Package: decontam

Version: 1.3.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:decontam.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings decontam_1.3.1.tar.gz

StartedAt: 2019-04-09 02:11:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:12:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 73.5 seconds

RetCode: 0

Status:  OK

CheckDir: decontam.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:decontam.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings decontam_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/decontam.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 'decontam/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decontam' version '1.3.1'
* package encoding: UTF-8
* 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 'decontam' 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
plot_condition: no visible binding for global variable 'Condition'
plot_condition: no visible binding for global variable 'DNA_conc'
plot_frequency: no visible binding for global variable 'DNA_conc'
plot_frequency: no visible binding for global variable
  'taxon_abundance'
plot_frequency: no visible binding for global variable 'Type'
plot_frequency: no visible binding for global variable 'contam'
plot_frequency: no visible binding for global variable 'non.contam'
Undefined global functions or variables:
  Condition DNA_conc Type contam non.contam taxon_abundance
* 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
isNotContaminant 6.12   0.42    6.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
isNotContaminant 5.02   0.13    5.14
* 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/decontam.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/decontam_1.3.1.tar.gz && rm -rf decontam.buildbin-libdir && mkdir decontam.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=decontam.buildbin-libdir decontam_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL decontam_1.3.1.zip && rm decontam_1.3.1.tar.gz decontam_1.3.1.zip
###
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  % 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  770k  100  770k    0     0  10.8M      0 --:--:-- --:--:-- --:--:-- 12.1M

install for i386

* installing *source* package 'decontam' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'decontam'
    finding HTML links ... done
    isContaminant                           html  
    isNotContaminant                        html  
    plot_condition                          html  
    plot_frequency                          html  
    finding level-2 HTML links ... done

** 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 'decontam' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'decontam' as decontam_1.3.1.zip
* DONE (decontam)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'decontam' successfully unpacked and MD5 sums checked