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CHECK report for amplican on malbec2

This page was generated on 2018-10-17 08:30:40 -0400 (Wed, 17 Oct 2018).

Package 41/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.2.1
Eivind Valen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/amplican
Branch: RELEASE_3_7
Last Commit: 54d0eff
Last Changed Date: 2018-06-14 17:16:48 -0400 (Thu, 14 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: amplican
Version: 1.2.1
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings amplican_1.2.1.tar.gz
StartedAt: 2018-10-15 22:23:39 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:25:28 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 108.9 seconds
RetCode: 0
Status:  OK 
CheckDir: amplican.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:amplican.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings amplican_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/amplican.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.1’
* 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
* 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:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL amplican
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 57 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.356   0.440  17.815 

Example timings

amplican.Rcheck/amplican-Ex.timings

nameusersystemelapsed
AlignmentsExperimentSet-class1.2800.0201.299
amplicanAlign4.4560.2404.744
amplicanConsensus0.0840.0160.140
amplicanFilter0.0280.0000.028
amplicanMap0.1560.0000.159
amplicanNormalize0.0280.0000.027
amplicanOverlap0.0160.0000.017
amplicanPipeline2.2440.0122.282
amplicanReport0.0240.0000.026
amplicanSummarize0.0280.0000.029
amplican_print_reads0.3360.0040.341
assignedCount0.0280.0040.032
barcodeData-set0.0120.0000.009
barcodeData0.0120.0000.010
comb_along0.0320.0000.034
experimentData-set0.0080.0000.009
experimentData0.0080.0040.013
extractEvents1.7440.0281.774
findEOP0.0040.0000.004
findLQR0.0040.0000.005
findPD0.0040.0000.005
fwdReads-set0.0040.0000.005
fwdReads0.2560.0000.254
fwdReadsType-set0.0080.0000.007
fwdReadsType0.0040.0000.005
lookupAlignment0.2240.0000.222
metaplot_deletions0.2800.0000.281
metaplot_insertions0.1600.0040.164
metaplot_mismatches0.3280.0000.327
plot_cuts0.3960.0080.407
plot_deletions0.0560.0040.062
plot_height000
plot_heterogeneity0.3440.0040.349
plot_insertions0.460.000.46
plot_mismatches0.4920.0000.491
plot_variants0.7720.0000.772
readCounts-set0.0040.0000.005
readCounts0.0040.0000.005
rveReads-set0.0040.0000.006
rveReads0.2800.0040.283
rveReadsType-set0.0080.0000.006
rveReadsType0.0000.0040.004
unassignedCount0.0040.0000.004
unassignedData-set0.0040.0000.005
unassignedData0.0080.0000.006
writeAlignments0.0160.0000.017