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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:58 -0400 (Tue, 16 Apr 2019).
| Package 44/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| amplican 1.4.1 Eivind Valen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
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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_1.4.1.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
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL amplican ### ############################################################################## ############################################################################## * 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)
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
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.832 | 0.090 | 1.940 | |
| amplicanAlign | 7.830 | 0.304 | 8.211 | |
| amplicanConsensus | 0.379 | 0.398 | 0.136 | |
| amplicanFilter | 0.231 | 0.270 | 0.073 | |
| amplicanMap | 0.685 | 0.684 | 0.297 | |
| amplicanNormalize | 1.299 | 0.003 | 0.127 | |
| amplicanOverlap | 0.407 | 0.002 | 0.035 | |
| amplicanPipeline | 6.648 | 2.269 | 5.201 | |
| amplicanReport | 0.089 | 0.113 | 0.034 | |
| amplicanSummarize | 0.184 | 0.207 | 0.059 | |
| amplican_print_reads | 0.746 | 0.666 | 0.342 | |
| assignedCount | 0.024 | 0.001 | 0.028 | |
| barcodeData-set | 0.007 | 0.001 | 0.007 | |
| barcodeData | 0.011 | 0.000 | 0.012 | |
| comb_along | 0.041 | 0.003 | 0.045 | |
| experimentData-set | 0.01 | 0.00 | 0.01 | |
| experimentData | 0.017 | 0.002 | 0.019 | |
| extractEvents | 3.174 | 0.029 | 3.233 | |
| findEOP | 0.009 | 0.001 | 0.009 | |
| findLQR | 0.014 | 0.011 | 0.007 | |
| findPD | 0.023 | 0.033 | 0.007 | |
| fwdReads-set | 0.035 | 0.047 | 0.010 | |
| fwdReads | 0.873 | 0.747 | 0.491 | |
| fwdReadsType-set | 0.005 | 0.000 | 0.006 | |
| fwdReadsType | 0.005 | 0.000 | 0.004 | |
| lookupAlignment | 0.308 | 0.002 | 0.311 | |
| metaplot_deletions | 1.204 | 1.726 | 0.445 | |
| metaplot_insertions | 0.845 | 1.014 | 0.407 | |
| metaplot_mismatches | 1.637 | 0.500 | 0.405 | |
| plot_cuts | 0.895 | 0.976 | 0.472 | |
| plot_deletions | 0.262 | 0.376 | 0.100 | |
| plot_height | 0.003 | 0.005 | 0.001 | |
| plot_heterogeneity | 1.012 | 1.198 | 0.464 | |
| plot_insertions | 1.057 | 1.016 | 0.614 | |
| plot_mismatches | 1.046 | 0.916 | 0.599 | |
| plot_variants | 1.674 | 1.191 | 1.193 | |
| readCounts-set | 0.010 | 0.001 | 0.010 | |
| readCounts | 0.004 | 0.000 | 0.005 | |
| rveReads-set | 0.010 | 0.001 | 0.010 | |
| rveReads | 0.447 | 0.002 | 0.451 | |
| rveReadsType-set | 0.01 | 0.00 | 0.01 | |
| rveReadsType | 0.004 | 0.000 | 0.005 | |
| unassignedCount | 0.005 | 0.000 | 0.005 | |
| unassignedData-set | 0.005 | 0.000 | 0.006 | |
| unassignedData | 0.012 | 0.001 | 0.012 | |
| writeAlignments | 0.024 | 0.001 | 0.025 | |