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 08:58:46 -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: /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_1.2.1.tar.gz |
| StartedAt: 2018-10-16 19:50:15 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:52:58 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 163.2 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_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/amplican.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.1’
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
amplicanPipeline 5.121 1.539 3.698
amplicanAlign 6.301 0.338 6.714
* 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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
27.180 3.262 25.333
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.810 | 0.097 | 1.932 | |
| amplicanAlign | 6.301 | 0.338 | 6.714 | |
| amplicanConsensus | 0.182 | 0.026 | 0.209 | |
| amplicanFilter | 0.049 | 0.009 | 0.059 | |
| amplicanMap | 0.275 | 0.032 | 0.308 | |
| amplicanNormalize | 0.110 | 0.002 | 0.052 | |
| amplicanOverlap | 0.234 | 0.005 | 0.033 | |
| amplicanPipeline | 5.121 | 1.539 | 3.698 | |
| amplicanReport | 0.119 | 0.175 | 0.043 | |
| amplicanSummarize | 0.126 | 0.142 | 0.039 | |
| amplican_print_reads | 0.808 | 0.679 | 0.402 | |
| assignedCount | 0.030 | 0.001 | 0.031 | |
| barcodeData-set | 0.010 | 0.000 | 0.011 | |
| barcodeData | 0.011 | 0.001 | 0.012 | |
| comb_along | 0.035 | 0.003 | 0.039 | |
| experimentData-set | 0.011 | 0.000 | 0.011 | |
| experimentData | 0.016 | 0.001 | 0.017 | |
| extractEvents | 2.773 | 0.025 | 2.834 | |
| findEOP | 0.006 | 0.001 | 0.006 | |
| findLQR | 0.006 | 0.001 | 0.006 | |
| findPD | 0.006 | 0.000 | 0.006 | |
| fwdReads-set | 0.010 | 0.000 | 0.011 | |
| fwdReads | 0.369 | 0.002 | 0.379 | |
| fwdReadsType-set | 0.010 | 0.001 | 0.010 | |
| fwdReadsType | 0.007 | 0.000 | 0.007 | |
| lookupAlignment | 0.317 | 0.001 | 0.325 | |
| metaplot_deletions | 0.845 | 0.944 | 0.441 | |
| metaplot_insertions | 0.206 | 0.002 | 0.210 | |
| metaplot_mismatches | 0.472 | 0.003 | 0.480 | |
| plot_cuts | 0.512 | 0.004 | 0.520 | |
| plot_deletions | 0.281 | 0.317 | 0.110 | |
| plot_height | 0.008 | 0.010 | 0.003 | |
| plot_heterogeneity | 0.798 | 0.472 | 0.459 | |
| plot_insertions | 0.712 | 0.005 | 0.728 | |
| plot_mismatches | 0.678 | 0.005 | 0.689 | |
| plot_variants | 1.326 | 0.067 | 1.062 | |
| readCounts-set | 0.009 | 0.000 | 0.009 | |
| readCounts | 0.007 | 0.000 | 0.006 | |
| rveReads-set | 0.011 | 0.001 | 0.011 | |
| rveReads | 0.348 | 0.001 | 0.350 | |
| rveReadsType-set | 0.006 | 0.001 | 0.006 | |
| rveReadsType | 0.006 | 0.000 | 0.007 | |
| unassignedCount | 0.008 | 0.000 | 0.009 | |
| unassignedData-set | 0.011 | 0.001 | 0.012 | |
| unassignedData | 0.011 | 0.001 | 0.012 | |
| writeAlignments | 0.023 | 0.001 | 0.023 | |