Eivind Valen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/amplican |
| Branch: RELEASE_3_6 |
| Last Commit: cc2b529 |
| Last Changed Date: 2017-10-30 12:41:46 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:41 -0400 (Thu, 12 Apr 2018).
| Package 40/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| amplican 1.0.0 Eivind Valen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: amplican |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz |
| StartedAt: 2018-04-11 21:23:40 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:26:05 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 144.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: amplican.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 ... NOTE
installed size is 13.1Mb
sub-directories of 1Mb or more:
doc 12.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... 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 ... NOTE
Package unavailable to check Rd xrefs: ‘CrispRVariants’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
metaplot_deletions 5.836 0.052 6.298
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck/00check.log’
for details.
amplican.Rcheck/00install.out
* installing *source* package ‘amplican’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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: 74 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
26.628 0.336 26.669
amplican.Rcheck/amplican-Ex.timings
| name | user | system | elapsed | |
| AlignmentsExperimentSet-class | 1.604 | 0.016 | 1.622 | |
| amplicanAlign | 4.496 | 0.080 | 4.612 | |
| amplicanConsensus | 0.036 | 0.000 | 0.030 | |
| amplicanFilter | 0.348 | 0.012 | 0.146 | |
| amplicanMap | 0.976 | 0.000 | 0.976 | |
| amplicanNormalize | 0.224 | 0.000 | 0.207 | |
| amplicanOverlap | 0.068 | 0.000 | 0.069 | |
| amplicanPipeline | 4.836 | 0.052 | 4.292 | |
| amplicanReport | 0.084 | 0.012 | 0.093 | |
| amplicanSummarize | 0.276 | 0.000 | 0.083 | |
| amplican_print_reads | 0.332 | 0.008 | 0.341 | |
| assignedCount | 0.064 | 0.000 | 0.063 | |
| barcodeData-set | 0.004 | 0.000 | 0.005 | |
| barcodeData | 0.008 | 0.000 | 0.005 | |
| comb_along | 0.012 | 0.004 | 0.018 | |
| experimentData-set | 0.004 | 0.000 | 0.005 | |
| experimentData | 0.004 | 0.004 | 0.007 | |
| extractEvents | 1.992 | 0.012 | 2.005 | |
| findEOP | 0.004 | 0.000 | 0.004 | |
| findLQR | 0.004 | 0.000 | 0.003 | |
| findPD | 0.004 | 0.000 | 0.003 | |
| fwdReads-set | 0.008 | 0.000 | 0.006 | |
| fwdReads | 0.084 | 0.000 | 0.082 | |
| lookupAlignment | 0.412 | 0.000 | 0.412 | |
| metaplot_deletions | 5.836 | 0.052 | 6.298 | |
| metaplot_insertions | 0.568 | 0.000 | 0.566 | |
| metaplot_mismatches | 0.008 | 0.000 | 0.006 | |
| plot_cuts | 0.496 | 0.000 | 0.496 | |
| plot_deletions | 0.352 | 0.000 | 0.311 | |
| plot_height | 0.000 | 0.000 | 0.001 | |
| plot_heterogeneity | 0.656 | 0.000 | 0.652 | |
| plot_insertions | 0.288 | 0.000 | 0.288 | |
| plot_mismatches | 0.284 | 0.000 | 0.286 | |
| plot_variants | 0.864 | 0.000 | 0.850 | |
| readCounts-set | 0.008 | 0.004 | 0.010 | |
| readCounts | 0.008 | 0.000 | 0.008 | |
| rveReads-set | 0.008 | 0.000 | 0.010 | |
| rveReads | 0.140 | 0.000 | 0.139 | |
| unassignedCount | 0.004 | 0.000 | 0.007 | |
| unassignedData-set | 0.008 | 0.000 | 0.005 | |
| unassignedData | 0.008 | 0.000 | 0.007 | |
| writeAlignments | 0.02 | 0.00 | 0.02 | |