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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scifer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings scifer_1.10.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/scifer.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scifer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scifer' version '1.10.0'
* 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 whether package 'scifer' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'E:/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     64.80   1.07   69.11
summarise_quality  59.42   0.23   59.79
secondary_peaks    20.36   0.15   23.43
summarise_abi_file 18.58   0.10   18.68
* 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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/scifer.Rcheck/00check.log'
for details.

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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL scifer
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'scifer' ...
** this is package 'scifer' version '1.10.0'
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scifer)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
> 
> test_check("scifer")


processing file: HC_report.Rmd
output file: HC_report.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc1144439206f83.html --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "E:\biocbuild\bbs-3.21-bioc\R\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 "E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpWo8acx\rmarkdown-str11444ac92434.html" 

Output created: E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpWo8acx/QC_report.html
[ FAIL 0 | WARN 11 | SKIP 4 | PASS 49 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Windows (4): 'test-igblast.R:21:9', 'test-igblast.R:43:9',
  'test-igblast.R:69:9', 'test-igblast.R:79:9'

[ FAIL 0 | WARN 11 | SKIP 4 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 181.95    2.62  187.98