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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Repitools_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Repitools.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 ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ 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 ‘Repitools’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... 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 ... WARNING
checkRd: (5) AdjustedCopyEstimate-class.Rd:16-34: \item in \describe must have non-empty label
checkRd: (5) BayMethList-class.Rd:58-88: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:29-50: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:57-60: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:61-64: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) ClusteredScoresList-class.Rd:75-78: \item in \describe must have non-empty label
checkRd: (5) CopyEstimate-class.Rd:14-23: \item in \describe must have non-empty label
checkRd: (5) GCAdjustParams-class.Rd:14-37: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:24-27: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:28-31: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:42-45: \item in \describe must have non-empty label
checkRd: (5) ScoresList-class.Rd:46-49: \item in \describe must have non-empty label
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Repitools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BayMethList
> ### Title: Class '"BayMethList"'
> ### Aliases: BayMethList BayMethList-class
> ###   BayMethList,GRanges,matrix,matrix,numeric-method
> ###   [,BayMethList,ANY,missing,ANY-method length length,BayMethList-method
> ###   control control<- control,BayMethList-method
> ###   control<-,BayMethList-method cpgDens cpgDens<-
> ###   cpgDens,BayMethList-method cpgDens<-,BayMethList-method
> ###   sampleInterest sampleInterest<- sampleInterest,BayMethList-method
> ###   sampleInterest<-,BayMethList-method show,BayMethList-method windows
> ###   windows<- windows,BayMethList-method windows<-,BayMethList-method
> ###   fOffset fOffset<- fOffset,BayMethList-method
> ###   fOffset<-,BayMethList-method priorTab priorTab<-
> ###   priorTab,BayMethList-method priorTab<-,BayMethList-method methEst
> ###   methEst<- methEst,BayMethList-method methEst<-,BayMethList-method
> ###   maskEmpBayes maskEmpBayes<- maskEmpBayes,BayMethList-method
> ###   maskEmpBayes<-,BayMethList-method ncontrol
> ###   ncontrol,BayMethList-method nsampleInterest
> ###   nsampleInterest,BayMethList-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>     if(require(BSgenome.Hsapiens.UCSC.hg18)){
+         windows <- genomeBlocks(Hsapiens, chrs="chr21", width=100, spacing=100)
+         cpgdens <- cpgDensityCalc(windows, organism=Hsapiens,  
+             w.function="linear", window=700)  
+         co <- matrix(rnbinom(length(windows), mu=10, size=2), ncol=1)
+         sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
+         bm <- BayMethList(windows=windows, control=co, sampleInterest=sI,
+             cpgDens=cpgdens)
+ 
+         cat("Number of genomic regions", length(bm), "\n")
+         cat("Number of fully methylated control samples:", ncontrol(bm), "\n")
+         cat("Number of samples of interest:", nsampleInterest(bm), "\n")
+         bm[2:20]
+     }
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
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: GenomeInfoDb
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: rtracklayer

Attaching package: ‘rtracklayer’

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

    blocks

Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’
 ERROR
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  > correctLookupTable[1, c(50, 51)] <- 1
  > correctLookupTable[1, c(60, 61)] <- 4
  > correctLookupTable[2, c(90, 91)] <- 2
  > correctLookupTable[4, c(45, 46)] <- 1
  > correctLookupTable[4, c(55, 56)] <- 4
  > correctLookupTable[6, c(49, 50)] <- 6
  > correctLookupTable[6, c(51, 52)] <- 7
  > 
  > if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
  +     stop("Error in makeWindowLookupTable function")
  > cat("makeWindowLookupTable tested fine.\n")
  makeWindowLookupTable tested fine.
  > 
  > cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Repitools_vignette.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Repitools
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Repitools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -c const.c -o const.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -c hyp2f1.c -o hyp2f1.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -c mtherr.c -o mtherr.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-Repitools/00new/Repitools/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Repitools)

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("Repitools")
Loading required package: Repitools
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

> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
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: GenomeInfoDb
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: rtracklayer

Attaching package: 'rtracklayer'

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

    blocks

> options(warn = -1)
> 
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
> 
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
> 
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) 
+ 	stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
> 
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
> 
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+     stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
> 
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
Killed