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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DEScan2_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEScan2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEScan2’ version ‘1.22.0’
* 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 ‘DEScan2’ can be installed ... WARNING
Found the following significant warnings:
  Warning: saveGRangesAsTsv.Rd:34: unknown macro '\t'
See ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... NOTE
.addScoreCol: no visible global function definition for ‘mcols<-’
Undefined global functions or variables:
  mcols<-
* checking Rd files ... WARNING
prepare_Rd: saveGRangesAsTsv.Rd:34: unknown macro '\t'
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DEScan2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binnedCoverage
> ### Title: binnedCoverage
> ### Aliases: binnedCoverage
> 
> ### ** Examples
> 
> ## dividing one chromosome in bins of 50 bp each
> seqinfo <- GenomeInfoDb::Seqinfo(genome="mm9")
> bins <- GenomicRanges::tileGenome(
+             seqlengths=GenomeInfoDb::seqlengths(seqinfo)[1],
+             tilewidth=50,
+             cut.last.tile.in.chrom=TRUE)
> gr <- GenomicRanges::GRanges(seqnames = S4Vectors::Rle("chr1", 100),
+             ranges=IRanges::IRanges(start = seq(from=10, to=1000, by=10),
+             end=seq(from=20, to=1010, by = 10)))
> cov <- GenomicRanges::coverage(x=gr)
> (binnedMaxCovGR <- binnedCoverage(bins, cov, "binned_cov"))
GRanges object with 3943909 ranges and 1 metadata column:
            seqnames              ranges strand |  binned_cov
               <Rle>           <IRanges>  <Rle> |   <integer>
        [1]     chr1                1-50      * |           2
        [2]     chr1              51-100      * |           2
        [3]     chr1             101-150      * |           2
        [4]     chr1             151-200      * |           2
        [5]     chr1             201-250      * |           2
        ...      ...                 ...    ... .         ...
  [3943905]     chr1 197195201-197195250      * | -2147483647
  [3943906]     chr1 197195251-197195300      * | -2147483647
  [3943907]     chr1 197195301-197195350      * | -2147483647
  [3943908]     chr1 197195351-197195400      * | -2147483647
  [3943909]     chr1 197195401-197195432      * | -2147483647
  -------
  seqinfo: 1 sequence from an unspecified genome
> (binnedMeanCovGR <- binnedCoverage(bins, cov, "binned_cov",
+                                 covMethod="mean", roundingMethod="floor"))
GRanges object with 3943909 ranges and 1 metadata column:
            seqnames              ranges strand | binned_cov
               <Rle>           <IRanges>  <Rle> |  <numeric>
        [1]     chr1                1-50      * |          0
        [2]     chr1              51-100      * |          1
        [3]     chr1             101-150      * |          1
        [4]     chr1             151-200      * |          1
        [5]     chr1             201-250      * |          1
        ...      ...                 ...    ... .        ...
  [3943905]     chr1 197195201-197195250      * |        NaN
  [3943906]     chr1 197195251-197195300      * |        NaN
  [3943907]     chr1 197195301-197195350      * |        NaN
  [3943908]     chr1 197195351-197195400      * |        NaN
  [3943909]     chr1 197195401-197195432      * |        NaN
  -------
  seqinfo: 1 sequence from an unspecified genome
> (binnedSumCovGR <- binnedCoverage(bins, cov, "binned_cov", covMethod="sum"))
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. └─DEScan2::findPeaks(...) at testPeaks.R:27:8
    2.   ├─GenomicRanges::GRangesList(...)
    3.   ├─BiocParallel::bplapply(...)
    4.   └─BiocParallel::bplapply(...)
    5.     └─BiocParallel:::.bpinit(...)
    6.       ├─BiocParallel::bploop(...)
    7.       └─BiocParallel:::bploop.lapply(...)
    8.         └─BiocParallel:::.bploop_impl(...)
    9.           └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
   10.             ├─BiocParallel:::.reducer_add(reducer, njob, value)
   11.             └─BiocParallel:::.reducer_add(reducer, njob, value)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL DEScan2
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘DEScan2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c rcpparma_max_win.cpp -o rcpparma_max_win.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o DEScan2.so RcppExports.o rcpparma_max_win.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-DEScan2/00new/DEScan2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: saveGRangesAsTsv.Rd:34: unknown macro '\t'
*** 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 (DEScan2)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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("DEScan2")
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 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: GenomeInfoDb
> 
> test_check("DEScan2")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 4 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testPeaks.R:27:9'): Test if new findPeaks works with bam and bed files ──
Error in `reducer$value.cache[[as.character(idx)]] <- values`: wrong args for environment subassignment
Backtrace:
     ▆
  1. └─DEScan2::findPeaks(...) at testPeaks.R:27:8
  2.   ├─GenomicRanges::GRangesList(...)
  3.   ├─BiocParallel::bplapply(...)
  4.   └─BiocParallel::bplapply(...)
  5.     └─BiocParallel:::.bpinit(...)
  6.       ├─BiocParallel::bploop(...)
  7.       └─BiocParallel:::bploop.lapply(...)
  8.         └─BiocParallel:::.bploop_impl(...)
  9.           └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 10.             ├─BiocParallel:::.reducer_add(reducer, njob, value)
 11.             └─BiocParallel:::.reducer_add(reducer, njob, value)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 4 ]
Error: Test failures
Execution halted