Package: amplican

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz

StartedAt: 2018-04-12 00:17:33 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:20:25 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: amplican.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 ... NOTE
  installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc  16.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... 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 ... NOTE
Package unavailable to check Rd xrefs: ‘CrispRVariants’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
metaplot_deletions 6.671  0.180   7.092
amplicanAlign      5.541  0.154   5.798
amplicanPipeline   4.976  0.182   4.897
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00check.log’
for details.

* installing *source* package ‘amplican’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (amplican)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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: 74 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 29.186   0.881  29.913 

name	user	system	elapsed
AlignmentsExperimentSet-class	1.900	0.046	1.985
amplicanAlign	5.541	0.154	5.798
amplicanConsensus	0.046	0.003	0.045
amplicanFilter	0.180	0.029	0.106
amplicanMap	1.444	0.052	1.337
amplicanNormalize	0.317	0.019	0.281
amplicanOverlap	0.153	0.024	0.090
amplicanPipeline	4.976	0.182	4.897
amplicanReport	0.131	0.026	0.100
amplicanSummarize	0.066	0.006	0.060
amplican_print_reads	0.596	0.050	0.482
assignedCount	0.092	0.001	0.094
barcodeData-set	0.008	0.001	0.008
barcodeData	0.008	0.000	0.009
comb_along	0.034	0.002	0.038
experimentData-set	0.008	0.000	0.009
experimentData	0.013	0.001	0.014
extractEvents	2.545	0.022	2.627
findEOP	0.005	0.001	0.005
findLQR	0.004	0.000	0.004
findPD	0.004	0.001	0.005
fwdReads-set	0.008	0.001	0.008
fwdReads	0.094	0.001	0.098
lookupAlignment	0.564	0.002	0.572
metaplot_deletions	6.671	0.180	7.092
metaplot_insertions	0.730	0.002	0.747
metaplot_mismatches	0.009	0.001	0.009
plot_cuts	0.636	0.003	0.644
plot_deletions	0.669	0.118	0.405
plot_height	0.001	0.001	0.001
plot_heterogeneity	1.049	0.073	0.833
plot_insertions	0.337	0.002	0.346
plot_mismatches	0.325	0.002	0.337
plot_variants	1.765	0.050	1.498
readCounts-set	0.005	0.000	0.006
readCounts	0.005	0.000	0.006
rveReads-set	0.005	0.000	0.005
rveReads	0.119	0.006	0.130
unassignedCount	0.007	0.001	0.007
unassignedData-set	0.008	0.001	0.008
unassignedData	0.009	0.001	0.010
writeAlignments	0.022	0.004	0.027