##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SeqSQC.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.29.0’
* 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-3.21-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 8.497   0.84   9.961
* 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-3.21-bioc/meat/SeqSQC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqSQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SeqSQC’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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’
** testing if installed package can be loaded from final location
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’
** testing if installed package keeps a record of temporary installation path
* DONE (SeqSQC)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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(SeqSQC)
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: SNPRelate
Loading required package: gdsfmt
Warning messages:
1: replacing previous import 'S4Vectors::rename' by 'plotly::rename' when loading 'SeqSQC' 
2: replacing previous import 'IRanges::slice' by 'plotly::slice' when loading 'SeqSQC' 
3: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'SeqSQC' 
> 
> test_check("SeqSQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  2.298   0.126   2.470