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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:breakpointR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings breakpointR_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/breakpointR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘breakpointR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘breakpointR’ version ‘1.17.0’
* 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 ‘breakpointR’ 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 loading without being on the library search path ... 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
genotyping         15.530  0.207  15.743
hotspotter          7.515  0.187   7.712
synchronizeReadDir  5.636  0.051   5.687
exportRegions       2.757  1.426   5.829
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘breakpointR.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘breakpointR.Rnw’ using knitr
breakpointr            package:breakpointR             R Documentation

_M_a_i_n _f_u_n_c_t_i_o_n _f_o_r _t_h_e '_b_r_e_a_k_p_o_i_n_t_R' _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function is an easy-to-use wrapper to find breakpoints with
     'runBreakpointr' in parallel, write the results to file, plot
     results and find hotspots.

_U_s_a_g_e:

     breakpointr(
       inputfolder,
       outputfolder,
       configfile = NULL,
       numCPU = 1,
       reuse.existing.files = FALSE,
       windowsize = 1e+06,
       binMethod = "size",
       multi.sizes = NULL,
       pairedEndReads = FALSE,
       pair2frgm = FALSE,
       chromosomes = NULL,
       min.mapq = 10,
       filtAlt = FALSE,
       genoT = "fisher",
       trim = 10,
       peakTh = 0.33,
       zlim = 3.291,
       background = 0.05,
       minReads = 10,
       maskRegions = NULL,
       callHotSpots = FALSE,
       conf = 0.99
     )
     
_A_r_g_u_m_e_n_t_s:

inputfolder: Folder with BAM files.

outputfolder: Folder to output the results. If it does not exist it
          will be created.

configfile: A file specifying the parameters of this function (without
          'inputfolder', 'outputfolder' and 'configfile'). Having the
          parameters in a file can be handy if many samples with the
          same parameter settings are to be run. If a 'configfile' is
          specified, it will take priority over the command line
          parameters.

  numCPU: The numbers of CPUs that are used. Should not be more than
          available on your machine.

reuse.existing.files: A logical indicating whether or not existing
          files in 'outputfolder' should be reused.

windowsize: The window size used to calculate deltaWs, either number of
          reads or genomic size depending on 'binMethod'.

binMethod: Method used to calculate optimal number of reads in the
          window ("size", "reads"). By default 'binMethod='size''.

multi.sizes: User defined multiplications of the original window size.

pairedEndReads: Set to 'TRUE' if you have paired-end reads in your
          file.

pair2frgm: Set to 'TRUE' if every paired-end read should be merged into
          a single fragment.

chromosomes: If only a subset of the chromosomes should be binned,
          specify them here.

min.mapq: Minimum mapping quality when importing from BAM files.

 filtAlt: Set to 'TRUE' if you want to filter out alternative
          alignments defined in 'XA' tag.

   genoT: A method ('fisher' or 'binom') to genotype regions defined by
          a set of breakpoints.

    trim: The amount of outliers in deltaWs removed to calculate the
          stdev (10 will remove top 10% and bottom 10% of deltaWs).

  peakTh: The treshold that the peak deltaWs must pass to be considered
          a breakpoint (e.g. 0.33 is 1/3 of max(deltaW)).

    zlim: The number of stdev that the deltaW must pass the peakTh
          (ensures only significantly higher peaks are considered).

background: The percent (e.g. 0.05 = 5%) of background reads allowed
          for WW or CC genotype calls.

minReads: The minimal number of reads between two breaks required for
          genotyping.

maskRegions: List of regions to be excluded from the analysis
          (tab-separated file: chromosomes start end).

callHotSpots: Search for regions of high abundance of breakpoints in
          single cells.

    conf: Desired confidence interval of localized breakpoints.

_V_a_l_u_e:

     'NULL'

_A_u_t_h_o_r(_s):

     David Porubsky, Aaron Taudt, Ashley Sanders

_E_x_a_m_p_l_e_s:

     ## Not run:
     
     ## The following call produces plots and genome browser files for all BAM files in "my-data-folder"
     breakpointr(inputfolder="my-data-folder", outputfolder="my-output-folder")
     ## End(Not run)
     

Killed

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/breakpointR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL breakpointR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘breakpointR’ ...
** using staged installation
** R
** 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 (breakpointR)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(breakpointR)
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: cowplot
Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 21.014   1.149  22.204