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CHECK report for cellity on tokay1

This page was generated on 2020-08-12 11:44:19 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cellity PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 242/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellity 1.17.0
Tomislav Ilicic
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/cellity
Branch: master
Last Commit: 5a480a2
Last Changed Date: 2020-04-27 14:54:50 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellity
Version: 1.17.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellity.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cellity_1.17.0.tar.gz
StartedAt: 2020-08-12 02:48:09 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 02:54:51 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 401.6 seconds
RetCode: 0
Status:  OK  
CheckDir: cellity.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellity.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cellity_1.17.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/cellity.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cellity' version '1.17.0'
* 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 'cellity' 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
assess_cell_quality_SVM 32.21   0.25   32.48
extract_features         1.78   0.23    6.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
assess_cell_quality_SVM 27.81   0.08   27.89
* 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: OK


Installation output

cellity.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/cellity_1.17.0.tar.gz && rm -rf cellity.buildbin-libdir && mkdir cellity.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellity.buildbin-libdir cellity_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL cellity_1.17.0.zip && rm cellity_1.17.0.tar.gz cellity_1.17.0.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  824k  100  824k    0     0  10.0M      0 --:--:-- --:--:-- --:--:-- 10.5M

install for i386

* installing *source* package 'cellity' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cellity'
    finding HTML links ... done
    assess_cell_quality_PCA                 html  
    assess_cell_quality_SVM                 html  
    cellity-package                         html  
    extra_human_genes                       html  
    extra_mouse_genes                       html  
    extract_features                        html  
    feature_generation                      html  
    feature_info                            html  
    mES1_features                           html  
    mES1_labels                             html  
    multiplot                               html  
    normalise_by_factor                     html  
    param_mES_all                           html  
    param_mES_common                        html  
    plot_pca                                html  
    sample_counts                           html  
    sample_stats                            html  
    simple_cap                              html  
    sum_prop                                html  
    training_mES_features                   html  
    training_mES_labels                     html  
    uni.plot                                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 'cellity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellity' as cellity_1.17.0.zip
* DONE (cellity)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'cellity' successfully unpacked and MD5 sums checked

Tests output

cellity.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(cellity)


sROC 0.1-2 loaded

> 
> test_check("cellity")
[1] "[INFO]:Extracting features"
[1] "[INFO]:Features extracted."
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  34.53    1.09   35.60 

cellity.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(cellity)


sROC 0.1-2 loaded

> 
> test_check("cellity")
[1] "[INFO]:Extracting features"
[1] "[INFO]:Features extracted."
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.53    0.78   46.53 

Example timings

cellity.Rcheck/examples_i386/cellity-Ex.timings

nameusersystemelapsed
assess_cell_quality_PCA0.080.070.14
assess_cell_quality_SVM32.21 0.2532.48
extract_features1.780.236.75
normalise_by_factor0.030.000.03

cellity.Rcheck/examples_x64/cellity-Ex.timings

nameusersystemelapsed
assess_cell_quality_PCA0.10.00.1
assess_cell_quality_SVM27.81 0.0827.89
extract_features1.300.121.42
normalise_by_factor0.030.000.03