Mac ARM64 build report for BioC 3.17 - CHECK results for scTGIF on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (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: scTGIF

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTGIF_1.14.0.tar.gz

StartedAt: 2023-10-18 23:33:38 -0400 (Wed, 18 Oct 2023)

EndedAt: 2023-10-18 23:44:08 -0400 (Wed, 18 Oct 2023)

EllapsedTime: 629.7 seconds

RetCode: 0

Status: OK

CheckDir: scTGIF.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTGIF_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scTGIF.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 ‘scTGIF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTGIF’ version ‘1.14.0’
* 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-3.17-bioc-mac-arm64/meat/scTGIF.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scTGIF
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)


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("scTGIF")
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)
> 
> 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 3 | WARN 0 | SKIP 0 | PASS 5 ]

── 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 

── Error ('test_convertRowID.R:53:1'): (code run outside of `test_that()`) ─────
Error in `i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value, 
    "value"), check = FALSE)`: Length of new attribute value must be 1 or 5, the number of target edges, not 4
Backtrace:
    ▆
 1. └─scTGIF::convertRowID(input, rowID, LtoR, "large.mean") at test_convertRowID.R:53:0
 2.   └─scTGIF (local) f(input, rowID, LtoR, score, unique.right)
 3.     └─igraph::`E<-`(`*tmp*`, value = `*vtmp*`)
 4.       └─igraph:::i_set_edge_attr(...)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ]
> 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) at 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) at 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) at 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) at test_cellMarkerToGmt.R:141:0
 2.   └─GSEABase:::.warningf(...)

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 18.332   1.208  34.715

name	user	system	elapsed
DistalLungEpithelium	0.019	0.002	0.031
calcTGIF	0.003	0.000	0.007
cellMarkerToGmt	0.352	0.024	0.658
convertRowID	0.032	0.010	0.106
label.DistalLungEpithelium	0.001	0.002	0.004
pca.DistalLungEpithelium	0.001	0.001	0.002
reportTGIF	0.008	0.001	0.014
settingTGIF	0.001	0.000	0.005

CHECK results for scTGIF on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings