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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CircSeqAlignTk.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CircSeqAlignTk_1.1.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/CircSeqAlignTk.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 'CircSeqAlignTk/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CircSeqAlignTk' version '1.1.0'
* 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 'CircSeqAlignTk' 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 ... OK
* 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 'CircSeqAlignTk-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: align_reads
> ### Title: Align sequence reads to a genome sequence
> ### Aliases: align_reads
> 
> ### ** Examples
> 
> output_dpath <- tempdir()
> 
> genome_seq <- system.file(package="CircSeqAlignTk", "extdata", "FR851463.fa")
> fq <- system.file(package="CircSeqAlignTk", "extdata", "srna.fq.gz")
> 
> ref_index <- build_index(input = genome_seq,
+                          output = file.path(output_dpath, 'index'))
Building a SMALL index
Building a SMALL index
> aln <- align_reads(input = fq, index = ref_index,
+                    output = file.path(output_dpath, 'align_results'))
Warning in check_overwrite(c(aln@fastq, aln@bam, aln@clean_bam), overwrite) :
  The following files are found.
  - F:\biocbuild\bbs-3.17-bioc\R\library\CircSeqAlignTk\extdata/srna.fq.gz
These files will be overwrite.

Started align sequence reads onto the type 1 reference sequence ...
Saw ASCII character 10 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
Can't spawn ""F:\biocbuild\bbs-3.17-bioc\R\library\Rbowtie2\bowtie2-align-s.exe" --wrapper basic-0 --threads 1 -x "F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpemYQJR/index/refseq.t1" -S "F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpemYQJR/file4774438b6b5f.sam" -U "F:/biocbuild/bbs-3.17-bioc/R/library/CircSeqAlignTk/extdata/srna.fq.gz"": No such file or directory at F:/biocbuild/bbs-3.17-bioc/R/library/Rbowtie2/bowtie2 line 629.
(ERR): bowtie2-align exited with value 255
Error in value[[3L]](cond) : 'asBam' failed to open SAM/BAM file
  file: 'F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpemYQJR\file4774438b6b5f.sam'
  SAM file: 'F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpemYQJR\file4774438b6b5f.sam'
Calls: align_reads ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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. └─CircSeqAlignTk::align_reads(input = fq, index = ref_index, output = "tmp_bt2output") at test_workflow.R:9:4
   2.   └─CircSeqAlignTk:::.align_reads(...)
   3.     ├─Rsamtools::asBam(output_sam)
   4.     └─Rsamtools::asBam(output_sam)
   5.       └─Rsamtools (local) .local(file, destination, ...)
   6.         └─base::tryCatch(...)
   7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.               └─value[[3L]](cond)
  ── Error ('test_workflow.R:105'): workflow - reads without adapter and mismatches correctly aligned ──
  Error in `fwd_pred - fwd_true`: non-conformable arrays
  
  [ FAIL 2 | WARN 12 | SKIP 3 | PASS 0 ]
  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
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/CircSeqAlignTk.Rcheck/00check.log'
for details.