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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:40 -0400 (Wed, 17 Oct 2018).
| Package 41/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| amplican 1.2.1 Eivind Valen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL amplican ### ############################################################################## ############################################################################## * 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)
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
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.280 | 0.020 | 1.299 | |
| amplicanAlign | 4.456 | 0.240 | 4.744 | |
| amplicanConsensus | 0.084 | 0.016 | 0.140 | |
| amplicanFilter | 0.028 | 0.000 | 0.028 | |
| amplicanMap | 0.156 | 0.000 | 0.159 | |
| amplicanNormalize | 0.028 | 0.000 | 0.027 | |
| amplicanOverlap | 0.016 | 0.000 | 0.017 | |
| amplicanPipeline | 2.244 | 0.012 | 2.282 | |
| amplicanReport | 0.024 | 0.000 | 0.026 | |
| amplicanSummarize | 0.028 | 0.000 | 0.029 | |
| amplican_print_reads | 0.336 | 0.004 | 0.341 | |
| assignedCount | 0.028 | 0.004 | 0.032 | |
| barcodeData-set | 0.012 | 0.000 | 0.009 | |
| barcodeData | 0.012 | 0.000 | 0.010 | |
| comb_along | 0.032 | 0.000 | 0.034 | |
| experimentData-set | 0.008 | 0.000 | 0.009 | |
| experimentData | 0.008 | 0.004 | 0.013 | |
| extractEvents | 1.744 | 0.028 | 1.774 | |
| findEOP | 0.004 | 0.000 | 0.004 | |
| findLQR | 0.004 | 0.000 | 0.005 | |
| findPD | 0.004 | 0.000 | 0.005 | |
| fwdReads-set | 0.004 | 0.000 | 0.005 | |
| fwdReads | 0.256 | 0.000 | 0.254 | |
| fwdReadsType-set | 0.008 | 0.000 | 0.007 | |
| fwdReadsType | 0.004 | 0.000 | 0.005 | |
| lookupAlignment | 0.224 | 0.000 | 0.222 | |
| metaplot_deletions | 0.280 | 0.000 | 0.281 | |
| metaplot_insertions | 0.160 | 0.004 | 0.164 | |
| metaplot_mismatches | 0.328 | 0.000 | 0.327 | |
| plot_cuts | 0.396 | 0.008 | 0.407 | |
| plot_deletions | 0.056 | 0.004 | 0.062 | |
| plot_height | 0 | 0 | 0 | |
| plot_heterogeneity | 0.344 | 0.004 | 0.349 | |
| plot_insertions | 0.46 | 0.00 | 0.46 | |
| plot_mismatches | 0.492 | 0.000 | 0.491 | |
| plot_variants | 0.772 | 0.000 | 0.772 | |
| readCounts-set | 0.004 | 0.000 | 0.005 | |
| readCounts | 0.004 | 0.000 | 0.005 | |
| rveReads-set | 0.004 | 0.000 | 0.006 | |
| rveReads | 0.280 | 0.004 | 0.283 | |
| rveReadsType-set | 0.008 | 0.000 | 0.006 | |
| rveReadsType | 0.000 | 0.004 | 0.004 | |
| unassignedCount | 0.004 | 0.000 | 0.004 | |
| unassignedData-set | 0.004 | 0.000 | 0.005 | |
| unassignedData | 0.008 | 0.000 | 0.006 | |
| writeAlignments | 0.016 | 0.000 | 0.017 | |