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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings amplican_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/amplican.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.31.0’
* 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 ‘amplican’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘get_seq’
* 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
checkRd: (-1) amplicanAlign.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:65-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanAlign.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:60-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipeline.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:60-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:107-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanPipelineConservative.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amplicanSummarize.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAlignment.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot_variants.Rd:77-78: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlignmentsExperimentSet-class.Rd: PairwiseAlignmentsSingleSubject,
    GRanges
  amplicanAlign.Rd: nucleotideSubstitutionMatrix
  amplicanMap.Rd: GRanges
  amplicanPipeline.Rd: nucleotideSubstitutionMatrix
  amplicanPipelineConservative.Rd: nucleotideSubstitutionMatrix
  cigarsToEvents.Rd: GRanges
  cumsumw.Rd: IRanges
  defGR.Rd: IRanges, GRanges
  extractEvents.Rd: GRanges
  findPD.Rd: GRanges
  fwdReads-set.Rd: PairwiseAlignmentsSingleSubject
  fwdReadsType-set.Rd: PairwiseAlignmentsSingleSubject
  getEventInfo.Rd: PairwiseAlignmentsSingleSubject, GRanges
  getEvents.Rd: pairwiseAlignment, GRanges
  makeAlignment.Rd: nucleotideSubstitutionMatrix
  pairToEvents.Rd: GRanges
  readCounts-set.Rd: PairwiseAlignmentsSingleSubject
  rveReads-set.Rd: PairwiseAlignmentsSingleSubject
  rveReadsType-set.Rd: PairwiseAlignmentsSingleSubject
  unassignedData-set.Rd: PairwiseAlignmentsSingleSubject
  upperGroups.Rd: IRanges
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 ... NOTE
Documented arguments not in \usage in Rd file 'getEventInfo.Rd':
  ‘ampl_len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘amplican-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: amplicanAlign
> ### Title: Align reads to amplicons.
> ### Aliases: amplicanAlign
> 
> ### ** Examples
> 
> # path to example config file
> config <- system.file("extdata", "config.csv", package = "amplican")
> # path to example fastq files
> fastq_folder <- system.file("extdata", package = "amplican")
> aln <- amplicanAlign(config, fastq_folder)
Checking configuration file...
Making alignments...
Error in .call_fun_in_pwalign("nucleotideSubstitutionMatrix", ...) : 
  nucleotideSubstitutionMatrix() has moved from Biostrings to the pwalign
  package, and is formally defunct in Biostrings >= 2.77.1. Please call
  pwalign::nucleotideSubstitutionMatrix() to get rid of this error.
Calls: amplicanAlign ... <Anonymous> -> <Anonymous> -> .call_fun_in_pwalign -> .Defunct
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:
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─amplican::amplicanPipeline(...)
    7.   ├─amplican::amplicanAlign(...)
    8.   │ ├─BiocParallel::bplapply(...)
    9.   │ └─BiocParallel::bplapply(...)
   10.   └─Biostrings::nucleotideSubstitutionMatrix(...)
   11.     └─Biostrings:::.call_fun_in_pwalign(...)
   12.       └─base::.Defunct(msg = wmsg(msg))
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 44 ]
  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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/amplican.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL amplican
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘amplican’ ...
** this is package ‘amplican’ version ‘1.31.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bezier.cpp -o bezier.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o amplican.so RcppExports.o bezier.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-amplican/00new/amplican/libs
** 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
** 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 (amplican)

R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(amplican)
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: pwalign

Attaching package: 'pwalign'

The following objects are masked from 'package:Biostrings':

    PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned,
    alignedPattern, alignedSubject, compareStrings, deletion,
    errorSubstitutionMatrices, indel, insertion, mismatchSummary,
    mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
    pairwiseAlignment, pattern, pid, qualitySubstitutionMatrices,
    stringDist, unaligned, writePairwiseAlignments

Loading required package: data.table

Attaching package: 'data.table'

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

version: 1.31.0
Please consider supporting this software by citing:

Labun et al. 2019
Accurate analysis of genuine CRISPR editing events with ampliCan.
Genome Res. 2019 Mar 8
doi: 10.1101/gr.244293.118

> 
> test_check("amplican")
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 44 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_alignment_helpers.R:22:3'): getEventInfo returns correct GRanges ──
<defunctError/error/condition>
Error in `.call_fun_in_pwalign("pairwiseAlignment", ...)`: pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
  formally defunct in Biostrings >= 2.77.1. Please call
  pwalign::pairwiseAlignment() to get rid of this error.
Backtrace:
    ▆
 1. └─Biostrings::pairwiseAlignment(...) at test_alignment_helpers.R:22:3
 2.   └─Biostrings:::.call_fun_in_pwalign("pairwiseAlignment", ...)
 3.     └─base::.Defunct(msg = wmsg(msg))
── Error ('test_amplican.R:25:3'): amplican runs through example files without any issues ──
<defunctError/error/condition>
Error in `.call_fun_in_pwalign("nucleotideSubstitutionMatrix", ...)`: nucleotideSubstitutionMatrix() has moved from Biostrings to the pwalign
  package, and is formally defunct in Biostrings >= 2.77.1. Please call
  pwalign::nucleotideSubstitutionMatrix() to get rid of this error.
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test_amplican.R:25:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─amplican::amplicanPipeline(...)
  7.   ├─amplican::amplicanAlign(...)
  8.   │ ├─BiocParallel::bplapply(...)
  9.   │ └─BiocParallel::bplapply(...)
 10.   └─Biostrings::nucleotideSubstitutionMatrix(...)
 11.     └─Biostrings:::.call_fun_in_pwalign(...)
 12.       └─base::.Defunct(msg = wmsg(msg))

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted