##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings amplican_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘amplican’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
amplicanAlign    6.626  0.285   6.914
amplicanPipeline 6.829  0.075   6.887
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL amplican
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘amplican’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c bezier.cpp -o bezier.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o amplican.so RcppExports.o bezier.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 1.29.0
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 0 | WARN 11 | SKIP 0 | PASS 57 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 57 ]
> 
> proc.time()
   user  system elapsed 
 22.084   1.121  23.155