Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:05:11 -0400 (Mon, 20 Sep 2021).

CHECK results for diffcyt on tokay2

To the developers/maintainers of the diffcyt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffcyt.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 497/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffcyt 1.12.0  (landing page)
Lukas M. Weber
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/diffcyt
git_branch: RELEASE_3_13
git_last_commit: 7e8f4d3
git_last_commit_date: 2021-05-19 12:34:44 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffcyt
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffcyt_1.12.0.tar.gz
StartedAt: 2021-09-19 21:37:51 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 21:44:32 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 401.2 seconds
RetCode: 0
Status:   OK  
CheckDir: diffcyt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffcyt_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diffcyt.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.12.0'
* 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 (user + system) or elapsed time > 5s
            user system elapsed
diffcyt     8.84   0.55    9.40
testDA_GLMM 7.62   0.15    7.80
plotHeatmap 4.99   0.10    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
diffcyt     9.57   0.07    9.66
testDA_GLMM 9.08   0.00    9.08
topTable    6.57   0.00    6.58
plotHeatmap 6.11   0.08    6.18
testDS_LMM  5.61   0.03    5.64
* 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-3.13-bioc/meat/diffcyt.Rcheck/00check.log'
for details.



Installation output

diffcyt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/diffcyt_1.12.0.tar.gz && rm -rf diffcyt.buildbin-libdir && mkdir diffcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffcyt.buildbin-libdir diffcyt_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL diffcyt_1.12.0.zip && rm diffcyt_1.12.0.tar.gz diffcyt_1.12.0.zip
###
##############################################################################
##############################################################################


  % 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  183k  100  183k    0     0   362k      0 --:--:-- --:--:-- --:--:--  363k

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_1.12.0.zip
* DONE (diffcyt)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'diffcyt' successfully unpacked and MD5 sums checked

Tests output

diffcyt.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  10.23    0.89   11.09 

diffcyt.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  11.26    0.50   11.75 

Example timings

diffcyt.Rcheck/examples_i386/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts1.80.22.0
calcMedians1.620.061.69
calcMediansByClusterMarker1.280.001.28
calcMediansBySampleMarker1.160.001.16
createContrast000
createDesignMatrix000
createFormula000
diffcyt8.840.559.40
generateClusters1.030.141.17
plotHeatmap4.990.105.08
prepareData0.030.000.03
testDA_GLMM7.620.157.80
testDA_edgeR1.470.001.47
testDA_voom1.330.021.34
testDS_LMM3.940.013.96
testDS_limma2.190.102.28
topTable4.090.074.17
transformData0.060.000.06

diffcyt.Rcheck/examples_x64/diffcyt-Ex.timings

nameusersystemelapsed
calcCounts2.190.062.25
calcMedians2.190.062.25
calcMediansByClusterMarker1.640.051.69
calcMediansBySampleMarker1.440.021.45
createContrast000
createDesignMatrix0.020.000.01
createFormula000
diffcyt9.570.079.66
generateClusters1.360.021.38
plotHeatmap6.110.086.18
prepareData0.030.000.03
testDA_GLMM9.080.009.08
testDA_edgeR1.670.011.69
testDA_voom1.550.001.55
testDS_LMM5.610.035.64
testDS_limma3.890.003.89
topTable6.570.006.58
transformData0.110.000.11