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

CHECK results for scTensor on nebbiolo1

To the developers/maintainers of the scTensor package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTensor.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1718/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTensor 2.2.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/scTensor
git_branch: RELEASE_3_13
git_last_commit: adb0ecb
git_last_commit_date: 2021-05-19 12:39:42 -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: scTensor
Version: 2.2.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scTensor_2.2.0.tar.gz
StartedAt: 2021-09-14 11:33:21 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 11:41:22 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 481.7 seconds
RetCode: 0
Status:   OK  
CheckDir: scTensor.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings scTensor_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/scTensor.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘2.2.0’
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/scTensor.Rcheck/00check.log’
for details.



Installation output

scTensor.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL scTensor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 3 ]

── Warning (test_cellCellFunctions.R:4:1): (code run outside of `test_that()`) ──
Package 'LRBase.Hsa.eg.db' is deprecated and will be removed from
  Bioconductor version 3.14. For details, check the vignette of
  'AHLRBaseDbs'.
Backtrace:
  1. base::library(LRBase.Hsa.eg.db) test_cellCellFunctions.R:4:0
  6. base::attachNamespace(ns, pos = pos, deps, exclude, include.only)
  7. base:::runHook(".onAttach", ns, dirname(nspath), nsname)
 12. LRBase.Hsa.eg.db:::fun(libname, pkgname)
 13. base::.Deprecated(msg = paste(strwrap(msg, exdent = 2), collapse = "\n"))

── 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 1 | 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 
 25.366   2.843  28.017 

Example timings

scTensor.Rcheck/scTensor-Ex.timings

nameusersystemelapsed
GermMale0.0130.0000.013
cellCellDecomp0.0030.0000.003
cellCellRanks0.0010.0000.001
cellCellReport0.0030.0000.004
cellCellSetting0.0010.0000.001
cellCellSimulate0.0010.0000.001
convertToNCBIGeneID0.0010.0010.001
getParam0.0000.0020.002
labelGermMale0.0010.0000.002
m0.0020.0000.002
newCCSParams0.0000.0000.001
scTensor-package0.0000.0000.001
setParam0.0020.0000.002
tsneGermMale0.0020.0000.001
v0.0010.0020.002