Package: sSeq

Version: 1.20.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sSeq_1.20.1.tar.gz

StartedAt: 2019-04-13 05:44:31 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:58:00 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 809.5 seconds

RetCode: 0

Status:  OK

CheckDir: sSeq.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sSeq_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sSeq.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 'sSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sSeq' version '1.20.1'
* 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 'sSeq' 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
'library' or 'require' call to 'caTools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'caTools'
  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 ... OK
* checking R code for possible problems ... NOTE
drawMA_vol: no visible global function definition for 'par'
drawMA_vol: no visible global function definition for 'plot'
drawMA_vol: no visible global function definition for 'points'
drawMA_vol: no visible global function definition for 'abline'
ecdfAUC: no visible global function definition for 'ecdf'
ecdfAUC: no visible global function definition for 'trapz'
ecdfAUC: no visible global function definition for 'plot'
ecdfAUC: no visible global function definition for 'mtext'
ecdfAUC: no visible global function definition for 'axis'
ecdfAUC: no visible global function definition for 'box'
ecdfAUC: no visible global function definition for 'lines'
ecdfAUC: no visible global function definition for 'abline'
ecdfAUC: no visible global function definition for 'legend'
exactNBtest1: no visible global function definition for 'dnbinom'
getAdjustDisp: no visible global function definition for 'quantile'
getAdjustDisp: no visible global function definition for 'var'
getNormFactor : <anonymous>: no visible global function definition for
  'median'
getQ: no visible global function definition for 'quantile'
getQ: no visible global function definition for 'cov'
getQ: no visible global function definition for 'var'
getQ: no visible global function definition for 'plot'
getQ: no visible global function definition for 'abline'
getQ: no visible global function definition for 'mtext'
getT: no visible global function definition for 'quantile'
getT: no visible global function definition for 'sd'
getT: no visible global function definition for 'cov'
getT: no visible global function definition for 'var'
getT: no visible global function definition for 'plot'
getT: no visible global function definition for 'mtext'
getT: no visible global function definition for 'axis'
getT: no visible global function definition for 'abline'
getTgroup: no visible global function definition for 'quantile'
getTgroup: no visible global function definition for 'cov'
getTgroup: no visible global function definition for 'var'
getTgroup: no visible global function definition for 'plot'
getTgroup: no visible global function definition for 'mtext'
getTgroup: no visible global function definition for 'box'
getTgroup: no visible global function definition for 'axis'
getTgroup: no visible global function definition for 'abline'
nbinomTestForMatricesSH : int.func: no visible global function
  definition for 'median'
nbinomTestForMatricesSH: no visible global function definition for
  'dnbinom'
nbinomTestForMatricesSH: no visible global function definition for
  'pchisq'
plotDispersion: no visible global function definition for 'brewer.pal'
plotDispersion: no visible global function definition for
  'smoothScatter'
plotDispersion: no visible binding for global variable 'blues9'
plotDispersion: no visible global function definition for 'points'
plotDispersion: no visible global function definition for 'legend'
plotDispersion: no visible global function definition for 'plot'
rnbinomMV: no visible global function definition for 'rnbinom'
rowVars: no visible binding for global variable 'var'
sim: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis blues9 box brewer.pal cov dnbinom ecdf legend lines
  median mtext par pchisq plot points quantile rnbinom rnorm sd
  smoothScatter trapz var
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "mtext", "par", "plot", "points", "smoothScatter")
  importFrom("stats", "cov", "dnbinom", "ecdf", "median", "pchisq",
             "quantile", "rnbinom", "rnorm", "sd", "var")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getTgroup    132.28   1.05  133.33
nbTestSH     128.52   1.06  129.59
sSeq-package 123.78   0.42  124.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
nbTestSH     108.92   1.00  109.92
getTgroup    104.19   1.04  105.22
sSeq-package 104.19   0.67  104.86
* 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-3.8-bioc/meat/sSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sSeq_1.20.1.tar.gz && rm -rf sSeq.buildbin-libdir && mkdir sSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sSeq.buildbin-libdir sSeq_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sSeq_1.20.1.zip && rm sSeq_1.20.1.tar.gz sSeq_1.20.1.zip
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install for i386

* installing *source* package 'sSeq' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sSeq'
    finding HTML links ... done
    Hammer2months                           html  
    Sultan                                  html  
    Tuch                                    html  
    countsTable                             html  
    drawMA_vol                              html  
    ecdfAUC                                 html  
    equalSpace                              html  
    exactNBtest1                            html  
    getAdjustDisp                           html  
    getNormFactor                           html  
    getQ                                    html  
    getT                                    html  
    getTgroup                               html  
    nbTestSH                                html  
    nbinomTestForMatricesSH                 html  
    plotDispersion                          html  
    rnbinomMV                               html  
    rowVars                                 html  
    sSeq-package                            html  
    sim                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sSeq' as sSeq_1.20.1.zip
* DONE (sSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL