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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1824/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scBFA 1.14.0  (landing page)
Ruoxin Li
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/scBFA
git_branch: RELEASE_3_17
git_last_commit: c3759a5
git_last_commit_date: 2023-04-25 11:11:32 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for scBFA on kjohnson2


To the developers/maintainers of the scBFA package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: scBFA
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBFA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBFA_1.14.0.tar.gz
StartedAt: 2023-10-18 21:50:51 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 22:00:44 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 592.9 seconds
RetCode: 0
Status:   OK  
CheckDir: scBFA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBFA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBFA_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scBFA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBFA/DESCRIPTION’ ... OK
* this is package ‘scBFA’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
diagnose 5.55  0.152  10.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scBFA.Rcheck/00check.log’
for details.



Installation output

scBFA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scBFA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* 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
** 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
* DONE (scBFA)

Tests output

scBFA.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> test_check("scBFA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 15.837   0.989  30.098 

Example timings

scBFA.Rcheck/scBFA-Ex.timings

nameusersystemelapsed
BinaryPCA1.7560.0583.252
diagnose 5.550 0.15210.089
getGeneExpr0.0010.0000.002
getLoading0.3880.0050.710
getScore0.3600.0040.654
scNoiseSim0.1680.0040.288
scbfa2.4010.0444.386