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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SeqSQC_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SeqSQC.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SeqSQC/DESCRIPTION’ ... OK
* this is package ‘SeqSQC’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
 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 ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SeqSQC’
  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 ‘/home/biocbuild/bbs-3.22-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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘SeqSQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LoadVfile
> ### Title: Data preprocessing for VCF or plink input from NGS or GWAS data.
> ### Aliases: LoadVfile
> 
> ### ** Examples
> 
> infile <- system.file("extdata", "example_sub.vcf", package="SeqSQC")
> sample.annot <- system.file("extdata", "sampleAnnotation.txt", package="SeqSQC")
> cr <- system.file("extdata", "CCDS.Hs37.3.reduced_chr1.bed", package="SeqSQC")
> outfile <- file.path(tempdir(), "testWrapUp")
> seqfile <- LoadVfile(vfile = infile, output = outfile, capture.region = cr,
+ sample.annot = sample.annot)
Load vcf file ...
Start file conversion from VCF to SNP GDS ...
Method: extracting biallelic SNPs
Number of samples: 5
Parsing "/home/biocbuild/bbs-3.22-bioc/R/site-library/SeqSQC/extdata/example_sub.vcf" ...
	import 1000 variants.
+ genotype   { Bit2 5x1000, 1.2K } *
SNP genotypes: 5 samples, 1000 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpyTwRdj/filef5cf81c367fbe' (12.4K)
    # of fragments: 48
    save to '/tmp/RtmpyTwRdj/filef5cf81c367fbe.tmp'
    rename '/tmp/RtmpyTwRdj/filef5cf81c367fbe.tmp' (10.7K, reduced: 1.6K)
    # of fragments: 20
Load study cohort annotation file ...
Load 1kg data to temp directory...
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: LoadVfile ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from vignette.Rmd:71-73 [loadVfile]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─SeqSQC::LoadVfile(...)
 2.   └─ExperimentHub::ExperimentHub()
 3.     └─AnnotationHub::.Hub(...)
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SeqSQC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SeqSQC
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SeqSQC’ ...
** this is package ‘SeqSQC’ version ‘1.32.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SeqSQC’
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 ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SeqSQC’
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 ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SeqSQC’
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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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(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
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Warning messages:
1: replacing previous import 'e1071::element' by 'ggplot2::element' when loading 'SeqSQC' 
2: replacing previous import 'S4Vectors::rename' by 'plotly::rename' when loading 'SeqSQC' 
3: replacing previous import 'IRanges::slice' by 'plotly::slice' when loading 'SeqSQC' 
4: 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 
  5.533   0.332   5.855