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CHECK report for decontam on tokay2

This page was generated on 2019-04-09 12:38:10 -0400 (Tue, 09 Apr 2019).

Package 395/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decontam 1.3.1
Benjamin Callahan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/decontam
Branch: master
Last Commit: e772b2f
Last Changed Date: 2019-01-04 13:28:18 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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### Running 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
###
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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.



Installation output

decontam.Rcheck/00install.out

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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

Tests output


Example timings

decontam.Rcheck/examples_i386/decontam-Ex.timings

nameusersystemelapsed
isContaminant3.290.033.36
isNotContaminant6.120.426.55
plot_condition1.310.061.50
plot_frequency2.550.032.58

decontam.Rcheck/examples_x64/decontam-Ex.timings

nameusersystemelapsed
isContaminant303
isNotContaminant5.020.135.14
plot_condition1.160.031.19
plot_frequency2.560.012.58