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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings amplican_1.29.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'amplican/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'amplican' version '1.29.0'
* 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 'amplican' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/amplican/libs/x64/amplican.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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
amplicanPipeline 8.94   0.25    9.45
amplicanAlign    8.17   0.50    8.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 5 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck/00check.log'
for details.