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CHECK report for scTGIF on merida1

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

To the developers/maintainers of the scTGIF package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1664/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scTGIF 1.4.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scTGIF
Branch: RELEASE_3_12
Last Commit: f21027e
Last Changed Date: 2020-10-27 11:51:21 -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: scTGIF
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTGIF_1.4.0.tar.gz
StartedAt: 2021-05-06 06:03:47 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:09:35 -0400 (Thu, 06 May 2021)
EllapsedTime: 347.8 seconds
RetCode: 0
Status:   OK  
CheckDir: scTGIF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scTGIF_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/scTGIF.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 ‘scTGIF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTGIF’ version ‘1.4.0’
* 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 ‘scTGIF’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘schex:::.make_hexbin_function’
  See the note in ?`:::` about the use of this operator.
* 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 ... 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/scTGIF.Rcheck/00check.log’
for details.

Installation output

scTGIF.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘scTGIF’ ...
** using staged installation
** R
** data
** inst
** 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 (scTGIF)

Tests output

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

══ Testing test_DistalLungEpithelium.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 ] Done!
> test_file("testthat/test_TGIFFunctions.R")

══ Testing test_TGIFFunctions.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 ] Done!
> test_file("testthat/test_convertRowID.R")

══ Testing test_convertRowID.R ═════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
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[ 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 ]
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[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
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[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 5 ]
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 6 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 6 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 7 ]
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[ FAIL 3 | WARN 3 | SKIP 0 | PASS 8 ]
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[ FAIL 3 | WARN 3 | SKIP 0 | PASS 9 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 10 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 11 ]
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 12 ]
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[ FAIL 4 | WARN 3 | SKIP 0 | PASS 12 ]
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[ FAIL 5 | WARN 3 | SKIP 0 | PASS 12 ]
[ FAIL 5 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 5 | SKIP 0 | PASS 12 ]
[ FAIL 6 | WARN 5 | SKIP 0 | PASS 13 ]
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 13 ]
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 14 ]

── Failure (test_convertRowID.R:48:1): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Failure (test_convertRowID.R:51:1): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning (test_convertRowID.R:53:1): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.mean") test_convertRowID.R:53:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure (test_convertRowID.R:54:1): (code run outside of `test_that()`) ─────
identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning (test_convertRowID.R:56:1): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.var") test_convertRowID.R:56:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Warning (test_convertRowID.R:59:1): (code run outside of `test_that()`) ─────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.cv2") test_convertRowID.R:59:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure (test_convertRowID.R:112:1): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Failure (test_convertRowID.R:115:1): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning (test_convertRowID.R:117:1): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.mean") test_convertRowID.R:117:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Failure (test_convertRowID.R:118:1): (code run outside of `test_that()`) ────
identical(rownames(out$output), c("5", "2", "7")) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

── Warning (test_convertRowID.R:120:1): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.var") test_convertRowID.R:120:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)

── Warning (test_convertRowID.R:123:1): (code run outside of `test_that()`) ────
number of items to replace is not a multiple of replacement length
Backtrace:
 1. scTGIF::convertRowID(input, rowID, LtoR, "large.cv2") test_convertRowID.R:123:0
 2. scTGIF:::f(input, rowID, LtoR, score, unique.right)
 3. igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4. igraph:::i_set_edge_attr(...)


[ FAIL 6 | WARN 6 | SKIP 0 | PASS 14 ]
> test_file("testthat/test_cellMarkerToGmt.R")

══ Testing test_cellMarkerToGmt.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 2 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 5 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 10 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 13 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]

── Warning (test_cellMarkerToGmt.R:134:1): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Meniscus
Backtrace:
 1. GSEABase::getGmt(outfile2_1) test_cellMarkerToGmt.R:134:0
 2. GSEABase:::.warningf(...)

── Warning (test_cellMarkerToGmt.R:135:1): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Meniscus
Backtrace:
 1. GSEABase::getGmt(outfile2_2) test_cellMarkerToGmt.R:135:0
 2. GSEABase:::.warningf(...)

── Warning (test_cellMarkerToGmt.R:140:1): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Pancreas
Backtrace:
 1. GSEABase::getGmt(outfile3_1) test_cellMarkerToGmt.R:140:0
 2. GSEABase:::.warningf(...)

── Warning (test_cellMarkerToGmt.R:141:1): (code run outside of `test_that()`) ──
1 record(s) contain duplicate ids: Pancreas
Backtrace:
 1. GSEABase::getGmt(outfile3_2) test_cellMarkerToGmt.R:141:0
 2. GSEABase:::.warningf(...)


[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 18.946   1.779  20.786

Example timings

scTGIF.Rcheck/scTGIF-Ex.timings

nameusersystemelapsed
DistalLungEpithelium0.0310.0040.036
calcTGIF0.0030.0010.004
cellMarkerToGmt0.4050.0420.447
convertRowID0.0370.0130.050
label.DistalLungEpithelium0.0020.0010.002
pca.DistalLungEpithelium0.0010.0010.002
reportTGIF0.0190.0020.020
settingTGIF0.0010.0010.001