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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReQON.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ReQON_1.45.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReQON.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ReQON/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReQON’ version ‘1.45.0’
* 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 ‘ReQON’ can be installed ... OK
* 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 ... OK
* checking R 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
Packages in Depends field not imported from:
  ‘Rsamtools’ ‘seqbias’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FWSEplot: no visible global function definition for ‘title’
FWSEplot: no visible global function definition for ‘rgb’
FWSEplot: no visible global function definition for ‘points’
QualFreqPlot: no visible global function definition for ‘title’
ReQON: no visible global function definition for ‘glm.fit’
ReQON: no visible global function definition for ‘binomial’
ReadPosErrorPlot: no visible global function definition for ‘title’
Undefined global functions or variables:
  binomial glm.fit points rgb title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "points", "title")
  importFrom("stats", "binomial", "glm.fit")
to your NAMESPACE file.
* 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 ‘ReQON-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ReQON
> ### Title: Recalibrating Quality Of Nucleotides
> ### Aliases: ReQON
> 
> ### ** Examples
> 
> ## Read in sample data from seqbias package
> library( ReQON )
> library( seqbias )
> library( Rsamtools )
> ref_fn <- system.file( "extra/example.fa", package = "seqbias" )
> ref_f <- FaFile( ref_fn )
> open.FaFile( ref_f )
> reads_fn <- system.file( "extra/example.bam", package = "seqbias" )
> 
> ## Set up file of reference sequence
> seqs <- scanFa( ref_f )
> len <- length( seqs[[1]] )
> ref <- matrix( nrow = len, ncol = 3 )
> ref[,1] <- rep( "seq1", len )
> ref[,2] <- c( 1:len )
> str <- toString( subseq( seqs[[1]], 1, len ) )
> s <- strsplit( str, NULL )
> ref[,3] <- s[[1]]
> write.table( ref, file = "ref_seq.txt", sep = "\t", quote = FALSE,
+    row.names = FALSE, col.names = FALSE )
> 
> ## Recalibrate File
> sorted <- sortBam( reads_fn, tempfile() )
> indexBam( sorted )
      /tmp/Rtmp71hRRf/file3c1a4646c9dbc5.bam 
"/tmp/Rtmp71hRRf/file3c1a4646c9dbc5.bam.bai" 
> reg <- paste( "seq1:1-", len, sep = "" )
> diagnostics <- ReQON( sorted, "Recalibrated_example.bam", reg, 
+    RefSeq = "ref_seq.txt", nerr = 20, nraf = 0.25, 
+    plotname = "Recalibrated_example_plots.pdf" )

Start time: Tue Feb  7 13:14:07 2023


Reading in bam file
[Tue Feb 07 13:14:09 UTC 2023] org.renci.sequencing.util.BAMUnpacker done
Runtime.totalMemory()=262144000

Number of bases in training set: 496485

Determining Sequencing Errors 

Training set error rate = 0.04211

Number of bases in filtered training set: 488070

Calculating Training Parameters 

Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ReQON.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘ReQON.Rnw’
  ...

Training set error rate = 0.04211

Number of bases in filtered training set: 488070

Calculating Training Parameters 

Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘ReQON.Rnw’ using Sweave
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: seqbias

Start time: Tue Feb  7 13:15:22 2023


Reading in bam file
[Tue Feb 07 13:15:25 UTC 2023] org.renci.sequencing.util.BAMUnpacker done
Runtime.totalMemory()=262144000

Number of bases in training set: 496485

Determining Sequencing Errors 

Training set error rate = 0.04211

Number of bases in filtered training set: 488070

Calculating Training Parameters 

Killed

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

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ReQON.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ReQON
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ReQON’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ReQON)