Package: dmrseq

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dmrseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings dmrseq_1.6.0.tar.gz

StartedAt: 2020-04-15 02:44:58 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:00:41 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 942.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dmrseq.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dmrseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings dmrseq_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/dmrseq.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dmrseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dmrseq' version '1.6.0'
* 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 'dmrseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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
plotDMRs: warning in rank(as.numeric(rowSums(cov.unique)), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
plotEmpiricalDistribution: no visible binding for global variable 'wt'
Undefined global functions or variables:
  wt
* 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' ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                           user system elapsed
getAnnot                  21.67   2.76   29.30
dmrseq                    13.43   2.13  194.53
plotEmpiricalDistribution  7.44   0.53    7.97
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                           user system elapsed
getAnnot                  23.62   1.56   31.55
dmrseq                    12.20   1.86  237.50
plotEmpiricalDistribution  6.86   0.72    7.60
* 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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/dmrseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/dmrseq_1.6.0.tar.gz && rm -rf dmrseq.buildbin-libdir && mkdir dmrseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dmrseq.buildbin-libdir dmrseq_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL dmrseq_1.6.0.zip && rm dmrseq_1.6.0.tar.gz dmrseq_1.6.0.zip
###
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100 2286k  100 2286k    0     0  5427k      0 --:--:-- --:--:-- --:--:-- 5470k

install for i386

* installing *source* package 'dmrseq' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dmrseq'
    finding HTML links ... done
    BS.chr21                                html  
    annot.chr21                             html  
    dmrPlotAnnotations                      html  
    dmrs.ex                                 html  
    dmrseq                                  html  
    getAnnot                                html  
    meanDiff                                html  
    plotDMRs                                html  
    plotEmpiricalDistribution               html  
    simDMRs                                 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 'dmrseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dmrseq' as dmrseq_1.6.0.zip
* DONE (dmrseq)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'dmrseq' successfully unpacked and MD5 sums checked