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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scTGIF_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scTGIF.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘scTGIF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTGIF’ version ‘1.20.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scTGIF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scTGIF
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 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:53:1
 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:134:1
 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:135:1
 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:140:1
 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:141:1
 2.   └─GSEABase:::.warningf(...)

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 12.991   0.840  13.829