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CHECK report for amplican on merida1

This page was generated on 2019-04-16 12:00:58 -0400 (Tue, 16 Apr 2019).

Package 44/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.4.1
Eivind Valen
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/amplican
Branch: RELEASE_3_8
Last Commit: ef9ebb4
Last Changed Date: 2019-01-04 13:18:44 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: amplican
Version: 1.4.1
Command: /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_1.4.1.tar.gz
StartedAt: 2019-04-15 22:19:36 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:22:28 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 171.9 seconds
RetCode: 0
Status:  OK 
CheckDir: amplican.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.4.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/amplican.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
amplicanPipeline 6.648  2.269   5.201
amplicanAlign    7.830  0.304   8.211
* 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: OK


Installation output

amplican.Rcheck/00install.out

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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/3.5/Resources/library’
* installing *source* package ‘amplican’ ...
** 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

amplican.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, 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: 59 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 31.545   8.745  27.382 

Example timings

amplican.Rcheck/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.8320.0901.940
amplicanAlign7.8300.3048.211
amplicanConsensus0.3790.3980.136
amplicanFilter0.2310.2700.073
amplicanMap0.6850.6840.297
amplicanNormalize1.2990.0030.127
amplicanOverlap0.4070.0020.035
amplicanPipeline6.6482.2695.201
amplicanReport0.0890.1130.034
amplicanSummarize0.1840.2070.059
amplican_print_reads0.7460.6660.342
assignedCount0.0240.0010.028
barcodeData-set0.0070.0010.007
barcodeData0.0110.0000.012
comb_along0.0410.0030.045
experimentData-set0.010.000.01
experimentData0.0170.0020.019
extractEvents3.1740.0293.233
findEOP0.0090.0010.009
findLQR0.0140.0110.007
findPD0.0230.0330.007
fwdReads-set0.0350.0470.010
fwdReads0.8730.7470.491
fwdReadsType-set0.0050.0000.006
fwdReadsType0.0050.0000.004
lookupAlignment0.3080.0020.311
metaplot_deletions1.2041.7260.445
metaplot_insertions0.8451.0140.407
metaplot_mismatches1.6370.5000.405
plot_cuts0.8950.9760.472
plot_deletions0.2620.3760.100
plot_height0.0030.0050.001
plot_heterogeneity1.0121.1980.464
plot_insertions1.0571.0160.614
plot_mismatches1.0460.9160.599
plot_variants1.6741.1911.193
readCounts-set0.0100.0010.010
readCounts0.0040.0000.005
rveReads-set0.0100.0010.010
rveReads0.4470.0020.451
rveReadsType-set0.010.000.01
rveReadsType0.0040.0000.005
unassignedCount0.0050.0000.005
unassignedData-set0.0050.0000.006
unassignedData0.0120.0010.012
writeAlignments0.0240.0010.025