Package: scmeth

Version: 1.3.3

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scmeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scmeth_1.3.3.tar.gz

StartedAt: 2019-04-09 05:47:16 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:55:58 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 521.6 seconds

RetCode: 0

Status:  OK

CheckDir: scmeth.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scmeth.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scmeth_1.3.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scmeth.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 'scmeth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scmeth' version '1.3.3'
* 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 'scmeth' 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
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
report          37.37   2.50   42.25
repMask         16.36   3.69   23.53
cpgDensity       5.20   0.32    7.47
featureCoverage  2.58   0.47    5.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
report  46.22   3.03   51.50
repMask 13.75   1.53   16.71
* 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/scmeth.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/scmeth_1.3.3.tar.gz && rm -rf scmeth.buildbin-libdir && mkdir scmeth.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scmeth.buildbin-libdir scmeth_1.3.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scmeth_1.3.3.zip && rm scmeth_1.3.3.tar.gz scmeth_1.3.3.zip
###
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100  729k  100  729k    0     0  10.2M      0 --:--:-- --:--:-- --:--:-- 11.4M

install for i386

* installing *source* package 'scmeth' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scmeth'
    finding HTML links ... done
    bsConversionPlot                        html  
    chromosomeCoverage                      html  
    coverage                                html  
    cpgDensity                              html  
    cpgDiscretization                       html  
    downsample                              html  
    featureCoverage                         html  
    mbiasplot                               html  
    methylationDist                         html  
    readmetrics                             html  
    repMask                                 html  
    report                                  html  
    scmeth                                  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 'scmeth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scmeth' as scmeth_1.3.3.zip
* DONE (scmeth)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scmeth' successfully unpacked and MD5 sums checked