##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Repitools_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Repitools.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.56.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 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 ... 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: (-1) ChromaResults-class.Rd:25: Lost braces
    25 |     \code{blocks:}{\code{GRanges} of the blocks used across the genome, with their calculated RPKM}
       |                   ^
checkRd: (-1) ChromaResults-class.Rd:26: Lost braces
    26 |     \code{regions:}{\code{IRangesList} of regions determined to be enriched}
       |                    ^
checkRd: (-1) ChromaResults-class.Rd:27: Lost braces
    27 |     \code{FDRTable:}{\code{data.frame} showing the FDR at each cutoff tested}
       |                     ^
checkRd: (-1) ChromaResults-class.Rd:28: Lost braces
    28 |     \code{cutoff:}{The cutoff used to determine enrichment}
       |                   ^
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdjustedCopyEstimate-class.Rd: GRanges-class, GRangesList-class
  BayMethList-class.Rd: GRanges-class
  ClusteredScoresList-class.Rd: GRanges-class
  CopyEstimate-class.Rd: GRanges-class, GRangesList-class
  GCAdjustParams-class.Rd: BSgenome-class
  MappabilitySource-class.Rd: BSgenome-class
  annoDF2GR.Rd: GRanges-class
  featureBlocks.Rd: GRanges-class
  featureScores.Rd: BSgenome-class
  mergeReplicates.Rd: GRangesList-class
  relativeCN.Rd: segment
  samplesList.Rd: GRangesList-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: empBayes
> ### Title: Function to calculate prior parameters using empirical Bayes.
> ### Aliases: empBayes
> ### Keywords: programming
> 
> ### ** 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)
+         bm <- determineOffset(bm)
+  
+         # mask out unannotated high copy number regions
+         # see Pickrell et al. (2011), Bioinformatics 27: 2144-2146.
+ 
+         # should take about 3 minutes for both sample of interests with 2 CPUs.
+         bm <- empBayes(bm, ngroups=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 object is masked from ‘package:utils’:

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
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: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

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

    blocks

CpG density calculated for a sample.


	You provided 1 SssI samples and 2 samples of interest

Offset is determined for sample of interest: 1

Offset is determined for sample of interest: 2


	Information: The program will take advantage of 10 CPUs from total 32
	If you would like to change this please cancel and set explicitly the argument 'ncpus'


Error in .check_ncores(cores) : 10 simultaneous processes spawned
Calls: empBayes -> mclapply -> .check_ncores
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
cpgDensityCalc    8.516  0.373   9.253
BayMethList-class 7.477  0.162   8.311
determineOffset   5.370  0.020   5.946
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Repitools
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Repitools’ ...
** this is package ‘Repitools’ version ‘1.56.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -Werror=format-security -c const.c -o const.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -Werror=format-security -c hyp2f1.c -o hyp2f1.o
hyp2f1.c: In function ‘hyp2f1’:
hyp2f1.c:126:8: warning: old-style function definition [-Wold-style-definition]
  126 | double hyp2f1( a, b, c, x )
      |        ^~~~~~
hyp2f1.c: In function ‘hyt2f1’:
hyp2f1.c:294:9: warning: old-style function definition [-Wold-style-definition]
  294 |  double hyt2f1( a, b, c, x, loss )
      |         ^~~~~~
hyp2f1.c: In function ‘hys2f1’:
hyp2f1.c:438:9: warning: old-style function definition [-Wold-style-definition]
  438 |  double hys2f1( a, b, c, x, loss )
      |         ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function ‘SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)’:
mmeansd.cpp:33:24: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
   33 |     int * x, nval, hs, is, i;
      |                        ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -Werror=format-security -c mtherr.c -o mtherr.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2  -Wall -Werror=format-security -c ringo_stuff.c -o ringo_stuff.o
ringo_stuff.c:13:24: warning: ‘Ringo_calls’ defined but not used [-Wunused-variable]
   13 | static R_CallMethodDef Ringo_calls[] = {
      |                        ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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
Warning in fun(libname, pkgname) :
  Package 'Repitools' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'Repitools' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (Repitools)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> require("Repitools")
Loading required package: Repitools
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

Warning message:
In fun(libname, pkgname) :
  Package 'Repitools' is deprecated and will be removed from Bioconductor
  version 3.23
> 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
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: BiocIO
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")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+     stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+     stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+     stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+     stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
> 
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+     stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
> 
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+     stop("Error in sequenceCalc function counting task")
> 
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+     stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
> 
> proc.time()
   user  system elapsed 
 89.072   2.962 101.218