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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqSQC_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqSQC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqSQC/DESCRIPTION’ ... OK
* this is package ‘SeqSQC’ version ‘1.28.0’
* 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 ‘SeqSQC’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’
  Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’
  Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqSQC.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’:
  Cannot process chunk/lines:
    Load benchmark data from ExperimentHub
  Cannot process chunk/lines:
    o added in the R script, will download only once with first time running of the LoadVfile() or sampleQC().
  Cannot process chunk/lines:
    Bioconductor submission check: 
  Cannot process chunk/lines:
    o Added unit test.
  Cannot process chunk/lines:
    o Added a NEWS file to keep track of changes
  Cannot process chunk/lines:
    o Added zzz.R to fix the no visible binding for global functions or variables. 
  Cannot process chunk/lines:
    o Added the "example_sub.vcf" for 1000 lines of variants to run as example in the package vignette.
  Cannot process chunk/lines:
    o Added accessor methods for SeqSQCclass data structure to get the slots of "gdsfile" and "QCresult".
  Cannot process chunk/lines:
    Vignettes: 
  Cannot process chunk/lines:
    o Added bioconductor installation and library load section in the vignette. 
  Cannot process chunk/lines:
    o Added runnable example vcf file added in "inst/extdata/example_sub.vcf", with 1000 lines of variants. 
  Cannot process chunk/lines:
    MAN: 
  Cannot process chunk/lines:
    o added package documentation for dataset, class, methods and constructor.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
LoadVfile  25.644  2.136  29.681
Inbreeding  7.597  0.152   7.794
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqSQC.Rcheck/00check.log’
for details.