Package: subSeq

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings subSeq_1.14.0.tar.gz

StartedAt: 2019-10-16 07:25:40 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:30:22 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 282.0 seconds

RetCode: 0

Status:  OK

CheckDir: subSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings subSeq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/subSeq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'subSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'subSeq' version '1.14.0'
* 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 'subSeq' 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
DESeq2: no visible global function definition for 'selectMethod'
ccc: no visible global function definition for 'cov'
ccc: no visible global function definition for 'var'
generateSubsampledMatrix : : no visible global function
  definition for 'rbinom'
plot.subsamples: no visible global function definition for 'plot'
plot.summary.subsamples: no visible binding for global variable
  'metric'
plot.summary.subsamples: no visible binding for global variable 'value'
plot.summary.subsamples: no visible binding for global variable
  'significant'
plot.summary.subsamples: no visible binding for global variable
  'percent'
plot.summary.subsamples: no visible binding for global variable
  'method'
plot.summary.subsamples: no visible binding for global variable 'depth'
plot.summary.subsamples: no visible binding for global variable
  'average.depth'
plot.summary.subsamples: no visible binding for global variable
  'average.value'
subsample: no visible binding for global variable 'proportion'
subsample: no visible binding for global variable 'replication'
subsample: no visible binding for global variable '.'
subsample: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'count'
summary.subsamples: no visible binding for global variable 'method'
summary.subsamples: no visible binding for global variable 'depth'
summary.subsamples: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'proportion'
summary.subsamples: no visible binding for global variable
  'replication'
summary.subsamples: no visible global function definition for
  'p.adjust'
summary.subsamples: no visible binding for global variable 'ID'
summary.subsamples: no visible binding for global variable 'padj'
summary.subsamples: no visible binding for global variable
  'coefficient'
summary.subsamples: no visible binding for global variable
  'o.coefficient'
summary.subsamples: no visible global function definition for 'cor'
summary.subsamples: no visible binding for global variable 'valid'
summary.subsamples: no visible binding for global variable 'o.lfdr'
summary.subsamples: no visible binding for global variable 'o.padj'
summary.subsamples: no visible binding for global variable
  'significant'
summary.subsamples: no visible binding for global variable 'estFDP'
summary.subsamples: no visible binding for global variable 'rFDP'
summary.subsamples: no visible binding for global variable 'metric'
summary.subsamples: no visible binding for global variable 'value'
summary.subsamples: no visible binding for global variable 'percent'
voomLimma: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  . ID average.depth average.value coefficient cor count cov depth
  estFDP method metric model.matrix o.coefficient o.lfdr o.padj
  p.adjust padj percent plot proportion pvalue rFDP rbinom replication
  selectMethod significant valid value var
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "selectMethod")
  importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
             "var")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
generateSubsampledMatrix 37.64   1.02   38.66
getSeed                  27.76   0.13   27.89
subsample                26.84   0.03   26.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
generateSubsampledMatrix 45.23   0.42   45.66
getSeed                  34.48   0.02   34.55
subsample                31.19   0.02   31.22
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/subSeq.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/subSeq_1.14.0.tar.gz && rm -rf subSeq.buildbin-libdir && mkdir subSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=subSeq.buildbin-libdir subSeq_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL subSeq_1.14.0.zip && rm subSeq_1.14.0.tar.gz subSeq_1.14.0.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 2774k  100 2774k    0     0  23.9M      0 --:--:-- --:--:-- --:--:-- 25.3M

install for i386

* installing *source* package 'subSeq' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'subSeq'
    finding HTML links ... done
    combineSubsamples                       html  
    generateSubsampledMatrix                html  
    getSeed                                 html  
    hammer                                  html  
    plot.subsamples                         html  
    plot.summary.subsamples                 html  
    ss                                      html  
    subsample                               html  
    summary.subsamples                      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 'subSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'subSeq' as subSeq_1.14.0.zip
* DONE (subSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'subSeq' successfully unpacked and MD5 sums checked