Package: macat

Version: 1.52.0

Command: rm -rf macat.buildbin-libdir macat.Rcheck && mkdir macat.buildbin-libdir macat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=macat.buildbin-libdir macat_1.52.0.tar.gz >macat.Rcheck\00install.out 2>&1 && cp macat.Rcheck\00install.out macat-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=macat.buildbin-libdir --install="check:macat-install.out" --force-multiarch --no-vignettes --timings macat_1.52.0.tar.gz

StartedAt: 2018-04-12 01:05:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:08:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 175.2 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf macat.buildbin-libdir macat.Rcheck && mkdir macat.buildbin-libdir macat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=macat.buildbin-libdir macat_1.52.0.tar.gz >macat.Rcheck\00install.out 2>&1 && cp macat.Rcheck\00install.out macat-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=macat.buildbin-libdir --install="check:macat-install.out" --force-multiarch --no-vignettes --timings macat_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/macat.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 'macat/DESCRIPTION' ... OK
* this is package 'macat' version '1.52.0'
* 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 'macat' 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
'library' or 'require' call to 'annotate' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'annotate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'annotate:::getTDRows'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
buildMACAT: no visible global function definition for 'featureNames'
buildMACAT: no visible global function definition for 'sampleNames'
buildMACAT: no visible global function definition for 'exprs'
compare.gammas: no visible global function definition for 'x11'
compare.gammas: no visible global function definition for 'lines'
compare.gammas: no visible global function definition for 'legend'
discreteKernelize: no visible binding for global variable 'quantile'
discretize: no visible binding for global variable 'quantile'
discretizeChromosome: no visible binding for global variable 'quantile'
discretizeOne: no visible binding for global variable 'quantile'
evalScoring: no visible binding for global variable 'quantile'
getHtml: no visible global function definition for 'browseURL'
loaddatapkg: no visible global function definition for
  'install.packages'
loaddatapkg: no visible global function definition for 'contrib.url'
plot.MACATevalScoring: no visible global function definition for 'x11'
plot.MACATevalScoring: no visible global function definition for 'png'
plot.MACATevalScoring: no visible global function definition for 'par'
plot.MACATevalScoring: no visible global function definition for
  'points'
plot.MACATevalScoring: no visible global function definition for
  'lines'
plot.MACATevalScoring: no visible global function definition for
  'title'
plot.MACATevalScoring: no visible global function definition for 'axis'
plot.MACATevalScoring: no visible global function definition for
  'mtext'
plot.MACATevalScoring: no visible global function definition for
  'dev.off'
plotSliding: no visible global function definition for 'lines'
preprocessedLoader: no visible global function definition for
  'read.delim'
preprocessedLoader: no visible global function definition for
  'read.table'
preprocessedLoader: no visible global function definition for
  'buildChromLocation'
preprocessedLoader: no visible global function definition for 'new'
preprocessedLoader: no visible global function definition for 'pData<-'
preprocessedLoader: no visible global function definition for
  'varLabels<-'
preprocessedLoader: no visible global function definition for
  'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'featureNames'
scoring : tscore: no visible global function definition for 'median'
scoring : tscoremat: no visible binding for global variable 'median'
scoring : pval: no visible binding for global variable 'pt'
scoring: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  addVigs2WinMenu axis browseURL buildChromLocation chromLocs
  contrib.url dev.off exprs featureNames install.packages legend lines
  median mtext new pData<- par png points pt quantile read.delim
  read.table sampleNames title varLabels<- x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "x11")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "points", "title")
  importFrom("methods", "new")
  importFrom("stats", "median", "pt", "quantile")
  importFrom("utils", "browseURL", "contrib.url", "install.packages",
             "read.delim", "read.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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* 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
discretize_tscores 13.59   0.02   13.61
get_results         6.01   0.00    6.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
discretize_tscores 25.45   0.05   25.50
get_results        18.39   0.00   18.39
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/macat.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'macat' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'macat'
    finding HTML links ... done
    buildMACAT                              html  
    compute_sliding                         html  
    discreteKernelize                       html  
    discretize                              html  
    discretizeAll                           html  
    discretize_tscores                      html  
    evalScoring                             html  
    evaluateParameters                      html  
    get_results                             html  
    html                                    html  
    kernelize                               html  
    kernelizeAll                            html  
    kernelizeToPython                       html  
    kernels                                 html  
    loaddatapkg                             html  
    macat-internal                          html  
    plot_MACATevalScoring                   html  
    preprocessedLoader                      html  
    pythondata                              html  
    scoring                                 html  
    stjd                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'macat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'macat' as macat_1.52.0.zip
* DONE (macat)
In R CMD INSTALL
In R CMD INSTALL