no visible global function definition for 'new'
backgd.sd: no visible global function definition for 'density'
backgd.sd: no visible global function definition for 'sd'
backgd.sd: no visible global function definition for 'quantile'
backgd.sd: no visible global function definition for 'acf'
backgd.sd: no visible global function definition for 'na.omit'
bpmapToProbeAnno: no visible global function definition for 'new'
cmarrt.ma: no visible global function definition for 'exprs'
cmarrt.peak : <anonymous>: no visible global function definition for
  'new'
correlate : <anonymous>: no visible global function definition for
  'cor'
correlationPlot: no visible global function definition for
  'colorRampPalette'
correlationPlot: no visible global function definition for 'brewer.pal'
correlationPlot: no visible global function definition for 'par'
correlationPlot: no visible global function definition for 'barplot'
correlationPlot: no visible global function definition for 'rect'
correlationPlot: no visible global function definition for 'text'
correlationPlot: no visible global function definition for 'axis'
correlationPlot: no visible global function definition for 'abline'
declare.bound: no visible global function definition for 'p.adjust'
densityscatter: no visible global function definition for
  'colorRampPalette'
densityscatter: no visible global function definition for 'points'
densityscatter: no visible global function definition for 'abline'
expressionByFeature: no visible global function definition for
  'featureNames'
expressionByFeature: no visible global function definition for 'median'
expressionByFeature: no visible global function definition for 'exprs'
getIntensities: no visible global function definition for 'exprs'
getProfiles: no visible global function definition for 'exprs'
getProfilesByBase: no visible global function definition for 'exprs'
getRatio: no visible binding for global variable 'median'
getRatio: no visible global function definition for 'exprs'
getRatio: no visible global function definition for 'new'
heatmapplot: no visible binding for global variable 'median'
heatmapplot: no visible global function definition for
  'colorRampPalette'
heatmapplot: no visible global function definition for 'levelplot'
heatmapplot : <anonymous>: no visible global function definition for
  'panel.levelplot'
heatmapplot : <anonymous>: no visible global function definition for
  'panel.abline'
heatmapplot : <anonymous>: no visible global function definition for
  'panel.axis'
kde2dplot: no visible global function definition for 'tail'
kde2dplot: no visible global function definition for 'topo.colors'
kde2dplot: no visible global function definition for 'par'
kde2dplot: no visible global function definition for 'contour'
kde2dplot: no visible global function definition for 'box'
ma.stat: no visible global function definition for 'filter'
ma.stat: no visible global function definition for 'pnorm'
makeProbeAnno: no visible global function definition for 'read.table'
makeSplines : spline: no visible global function definition for
  'predict'
normalize.Probes: no visible binding for global variable 'median'
normalize.Probes: no visible global function definition for 'exprs'
normalize.Probes: no visible global function definition for
  'normalizeBetweenArrays'
normalize.Probes: no visible global function definition for 'exprs<-'
normalize.Probes: no visible global function definition for
  'experimentData'
normalize.Probes: no visible global function definition for 'preproc<-'
normalize.Probes: no visible global function definition for
  'experimentData<-'
plotBoxes: no visible global function definition for 'exprs'
plotBoxes: no visible global function definition for 'boxplot'
plotBoxes: no visible global function definition for 'mtext'
plotDensity: no visible global function definition for 'exprs'
plotDensity: no visible global function definition for 'rainbow'
plotDensity: no visible global function definition for 'density'
plotDensity: no visible global function definition for 'lines'
plotDensity: no visible global function definition for 'legend'
plotDensity: no visible global function definition for 'par'
plotGCbias: no visible global function definition for 'boxplot'
plotImage: no visible global function definition for 'levelplot'
plotImage: no visible global function definition for 'rainbow'
plotMA: no visible global function definition for 'exprs'
plotMA: no visible global function definition for 'par'
plotMA: no visible global function definition for 'ma.plot'
plotPosBias: no visible global function definition for 'points'
plotProfiles: no visible global function definition for 'heat.colors'
plotProfiles: no visible global function definition for 'rainbow'
plotProfiles: no visible global function definition for
  'colorRampPalette'
plotProfiles: no visible global function definition for 'abline'
plotProfiles: no visible global function definition for 'axis'
plotProfiles: no visible global function definition for 'density'
plotProfiles: no visible global function definition for 'lines'
plotProfiles: no visible global function definition for 'legend'
plotRatioScatter: no visible global function definition for 'exprs'
plotRatioScatter: no visible global function definition for 'cor'
plotRatioScatter: no visible global function definition for 'hclust'
plotRatioScatter: no visible global function definition for 'pairs'
plotRatioScatter : <anonymous>: no visible global function definition
  for 'text'
plotRatioScatter : <anonymous>: no visible global function definition
  for 'cor'
plotRatioScatter : <anonymous>: no visible global function definition
  for 'points'
plotRatioScatter : <anonymous>: no visible global function definition
  for 'lines'
plotRatioScatter : <anonymous>: no visible global function definition
  for 'lowess'
plotScatter: no visible global function definition for 'exprs'
plotScatter: no visible global function definition for 'cor'
plotScatter: no visible global function definition for 'hclust'
plotScatter: no visible global function definition for 'pairs'
plotScatter : <anonymous>: no visible global function definition for
  'text'
plotScatter : <anonymous>: no visible global function definition for
  'cor'
plotScatter : <anonymous>: no visible global function definition for
  'points'
plotScatter : <anonymous>: no visible global function definition for
  'lines'
plotScatter : <anonymous>: no visible global function definition for
  'lowess'
plotcmarrt: no visible global function definition for 'par'
plotcmarrt: no visible global function definition for 'hist'
plotcmarrt: no visible global function definition for 'qqnorm'
plotcmarrt: no visible global function definition for 'abline'
profileplot: no visible global function definition for 'axis'
read.gffAnno: no visible global function definition for 'read.table'
readCelFile: no visible global function definition for 'new'
readCelFile: no visible global function definition for 'preproc<-'
readCelFile: no visible global function definition for 'featureNames<-'
singleclusterplot: no visible global function definition for 'title'
singleclusterplot : drawline: no visible global function definition for
  'lines'
singleclusterplot: no visible global function definition for
  'heat.colors'
singleclusterplot: no visible global function definition for 'rainbow'
singleclusterplot: no visible global function definition for
  'colorRampPalette'
singleclusterplot: no visible binding for global variable 'quantile'
singleclusterplot: no visible global function definition for 'polygon'
writeGFF: no visible global function definition for 'exprs'
writeGFF: no visible global function definition for 'write.table'
writePosFile: no visible global function definition for 'write.table'
writeWIG: no visible global function definition for 'exprs'
writeWIG: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline acf axis barplot box boxplot brewer.pal colorRampPalette
  contour cor density experimentData experimentData<- exprs exprs<-
  featureNames featureNames<- filter hclust heat.colors hist legend
  levelplot lines lowess ma.plot median mtext na.omit new
  normalizeBetweenArrays p.adjust pairs panel.abline panel.axis
  panel.levelplot par pnorm points polygon predict preproc<- qqnorm
  quantile rainbow read.table rect sd tail text title topo.colors
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors", "rainbow",
             "topo.colors")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "contour", "hist", "legend", "lines", "mtext", "pairs",
             "par", "points", "polygon", "rect", "text", "title")
  importFrom("methods", "new")
  importFrom("stats", "acf", "cor", "density", "filter", "hclust",
             "lowess", "median", "na.omit", "p.adjust", "pnorm",
             "predict", "qqnorm", "quantile", "sd")
  importFrom("utils", "read.table", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.9-bioc/R/library/Starr/libs/i386/Starr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Starr/libs/x64/Starr.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
plot.posBias 9.17   0.18    9.36
plot.gcBias  7.22   0.06    7.28
plot.ma      6.16   0.16    6.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot.posBias 13.26   0.10   13.36
plot.gcBias  10.27   0.05   10.32
plot.ma       6.82   0.09    6.91
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Starr_1.39.0.tar.gz && rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Starr.buildbin-libdir Starr_1.39.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Starr_1.39.0.zip && rm Starr_1.39.0.tar.gz Starr_1.39.0.zip
###
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100  702k  100  702k    0     0  8812k      0 --:--:-- --:--:-- --:--:-- 9622k

install for i386

* installing *source* package 'Starr' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ahocorasick.c -o ahocorasick.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c collect.c -o collect.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rm_small_peak.c -o rm_small_peak.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sort_by_genomic.c -o sort_by_genomic.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Starr.dll tmp.def ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Starr.buildbin-libdir/00LOCK-Starr/00new/Starr/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Starr'
    finding HTML links ... done
    RGlist2ExpressionSet                    html  
    backgd.sd                               html  
    bpmapToProbeAnno                        html  
    cmarrt.ma                               html  
    cmarrt.peak                             html  
    correlate                               html  
    correlationPlot                         html  
    declare.bound                           html  
    densityscatter                          html  
    expressionByFeature                     html  
    fill                                    html  
    fillNA                                  html  
    filterGenes                             html  
    getFeatures                             html  
    getIntensites                           html  
    getMeans                                html  
    getProfiles                             html  
    getProfilesByBase                       html  
    getRatio                                html  
    heatmapplot                             html  
    intersection                            html  
    kde2dplot                               html  
    list2matrix                             html  
    ma.stat                                 html  
    makeProbeAnno                           html  
    makeSplines                             html  
    mapFeatures                             html  
    match_ac                                html  
    normalize.Probes                        html  
    plot.Density                            html  
    plot.boxes                              html  
    plot.cmarrt                             html  
    plot.gcBias                             html  
    plot.image                              html  
    plot.ma                                 html  
    plot.posBias                            html  
    plot.ratioScatter                       html  
    plot.scatter                            html  
    plotProfiles                            html  
    profileplot                             html  
    rankPercentile.normalize                html  
    read.gffAnno                            html  
    readCelFile                             html  
    remap                                   html  
    rm.small.peak                           html  
    sameLength                              html  
    singleclusterplot                       html  
    sort.by.genomic                         html  
    substract                               html  
    whichIn                                 html  
    windowxy                                html  
    writeGFF                                html  
    writePosFile                            html  
    writeWIG                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Starr' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ahocorasick.c -o ahocorasick.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c collect.c -o collect.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rm_small_peak.c -o rm_small_peak.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sort_by_genomic.c -o sort_by_genomic.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Starr.dll tmp.def ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Starr.buildbin-libdir/Starr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Starr' as Starr_1.39.0.zip
* DONE (Starr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Starr' successfully unpacked and MD5 sums checked