Package: diffcyt

Version: 1.4.4

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings diffcyt_1.4.4.tar.gz

StartedAt: 2019-10-16 03:14:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:20:56 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 356.5 seconds

RetCode: 0

Status:  OK

CheckDir: diffcyt.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:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings diffcyt_1.4.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/diffcyt.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 'diffcyt/DESCRIPTION' ... OK
* this is package 'diffcyt' version '1.4.4'
* 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 'diffcyt' 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
calcCounts: no visible binding for global variable 'cluster_id'
calcCounts: no visible binding for global variable 'sample_id'
calcMedians: no visible binding for global variable 'cluster_id'
calcMedians: no visible binding for global variable 'sample_id'
calcMedians: no visible binding for global variable 'value'
calcMediansByClusterMarker: no visible binding for global variable
  'cluster_id'
calcMediansByClusterMarker: no visible binding for global variable
  'marker_id'
calcMediansByClusterMarker: no visible binding for global variable
  'value'
calcMediansBySampleMarker: no visible binding for global variable
  'sample_id'
calcMediansBySampleMarker: no visible binding for global variable
  'marker_id'
calcMediansBySampleMarker: no visible binding for global variable
  'value'
Undefined global functions or variables:
  cluster_id marker_id sample_id value
* 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
testDA_GLMM 7.28   0.04    7.58
diffcyt     6.51   0.19    6.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
diffcyt     12.64   0.03   12.67
testDA_GLMM 12.13   0.00   12.12
testDS_LMM   7.93   0.00    7.94
plotHeatmap  7.08   0.01    7.10
topTable     5.50   0.02    5.51
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/diffcyt.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/diffcyt_1.4.4.tar.gz && rm -rf diffcyt.buildbin-libdir && mkdir diffcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffcyt.buildbin-libdir diffcyt_1.4.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL diffcyt_1.4.4.zip && rm diffcyt_1.4.4.tar.gz diffcyt_1.4.4.zip
###
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install for i386

* installing *source* package 'diffcyt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'diffcyt'
    finding HTML links ... done
    calcCounts                              html  
    finding level-2 HTML links ... done

    calcMedians                             html  
    calcMediansByClusterMarker              html  
    calcMediansBySampleMarker               html  
    createContrast                          html  
    createDesignMatrix                      html  
    createFormula                           html  
    diffcyt                                 html  
    generateClusters                        html  
    plotHeatmap                             html  
    prepareData                             html  
    testDA_GLMM                             html  
    testDA_edgeR                            html  
    testDA_voom                             html  
    testDS_LMM                              html  
    testDS_limma                            html  
    topClusters                             html  
    topTable                                html  
    transformData                           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 'diffcyt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffcyt' as diffcyt_1.4.4.zip
* DONE (diffcyt)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'diffcyt' 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(diffcyt)
> 
> test_check("diffcyt")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.37    0.70    8.06 

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(diffcyt)
> 
> test_check("diffcyt")
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.56    0.50   13.04