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CHECK report for diffcyt on tokay1

This page was generated on 2019-04-13 11:29:09 -0400 (Sat, 13 Apr 2019).

Package 408/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.2.23
Lukas M. Weber
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/diffcyt
Branch: RELEASE_3_8
Last Commit: 8bdfd18
Last Changed Date: 2019-04-04 13:58:46 -0400 (Thu, 04 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: diffcyt
Version: 1.2.23
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diffcyt_1.2.23.tar.gz
StartedAt: 2019-04-13 01:48:26 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:54:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 361.4 seconds
RetCode: 0
Status:  OK  
CheckDir: diffcyt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings diffcyt_1.2.23.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/diffcyt.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.23'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 8.27   0.08    8.44
diffcyt     7.09   0.01    7.11
plotHeatmap 6.24   0.25    6.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testDA_GLMM 8.84   0.03    8.88
diffcyt     7.47   0.03    7.50
plotHeatmap 6.28   0.08    6.36
topTable    5.93   0.03    5.96
testDS_LMM  5.32   0.00    5.33
* 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-3.8-bioc/meat/diffcyt.Rcheck/00check.log'
for details.



Installation output

diffcyt.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/diffcyt_1.2.23.tar.gz && rm -rf diffcyt.buildbin-libdir && mkdir diffcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffcyt.buildbin-libdir diffcyt_1.2.23.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL diffcyt_1.2.23.zip && rm diffcyt_1.2.23.tar.gz diffcyt_1.2.23.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  188k  100  188k    0     0  4173k      0 --:--:-- --:--:-- --:--:-- 4498k

install for i386

* installing *source* package 'diffcyt' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'diffcyt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffcyt' as diffcyt_1.2.23.zip
* DONE (diffcyt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'diffcyt' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

diffcyt.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.37    0.79   10.15 

diffcyt.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.67    0.39    8.04 

Example timings

diffcyt.Rcheck/examples_i386/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts1.340.061.40
calcMedians1.340.021.36
calcMediansByClusterMarker1.050.021.06
calcMediansBySampleMarker0.890.030.93
createContrast000
createDesignMatrix0.020.000.01
createFormula000
diffcyt7.090.017.11
generateClusters1.060.061.13
plotHeatmap6.240.256.48
prepareData0.010.020.03
testDA_GLMM8.270.088.44
testDA_edgeR1.390.011.41
testDA_voom1.620.021.64
testDS_LMM3.930.003.92
testDS_limma1.710.001.72
topTable3.680.023.68
transformData0.040.000.05

diffcyt.Rcheck/examples_x64/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts1.440.041.48
calcMedians1.500.021.52
calcMediansByClusterMarker1.320.001.33
calcMediansBySampleMarker1.040.001.03
createContrast000
createDesignMatrix0.010.000.02
createFormula000
diffcyt7.470.037.50
generateClusters1.060.001.06
plotHeatmap6.280.086.36
prepareData0.040.000.03
testDA_GLMM8.840.038.88
testDA_edgeR1.440.001.43
testDA_voom1.610.001.61
testDS_LMM5.320.005.33
testDS_limma2.000.012.02
topTable5.930.035.96
transformData0.060.000.06