##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CircSeqAlignTk.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CircSeqAlignTk_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/CircSeqAlignTk.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 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 '1.4.0'
* 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-3.18-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 13 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
Can't spawn ""F:\biocbuild\bbs-3.18-bioc\R\library\Rbowtie2\bowtie2-align-s.exe" --wrapper basic-0 --threads 1 -x "F:/biocbuild/bbs-3.18-bioc/tmpdir/RtmpK4tWRT/index/refseq.t1" -S "F:/biocbuild/bbs-3.18-bioc/tmpdir/RtmpK4tWRT/file4110f33714a.sam" -U "F:/biocbuild/bbs-3.18-bioc/R/library/CircSeqAlignTk/extdata/srna.fq.gz"": No such file or directory at F:/biocbuild/bbs-3.18-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-3.18-bioc\tmpdir\RtmpK4tWRT\file4110f33714a.sam'
  SAM file: 'F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpK4tWRT\file4110f33714a.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:
    8. ├─base::as.data.frame(.)
    9. ├─dplyr::mutate(., strand = read_strand)
   10. ├─dplyr::arrange(., .data$read_length)
   11. ├─dplyr::mutate(...)
   12. ├─tidyr::pivot_longer(...)
   13. └─tidyr:::pivot_longer.data.frame(., !.data$position, names_to = "read_length", values_to = "coverage")
   14.   └─tidyr::build_longer_spec(...)
   15.     └─cli::cli_abort(...)
   16.       └─rlang::abort(...)
  ── Error ('test_workflow.R:105:9'): workflow - reads without adapter and mismatches correctly aligned ──
  Error in `fwd_pred - fwd_true`: non-conformable arrays
  
  [ FAIL 3 | WARN 12 | SKIP 2 | 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-3.18-bioc/meat/CircSeqAlignTk.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL CircSeqAlignTk
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'CircSeqAlignTk' ...
** using staged installation
** R
** 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 (CircSeqAlignTk)

R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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('CircSeqAlignTk')
> test_check('CircSeqAlignTk')
Building a SMALL index
Building a SMALL index
Saw ASCII character 13 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
Can't spawn ""F:\biocbuild\bbs-3.18-bioc\R\library\Rbowtie2\bowtie2-align-s.exe" --wrapper basic-0 --threads 1 -x "F:/biocbuild/bbs-3.18-bioc/tmpdir/RtmpYfJWUE/tmp_bt2index/refseq.t1" -S "F:/biocbuild/bbs-3.18-bioc/tmpdir/RtmpYfJWUE/file35d4f9c30d7.sam" -U "F:/biocbuild/bbs-3.18-bioc/R/library/CircSeqAlignTk/extdata/srna.fq.gz"": No such file or directory at F:/biocbuild/bbs-3.18-bioc/R/library/Rbowtie2/bowtie2 line 629.
(ERR): bowtie2-align exited with value 255
Settings:
  Output files: "tmp_ht2index/refseq.t1.*.ht2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:4, size_t:8
Input files DNA, FASTA:
  tmp_ht2index/refseq.t1.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 68 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 70
fchr[G]: 180
fchr[T]: 281
fchr[$]: 361
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4194625 bytes to primary GFM file: tmp_ht2index/refseq.t1.1.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t1.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 8421 bytes to primary GFM file: tmp_ht2index/refseq.t1.5.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t1.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 361
    gbwtLen: 362
    nodes: 362
    sz: 91
    gbwtSz: 91
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23
    offsSz: 92
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 2
    numLines: 2
    gbwtTotLen: 128
    gbwtTotSz: 128
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
Settings:
  Output files: "tmp_ht2index/refseq.t2.*.ht2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:4, size_t:8
Input files DNA, FASTA:
  tmp_ht2index/refseq.t2.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 68 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 70
fchr[G]: 180
fchr[T]: 281
fchr[$]: 361
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4194625 bytes to primary GFM file: tmp_ht2index/refseq.t2.1.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t2.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 8421 bytes to primary GFM file: tmp_ht2index/refseq.t2.5.ht2
Wrote 96 bytes to secondary GFM file: tmp_ht2index/refseq.t2.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 361
    gbwtLen: 362
    nodes: 362
    sz: 91
    gbwtSz: 91
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23
    offsSz: 92
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 2
    numLines: 2
    gbwtTotLen: 128
    gbwtTotSz: 128
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:01
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29007 (99.41%) aligned 0 times
    171 (0.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.59% overall alignment rate
29007 reads; of these:
  29007 (100.00%) were unpaired; of these:
    28978 (99.90%) aligned 0 times
    29 (0.10%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.10% overall alignment rate
29178 reads; of these:
  29178 (100.00%) were unpaired; of these:
    29007 (99.41%) aligned 0 times
    171 (0.59%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.59% overall alignment rate
29007 reads; of these:
  29007 (100.00%) were unpaired; of these:
    28978 (99.90%) aligned 0 times
    29 (0.10%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.10% overall alignment rate
Building a SMALL index
Building a SMALL index
0 reads
0.00% overall alignment rate
0 reads
0.00% overall alignment rate
Building a SMALL index
Building a SMALL index
84 reads; of these:
  84 (100.00%) were unpaired; of these:
    52 (61.90%) aligned 0 times
    32 (38.10%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
38.10% overall alignment rate
19 reads; of these:
  19 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    19 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
Building a SMALL index
Building a SMALL index
14 reads; of these:
  14 (100.00%) were unpaired; of these:
    2 (14.29%) aligned 0 times
    12 (85.71%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
85.71% overall alignment rate
2 reads; of these:
  2 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    2 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
2 reads; of these:
  2 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    2 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 reads
0.00% overall alignment rate
[ FAIL 3 | WARN 12 | SKIP 2 | PASS 0 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_workflow.R:16:1', 'test_workflow.R:56:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_workflow.R:9:5'): workflow with Bowtie2 ────────────────────────
Error in `value[[3L]](cond)`: 'asBam' failed to open SAM/BAM file
  file: 'F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpYfJWUE\file35d4f9c30d7.sam'
  SAM file: 'F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpYfJWUE\file35d4f9c30d7.sam'

Backtrace:
    ▆
 1. └─CircSeqAlignTk::align_reads(input = fq, index = ref_index, output = "tmp_bt2output") at test_workflow.R:9:5
 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:50:5'): workflow - no reads aligned on edges ────────
Error in `pivot_longer(., !.data$position, names_to = "read_length", values_to = "coverage")`: `cols` must select at least one column.
Backtrace:
     ▆
  1. ├─CircSeqAlignTk::calc_coverage(aln) at test_workflow.R:50:5
  2. │ ├─methods::new(...)
  3. │ │ ├─methods::initialize(value, ...)
  4. │ │ └─methods::initialize(value, ...)
  5. │ ├─base::rbind(...)
  6. │ └─CircSeqAlignTk:::reshape_coverage_df(mat_fwd, "+")
  7. │   └─... %>% as.data.frame()
  8. ├─base::as.data.frame(.)
  9. ├─dplyr::mutate(., strand = read_strand)
 10. ├─dplyr::arrange(., .data$read_length)
 11. ├─dplyr::mutate(...)
 12. ├─tidyr::pivot_longer(...)
 13. └─tidyr:::pivot_longer.data.frame(., !.data$position, names_to = "read_length", values_to = "coverage")
 14.   └─tidyr::build_longer_spec(...)
 15.     └─cli::cli_abort(...)
 16.       └─rlang::abort(...)
── Error ('test_workflow.R:105:9'): workflow - reads without adapter and mismatches correctly aligned ──
Error in `fwd_pred - fwd_true`: non-conformable arrays

[ FAIL 3 | WARN 12 | SKIP 2 | PASS 0 ]
Error: Test failures
Execution halted