Package: alevinQC

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alevinQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings alevinQC_1.0.0.tar.gz

StartedAt: 2019-10-16 01:53:16 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:56:30 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 193.9 seconds

RetCode: 0

Status:  OK

CheckDir: alevinQC.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:alevinQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings alevinQC_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/alevinQC.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 'alevinQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alevinQC' version '1.0.0'
* 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 'alevinQC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   8.1Mb
* 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
plotAlevinBarcodeCollapse: no visible binding for global variable
  'inFirstWhiteList'
plotAlevinBarcodeCollapse: no visible binding for global variable
  'collapsedFreq'
plotAlevinBarcodeCollapse: no visible binding for global variable
  'originalFreq'
plotAlevinKneeNbrGenes: no visible binding for global variable
  'inFirstWhiteList'
plotAlevinKneeNbrGenes: no visible binding for global variable
  'nbrGenesAboveZero'
plotAlevinKneeNbrGenes: no visible binding for global variable 'x'
plotAlevinKneeRaw: no visible binding for global variable 'ranking'
plotAlevinKneeRaw: no visible binding for global variable
  'originalFreq'
plotAlevinKneeRaw: no visible binding for global variable
  'inFirstWhiteList'
plotAlevinQuant: no visible binding for global variable
  'inFirstWhiteList'
plotAlevinQuant: no visible binding for global variable 'collapsedFreq'
plotAlevinQuant: no visible binding for global variable 'totalUMICount'
plotAlevinQuant: no visible binding for global variable
  'inFinalWhiteList'
plotAlevinQuant: no visible binding for global variable
  'nbrGenesAboveZero'
plotAlevinQuantPairs: no visible binding for global variable
  'inFirstWhiteList'
plotAlevinQuantPairs: no visible binding for global variable
  'inFinalWhiteList'
readAlevinQC: no visible binding for global variable 'V1'
readAlevinQC: no visible binding for global variable 'V2'
readAlevinQC: no visible binding for global variable 'CB'
readAlevinQC: no visible binding for global variable 'V3'
readAlevinQC: no visible binding for global variable 'V4'
readAlevinQC: no visible binding for global variable 'V5'
readAlevinQC: no visible binding for global variable 'inFirstWhiteList'
readAlevinQC: no visible binding for global variable 'inFinalWhiteList'
Undefined global functions or variables:
  CB V1 V2 V3 V4 V5 collapsedFreq inFinalWhiteList inFirstWhiteList
  nbrGenesAboveZero originalFreq ranking totalUMICount x
* 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
alevinQCReport       15.21   1.97   20.00
plotAlevinKneeRaw     8.33   1.06    9.40
plotAlevinQuantPairs  4.81   0.50    5.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
alevinQCReport    11.82   1.44   13.95
plotAlevinKneeRaw  6.12   0.73    6.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/alevinQC.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/alevinQC_1.0.0.tar.gz && rm -rf alevinQC.buildbin-libdir && mkdir alevinQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=alevinQC.buildbin-libdir alevinQC_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL alevinQC_1.0.0.zip && rm alevinQC_1.0.0.tar.gz alevinQC_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 4715k  100 4715k    0     0  13.0M      0 --:--:-- --:--:-- --:--:-- 13.3M

install for i386

* installing *source* package 'alevinQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'alevinQC'
    finding HTML links ... done
    alevinQCReport                          html  
    alevinQCShiny                           html  
    checkAlevinInputFiles                   html  
    plotAlevinBarcodeCollapse               html  
    plotAlevinKneeNbrGenes                  html  
    plotAlevinKneeRaw                       html  
    plotAlevinQuant                         html  
    plotAlevinQuantPairs                    html  
    readAlevinQC                            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 'alevinQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alevinQC' as alevinQC_1.0.0.zip
* DONE (alevinQC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'alevinQC' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alevinQC)
> 
> test_check("alevinQC")
== testthat results  ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.70    2.78   22.21 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alevinQC)
> 
> test_check("alevinQC")
== testthat results  ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.45    2.85   19.96