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CHECK report for scBFA on tokay2

This page was generated on 2020-10-17 11:57:45 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE scBFA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1585/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scBFA 1.2.0
Ruoxin Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/scBFA
Branch: RELEASE_3_11
Last Commit: b42ae7f
Last Changed Date: 2020-04-27 15:28:56 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scBFA
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scBFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings scBFA_1.2.0.tar.gz
StartedAt: 2020-10-17 07:57:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:11:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 809.2 seconds
RetCode: 0
Status:  OK  
CheckDir: scBFA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scBFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings scBFA_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/scBFA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scBFA/DESCRIPTION' ... OK
* this is package 'scBFA' version '1.2.0'
* 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 'scBFA' 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
InitBinaryFA: no visible global function definition for 'as'
diagnose: no visible binding for global variable 'disperPlot'
diagnose: no visible binding for global variable 'fitted_disper'
diagnose: no visible binding for global variable 'dataset_selection'
diagnose: no visible binding for global variable 'variance'
Undefined global functions or variables:
  as dataset_selection disperPlot fitted_disper variance
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
diagnose 5.39   0.23    5.63
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
diagnose 5.17   0.05    5.22
* 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-3.11-bioc/meat/scBFA.Rcheck/00check.log'
for details.



Installation output

scBFA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/scBFA_1.2.0.tar.gz && rm -rf scBFA.buildbin-libdir && mkdir scBFA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scBFA.buildbin-libdir scBFA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL scBFA_1.2.0.zip && rm scBFA_1.2.0.tar.gz scBFA_1.2.0.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
  0  876k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  876k  100  876k    0     0  8932k      0 --:--:-- --:--:-- --:--:-- 9429k

install for i386

* installing *source* package 'scBFA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scBFA'
    finding HTML links ... done
    BinaryPCA                               html  
    InitBinaryFA                            html  
    OptimBFA                                html  
    celltype                                html  
    celltype_toy                            html  
    diagnose                                html  
    disperPlot                              html  
    exprdata                                html  
    getGeneExpr                             html  
    getLoading                              html  
    getScore                                html  
    gradient                                html  
    gradient_chunk                          html  
    neg_loglikelihood                       html  
    neg_loglikelihood_chunk                 html  
    restore                                 html  
    scNoiseSim                              html  
    scbfa                                   html  
    zinb_toy                                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 'scBFA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scBFA' as scBFA_1.2.0.zip
* DONE (scBFA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'scBFA' successfully unpacked and MD5 sums checked

Tests output

scBFA.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(scBFA)
> 
> test_check("scBFA")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.14    1.68   31.10 

scBFA.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(scBFA)
> 
> test_check("scBFA")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.65    0.98   30.15 

Example timings

scBFA.Rcheck/examples_i386/scBFA-Ex.timings

nameusersystemelapsed
BinaryPCA0.840.090.94
diagnose5.390.235.63
getGeneExpr000
getLoading0.460.000.47
getScore0.500.140.64
scNoiseSim0.130.020.14
scbfa2.670.112.78

scBFA.Rcheck/examples_x64/scBFA-Ex.timings

nameusersystemelapsed
BinaryPCA1.720.051.77
diagnose5.170.055.22
getGeneExpr0.020.000.01
getLoading0.490.000.48
getScore0.470.000.47
scNoiseSim0.080.000.08
scbfa3.190.003.19