Mac ARM64 build report for BioC 3.20 - CHECK results for amplican on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4378
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /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_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/amplican.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.27.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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 ... OK
* 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
amplicanPipeline 7.739  1.097   9.173
amplicanAlign    7.689  0.804   8.497
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/amplican.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL amplican
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘amplican’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bezier.cpp -o bezier.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o amplican.so RcppExports.o bezier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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, 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: 1.27.0
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 
 24.161   1.961  26.196

Example timings

name	user	system	elapsed
AlignmentsExperimentSet-class	1.349	0.059	1.410
amplicanAlign	7.689	0.804	8.497
amplicanConsensus	0.221	0.003	0.226
amplicanFilter	0.025	0.007	0.033
amplicanMap	0.257	0.003	0.260
amplicanNormalize	0.034	0.001	0.035
amplicanOverlap	0.021	0.002	0.023
amplicanPipeline	7.739	1.097	9.173
amplicanReport	0.015	0.019	0.040
amplicanSummarize	0.021	0.003	0.026
amplican_print_reads	0.305	0.005	0.348
assignedCount	0.020	0.002	0.022
barcodeData-set	0.004	0.000	0.006
barcodeData	0.005	0.001	0.006
comb_along	0.021	0.003	0.025
experimentData-set	0.004	0.001	0.005
experimentData	0.008	0.002	0.011
extractEvents	2.680	0.020	2.892
findEOP	0.005	0.002	0.007
findLQR	0.004	0.001	0.005
findPD	0.004	0.002	0.005
fwdReads-set	0.003	0.000	0.004
fwdReads	0.330	0.002	0.333
fwdReadsType-set	0.004	0.001	0.005
fwdReadsType	0.003	0.001	0.003
geom_bezier	0.470	0.012	0.482
lookupAlignment	0.224	0.003	0.226
metaplot_deletions	0.201	0.006	0.207
metaplot_insertions	0.337	0.007	0.344
metaplot_mismatches	0.330	0.004	0.335
plot_cuts	0.229	0.005	0.233
plot_deletions	0.252	0.004	0.257
plot_height	0.000	0.000	0.001
plot_heterogeneity	0.196	0.003	0.200
plot_insertions	0.423	0.004	0.427
plot_mismatches	1.880	0.032	1.915
plot_variants	0.741	0.007	0.748
readCounts-set	0.004	0.001	0.005
readCounts	0.003	0.001	0.004
rveReads-set	0.004	0.001	0.004
rveReads	0.314	0.002	0.316
rveReadsType-set	0.004	0.000	0.005
rveReadsType	0.003	0.000	0.004
unassignedCount	0.003	0.001	0.003
unassignedData-set	0.003	0.001	0.004
unassignedData	0.005	0.001	0.006
writeAlignments	0.017	0.001	0.018

CHECK results for amplican on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings