##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bsseq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings bsseq_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/bsseq.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.44.0'
* 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 whether package 'bsseq' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking C++ specification ... 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 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots'
  'DelayedArray:::get_verbose_block_processing'
  'DelayedArray:::normarg_grid'
  'GenomicRanges:::.extract_groups_from_GenomicRanges'
  'GenomicRanges:::.get_circle_length'
  'GenomicRanges:::extraColumnSlotNames'
  'IRanges:::.shift_ranges_in_groups_to_first_circle'
  'S4Vectors:::normarg_names' 'S4Vectors:::numeric2integer'
  'S4Vectors:::sapply_isNULL' 'data.table:::funique'
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BSmooth.Rd: BiocParallelParam-class, SerialParam-class,
    MulticoreParam-class, SnowParam-class, BatchtoolsParam-class,
    getHDF5DumpChunkDim, getHDF5DumpCompressionLevel, HDF5Array-class,
    getAutoRealizationBackend, HDF5Matrix-class, RealizationSink-class
  BSseq-class.Rd: RangedSummarizedExperiment-class,
    setAutoRealizationBackend
  BSseq.Rd: DataFrame-class, GRanges-class, DelayedMatrix-class,
    HDF5Matrix-class
  BSseqStat-class.Rd: DelayedMatrix-class, HDF5Matrix-class
  BSseqTstat-class.Rd: DelayedMatrix-class, HDF5Matrix-class
  findLoci.Rd: BSgenome-class, DNAStringSet-class, GRanges-class
  getCoverage.Rd: DelayedMatrix-class
  getMeth.Rd: DelayedMatrix-class
  read.bismark.Rd: GenomicRanges-class, DataFrame-class,
    BiocParallelParam-class, SerialParam-class, MulticoreParam-class,
    SnowParam-class, BatchtoolsParam-class, getHDF5DumpChunkDim,
    getHDF5DumpCompressionLevel, HDF5Array-class,
    getAutoRealizationBackend, HDF5Matrix-class, RealizationSink-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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/bsseq/libs/x64/bsseq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'bsseq-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BSseq-class
> ### Title: Class BSseq
> ### Aliases: BSseq-class [,BSseq-method combine,BSseq,BSseq-method
> ###   combineList length,BSseq-method pData,BSseq-method
> ###   pData<-,BSseq,data.frame-method pData<-,BSseq,DataFrame-method
> ###   sampleNames,BSseq-method sampleNames<-,BSseq,ANY-method
> ###   updateObject,BSseq-method assays,BSseq-method assayNames,BSseq-method
> ###   show,BSseq-method getBSseq collapseBSseq strandCollapse orderBSseq
> ###   chrSelectBSseq hasBeenSmoothed
> ### Keywords: classes
> 
> ### ** Examples
> 
> M <- matrix(1:9, 3,3)
> colnames(M) <- c("A1", "A2", "A3")
> BStest <- BSseq(pos = 1:3, chr = c("chr1", "chr2", "chr1"), M = M, Cov = M + 2)
> chrSelectBSseq(BStest, seqnames = "chr1", order = TRUE)
An object of type 'BSseq' with
  2 methylation loci
  3 samples
has not been smoothed
All assays are in-memory
> collapseBSseq(BStest, group = c("A", "A", "B"))
An object of type 'BSseq' with
  3 methylation loci
  2 samples
has not been smoothed
All assays are in-memory
> 
> #-------------------------------------------------------------------------------
> # An example using a HDF5-backed BSseq object
> #
> hdf5_BStest <- realize(BStest, "HDF5Array")
> chrSelectBSseq(hdf5_BStest, seqnames = "chr1", order = TRUE)
An object of type 'BSseq' with
  2 methylation loci
  3 samples
has not been smoothed
Some assays are HDF5Array-backed
> collapseBSseq(
+     BSseq = hdf5_BStest,
+     group = c("A", "A", "B"),
+     BACKEND = "HDF5Array",
+     type = "integer")
Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error:
Error: There is not enough space on the disk.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
BSmooth.tstat 8.39   0.56    9.38
* 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:
  
  Backtrace:
      ▆
   1. ├─bsseq:::expect_equivalent_SE(...) at test_BSseq-class.R:59:5
   2. │ ├─base::stopifnot(is(SE1, "SummarizedExperiment"), is(SE2, "SummarizedExperiment")) at E:\biocbuild\bbs-3.21-bioc\meat\bsseq.Rcheck\tests\testthat\helper_make_test_data.R:12:5
   3. │ └─methods::is(SE1, "SummarizedExperiment")
   4. └─bsseq::strandCollapse(bsseq_pos, type = "integer")
   5.   └─bsseq:::.rowsum(...)
   6.     ├─BiocParallel::bplapply(...)
   7.     └─BiocParallel::bplapply(...)
   8.       └─BiocParallel:::.bpinit(...)
  
  [ FAIL 4 | WARN 6 | SKIP 6 | PASS 122 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/bsseq.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL bsseq
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'bsseq' ...
** this is package 'bsseq' version '1.44.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c check_M_and_Cov.cpp -o check_M_and_Cov.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c init.cpp -o init.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-bsseq/00new/bsseq/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bsseq)

R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(bsseq)
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

Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'IRanges'

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

    windows

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

> test_check("bsseq")
> > [ FAIL 4 | WARN 6 | SKIP 6 | PASS 122 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• Skipping tests that require SnowParam with multiple machines (1):
  'test_BSmooth.R:74:9'
• TODO: Remove these tests if no longer required (1): 'test_HDF5_utils.R:21:5'
• empty test (4): 'test_BSmooth.R:42:1', 'test_GitHub_issues.R:3:1',
  'test_combine.R:3:1', 'test_combine.R:28:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_BSmooth.R:21:5'): BSmooth properly inherits 'dir' ──────────────
Error in `!bpok`: invalid argument type
Backtrace:
    ▆
 1. └─bsseq::read.bismark(files = infile, BACKEND = "HDF5Array", BPPARAM = SerialParam()) at test_BSmooth.R:21:5
 2.   └─bsseq:::.constructCounts(...)
 3.     ├─base::stop(...)
 4.     │ └─base::.makeMessage(..., domain = domain)
 5.     │   └─base::lapply(list(...), as.character)
 6.     └─BiocGenerics::paste(files[!bpok], collapse = "\n  ")
── Error ('test_BSmooth.R:94:9'): Expected parallelisation backends work with on-disk realization backend ──
Error in `BSmooth(bsseq_test, BPPARAM = SerialParam())`: BSmooth() encountered errors: 4 of 4 smoothing tasks failed.
Backtrace:
    ▆
 1. └─bsseq::BSmooth(bsseq_test, BPPARAM = SerialParam()) at test_BSmooth.R:94:9
── Error ('test_BSmooth.R:150:5'): keep.se works ───────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'assay': BSmooth() encountered errors: 4 of 4 smoothing tasks failed.
Backtrace:
    ▆
 1. ├─testthat::expect_is(...) at test_BSmooth.R:150:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─SummarizedExperiment::assay(...)
 5. ├─bsseq::BSmooth(...)
 6. │ └─base::stop(...)
 7. └─base::.handleSimpleError(...)
 8.   └─base (local) h(simpleError(msg, call))
── Error ('test_BSseq-class.R:59:5'): strandCollapse() works on good input ─────
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  4 remote errors, element index: 1, 6, 11, 16
  16 unevaluated and other errors
  first remote error:
Error: There is not enough space on the disk.

Backtrace:
    ▆
 1. ├─bsseq:::expect_equivalent_SE(...) at test_BSseq-class.R:59:5
 2. │ ├─base::stopifnot(is(SE1, "SummarizedExperiment"), is(SE2, "SummarizedExperiment")) at E:\biocbuild\bbs-3.21-bioc\meat\bsseq.Rcheck\tests\testthat\helper_make_test_data.R:12:5
 3. │ └─methods::is(SE1, "SummarizedExperiment")
 4. └─bsseq::strandCollapse(bsseq_pos, type = "integer")
 5.   └─bsseq:::.rowsum(...)
 6.     ├─BiocParallel::bplapply(...)
 7.     └─BiocParallel::bplapply(...)
 8.       └─BiocParallel:::.bpinit(...)

[ FAIL 4 | WARN 6 | SKIP 6 | PASS 122 ]
Error: Test failures
Execution halted