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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scifer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scifer_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scifer.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scifer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scifer’ version ‘1.9.0’
* package encoding: UTF-8
* 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 ‘scifer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘basilisk::isMacOSX’ by ‘basilisk.utils::isMacOSX’ when loading ‘scifer’
  Warning: replacing previous import ‘basilisk::isMacOSXArm’ by ‘basilisk.utils::isMacOSXArm’ when loading ‘scifer’
  Warning: replacing previous import ‘basilisk::isWindows’ by ‘basilisk.utils::isWindows’ when loading ‘scifer’
Found the following additional notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/scifer.Rcheck/00install.out’ for details.
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New igblast wrapper function to run igblast on fasta sequences
    igblast function returns the output from a local igblast run with any custom database
    New function requires additional steps for ARM processors, please read the README
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘secondary_peaks’
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
quality_report    16.717  0.217  17.049
summarise_quality 14.776  0.052  14.994
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/scifer.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scifer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scifer’ ...
** this is package ‘scifer’ version ‘1.9.0’
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘basilisk::isMacOSX’ by ‘basilisk.utils::isMacOSX’ when loading ‘scifer’
Warning: replacing previous import ‘basilisk::isMacOSXArm’ by ‘basilisk.utils::isMacOSXArm’ when loading ‘scifer’
Warning: replacing previous import ‘basilisk::isWindows’ by ‘basilisk.utils::isWindows’ when loading ‘scifer’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘basilisk::isMacOSX’ by ‘basilisk.utils::isMacOSX’ when loading ‘scifer’
Warning: replacing previous import ‘basilisk::isMacOSXArm’ by ‘basilisk.utils::isMacOSXArm’ when loading ‘scifer’
Warning: replacing previous import ‘basilisk::isWindows’ by ‘basilisk.utils::isWindows’ when loading ‘scifer’
* DONE (scifer)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(scifer)
Warning messages:
1: replacing previous import 'basilisk::isMacOSX' by 'basilisk.utils::isMacOSX' when loading 'scifer' 
2: replacing previous import 'basilisk::isMacOSXArm' by 'basilisk.utils::isMacOSXArm' when loading 'scifer' 
3: replacing previous import 'basilisk::isWindows' by 'basilisk.utils::isWindows' when loading 'scifer' 
> 
> test_check("scifer")


processing file: HC_report.Rmd
2025-03-20 21:24:02.904 R[74043:772531273] XType: Using static font registry.
output file: HC_report.knit.md

/opt/homebrew/bin/pandoc +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpXHvE3I/QC_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXHvE3I/rmarkdown-str1213b6b845c8e.html 

Output created: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpXHvE3I/QC_report.html
[ FAIL 0 | WARN 7 | SKIP 4 | PASS 49 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• This test is not supported on MacOS with arm architecture. (4):
  'test-igblast.R:17:5', 'test-igblast.R:39:5', 'test-igblast.R:65:5',
  'test-igblast.R:75:3'

[ FAIL 0 | WARN 7 | SKIP 4 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 43.276   0.374  43.824