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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DeepBlueR_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DeepBlueR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DeepBlueR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepBlueR' version '1.25.0'
* 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 whether package 'DeepBlueR' can be installed ... 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 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 ... NOTE
prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'DeepBlueR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deepblue_export_bed
> ### Title: Export GenomicRanges result as BED file
> ### Aliases: deepblue_export_bed
> 
> ### ** Examples
> 
> query_id = deepblue_select_experiments (
+ experiment=c("GC_T14_10.CPG_methylation_calls.bs_call.GRCh38.20160531.wig"),
+ chromosome="chr1", start=0, end=50000000)
Called method: deepblue_select_experiments
Reported status was: okay
> cpg_islands = deepblue_select_annotations(annotation_name="CpG Islands",
+ genome="GRCh38", chromosome="chr1", start=0, end=50000000)
Called method: deepblue_select_annotations
Reported status was: okay
> overlapped = deepblue_aggregate (data_id=query_id, ranges_id=cpg_islands,
+                                 column="VALUE" )
Called method: deepblue_aggregate
Reported status was: okay
> request_id = deepblue_get_regions(query_id=overlapped,
+                                 output_format=
+                                      "CHROMOSOME,START,END,@AGG.MIN,@AGG.MAX,@AGG.MEAN,@AGG.VAR")
Called method: deepblue_get_regions
Reported status was: okay
> regions = deepblue_download_request_data(request_id=request_id)
Called method: deepblue_info
Reported status was: okay
fetching data
Called method: deepblue_info
Reported status was: okay
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726039&key=anonymous_key'
Content type 'application/x-bzip2' length 14872 bytes (14 KB)
==================================================
downloaded 14 KB

Decompressing downloaded file to F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\Rtmpei1O3h\file2b983c7d42b9_uncompress
Reading file from F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\Rtmpei1O3h\file2b983c7d42b9_uncompress
> temp_dir = tempdir()
> deepblue_export_bed(regions, target.directory = temp_dir,
+                   file.name = "GC_T14_10.CpG_islands")
Error in `stringr::str_replace_all()`:
! `string` must be a vector, not a <Rle> object.
Backtrace:
    ▆
 1. ├─DeepBlueR::deepblue_export_bed(...)
 2. │ └─stringr::str_replace_all(strand(result), "\\*", ".")
 3. │   └─stringr:::check_lengths(string, pattern, replacement)
 4. │     └─vctrs::vec_size_common(...)
 5. └─vctrs:::stop_scalar_type(`<fn>`(`<Rle>`), "string", `<env>`)
 6.   └─vctrs:::stop_vctrs(...)
 7.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
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: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DeepBlueR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DeepBlueR
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'DeepBlueR' ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Called method: deepblue_list_column_types
Reported status was: okay
Called method: deepblue_info
Reported status was: okay
** 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 (DeepBlueR)