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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NADfinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NADfinder_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NADfinder.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 ‘NADfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NADfinder’ version ‘1.23.0’
* 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 ‘NADfinder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   5.0Mb
* 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 ... WARNING
Killed

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NADfinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callPeaks
> ### Title: Call peaks using transformed, background corrected, and smoothed
> ###   ratios with biological replicates
> ### Aliases: callPeaks
> 
> ### ** Examples
> 
> 
> data(triplicate.count)
> se <- triplicate.count
> se <- log2se(se, transformation = "log2CPMRatio",
+              nucleolusCols = c("N18.subsampled.srt-2.bam",
+              "N18.subsampled.srt-3.bam",
+              "N18.subsampled.srt.bam"),
+              genomeCols = c("G18.subsampled.srt-2.bam",
+              "G18.subsampled.srt-3.bam",
+              "G18.subsampled.srt.bam"))
> se<- smoothRatiosByChromosome(se, chr="chr18")
> #add some variability to the data since the triplicate.count data was created using one sample only
> assays(se[[1]])$bcRatio[,2] <- assays(se[[1]])$bcRatio[,2] + 0.3
> assays(se[[1]])$bcRatio[,3] <- assays(se[[1]])$bcRatio[,3] - 0.3
> peaks <- callPeaks(se[[1]],
+                 cutoffAdjPvalue=0.001, countFilter=10)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  3.9639e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  1.1219e-16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.935
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 8.065
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 25
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 0.95
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  pseudoinverse used at 11.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  neighborhood radius 6.05
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  :
  There are other near singularities as well. 16
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘NADfinder.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘NADfinder.Rmd’ using rmarkdown
Killed

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

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/NADfinder.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NADfinder
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘NADfinder’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (NADfinder)

R Under development (unstable) (2023-01-14 r83615) -- "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.

> require("NADfinder") || stop("unable to load Package:NADfinder")
Loading required package: NADfinder
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: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians


[1] TRUE
> require("SummarizedExperiment") || 
+     stop("unable to load Package:SummarizedExperiment")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> 
> #test_check("NADfinder")
> 
> proc.time()
   user  system elapsed 
 27.646   1.077  29.741