Multiple platform build/check report for BioC 3.9 - CHECK report for amplican on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings amplican_1.5.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/amplican.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘amplican/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘amplican’ version ‘1.5.6’
* 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
* 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 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 or elapsed time > 5s
                  user system elapsed
amplicanPipeline 6.688  2.127   4.965
amplicanAlign    7.823  0.480   8.371
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/amplican.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL amplican
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘amplican’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c bezier.cpp -o bezier.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/3.6/Resources/library/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
* DONE (amplican)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(amplican)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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

> 
> test_check("amplican")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 59 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 32.042   7.840  27.951

Example timings

name	user	system	elapsed
AlignmentsExperimentSet-class	1.825	0.082	1.924
amplicanAlign	7.823	0.480	8.371
amplicanConsensus	0.446	0.398	0.122
amplicanFilter	0.261	0.240	0.067
amplicanMap	0.716	0.429	0.262
amplicanNormalize	0.252	0.143	0.072
amplicanOverlap	0.105	0.085	0.029
amplicanPipeline	6.688	2.127	4.965
amplicanReport	0.120	0.142	0.034
amplicanSummarize	0.236	0.174	0.053
amplican_print_reads	0.986	0.667	0.406
assignedCount	0.025	0.001	0.027
barcodeData-set	0.006	0.000	0.006
barcodeData	0.008	0.001	0.009
comb_along	0.040	0.003	0.043
experimentData-set	0.006	0.001	0.006
experimentData	0.015	0.001	0.016
extractEvents	3.055	0.030	3.117
findEOP	0.006	0.001	0.007
findLQR	0.020	0.010	0.008
findPD	0.032	0.031	0.007
fwdReads-set	0.037	0.040	0.010
fwdReads	1.006	0.699	0.495
fwdReadsType-set	0.009	0.000	0.009
fwdReadsType	0.008	0.000	0.009
geom_bezier	0.494	0.006	0.502
lookupAlignment	0.303	0.002	0.309
metaplot_deletions	0.981	0.575	0.403
metaplot_insertions	0.993	0.665	0.431
metaplot_mismatches	0.989	0.656	0.436
plot_cuts	1.013	0.635	0.461
plot_deletions	0.332	0.263	0.108
plot_height	0.004	0.004	0.001
plot_heterogeneity	1.243	0.784	0.548
plot_insertions	1.265	0.662	0.710
plot_mismatches	1.257	0.651	0.709
plot_variants	1.866	0.754	1.221
readCounts-set	0.006	0.000	0.006
readCounts	0.009	0.000	0.008
rveReads-set	0.006	0.000	0.006
rveReads	0.467	0.001	0.473
rveReadsType-set	0.009	0.001	0.011
rveReadsType	0.008	0.001	0.008
unassignedCount	0.007	0.000	0.007
unassignedData-set	0.010	0.001	0.010
unassignedData	0.009	0.001	0.010
writeAlignments	0.032	0.000	0.034

CHECK report for amplican on merida2

Summary

Command output

Installation output

Tests output

Example timings