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CHECK report for scTensor on merida1

This page was generated on 2021-05-06 12:36:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the scTensor package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1663/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 2.0.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scTensor
Branch: RELEASE_3_12
Last Commit: 0fafdd3
Last Changed Date: 2020-10-27 11:40:50 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: scTensor
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTensor_2.0.0.tar.gz
StartedAt: 2021-05-06 06:02:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:13:59 -0400 (Thu, 06 May 2021)
EllapsedTime: 686.9 seconds
RetCode: 0
Status:   OK  
CheckDir: scTensor.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTensor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTensor_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/scTensor.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scTensor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTensor’ version ‘2.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scTensor’ 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
.simulateDropoutCounts: no visible binding for global variable 'v'
.simulateDropoutCounts: no visible binding for global variable 'm'
Undefined global functions or variables:
  m v
* 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 ... OK
* 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-3.12-bioc/meat/scTensor.Rcheck/00check.log’
for details.



Installation output

scTensor.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scTensor
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘scTensor’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'show' in package 'scTensor'
** 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 (scTensor)

Tests output

scTensor.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("scTensor")


> 
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_GermMale.R")

══ Testing test_GermMale.R ═════════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

── Failure (test_GermMale.R:5:1): (code run outside of `test_that()`) ──────────
dim(GermMale) not equivalent to c(2547, 852).
1/2 mismatches
[1] 242 - 2547 == -2305


[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
> test_file("testthat/test_tsneGermMale.R")

══ Testing test_tsneGermMale.R ═════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
> test_file("testthat/test_labelGermMale.R")

══ Testing test_labelGermMale.R ════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
> test_file("testthat/test_cellCellFunctions.R")

══ Testing test_cellCellFunctions.R ════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 3 ]

── Failure (test_cellCellFunctions.R:21:1): (code run outside of `test_that()`) ──
is.null(metadata(sce)$lrbase) is not FALSE

`actual`:   TRUE 
`expected`: FALSE

── Failure (test_cellCellFunctions.R:22:1): (code run outside of `test_that()`) ──
is.null(metadata(sce)$color) is not FALSE

`actual`:   TRUE 
`expected`: FALSE

── Failure (test_cellCellFunctions.R:23:1): (code run outside of `test_that()`) ──
is.null(metadata(sce)$label) is not FALSE

`actual`:   TRUE 
`expected`: FALSE


[ FAIL 3 | WARN 0 | SKIP 0 | PASS 3 ]
> test_file("testthat/test_CCSParamsFunctions.R")

══ Testing test_CCSParamsFunctions.R ═══════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] Done!
> 
> proc.time()
   user  system elapsed 
 30.958   3.714  36.184 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.0640.0030.066
cellCellDecomp0.0030.0010.004
cellCellRanks0.0010.0010.002
cellCellReport0.0110.0020.014
cellCellSetting0.0020.0010.002
cellCellSimulate0.0010.0010.001
convertToNCBIGeneID0.0010.0010.001
getParam0.0010.0010.003
labelGermMale0.0030.0020.005
m0.0030.0020.006
newCCSParams000
scTensor-package0.0000.0010.001
setParam0.0050.0010.006
tsneGermMale0.0020.0020.003
v0.0020.0010.004