Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:45:39 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz |
StartedAt: 2018-04-12 00:17:33 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:20:25 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 171.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: amplican.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings amplican_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/amplican.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.0.0’ * 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 17.2Mb sub-directories of 1Mb or more: doc 16.6Mb * 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 6.671 0.180 7.092 amplicanAlign 5.541 0.154 5.798 amplicanPipeline 4.976 0.182 4.897 * 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 ‘/Users/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-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, 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 29.186 0.881 29.913
amplican.Rcheck/amplican-Ex.timings
name | user | system | elapsed | |
AlignmentsExperimentSet-class | 1.900 | 0.046 | 1.985 | |
amplicanAlign | 5.541 | 0.154 | 5.798 | |
amplicanConsensus | 0.046 | 0.003 | 0.045 | |
amplicanFilter | 0.180 | 0.029 | 0.106 | |
amplicanMap | 1.444 | 0.052 | 1.337 | |
amplicanNormalize | 0.317 | 0.019 | 0.281 | |
amplicanOverlap | 0.153 | 0.024 | 0.090 | |
amplicanPipeline | 4.976 | 0.182 | 4.897 | |
amplicanReport | 0.131 | 0.026 | 0.100 | |
amplicanSummarize | 0.066 | 0.006 | 0.060 | |
amplican_print_reads | 0.596 | 0.050 | 0.482 | |
assignedCount | 0.092 | 0.001 | 0.094 | |
barcodeData-set | 0.008 | 0.001 | 0.008 | |
barcodeData | 0.008 | 0.000 | 0.009 | |
comb_along | 0.034 | 0.002 | 0.038 | |
experimentData-set | 0.008 | 0.000 | 0.009 | |
experimentData | 0.013 | 0.001 | 0.014 | |
extractEvents | 2.545 | 0.022 | 2.627 | |
findEOP | 0.005 | 0.001 | 0.005 | |
findLQR | 0.004 | 0.000 | 0.004 | |
findPD | 0.004 | 0.001 | 0.005 | |
fwdReads-set | 0.008 | 0.001 | 0.008 | |
fwdReads | 0.094 | 0.001 | 0.098 | |
lookupAlignment | 0.564 | 0.002 | 0.572 | |
metaplot_deletions | 6.671 | 0.180 | 7.092 | |
metaplot_insertions | 0.730 | 0.002 | 0.747 | |
metaplot_mismatches | 0.009 | 0.001 | 0.009 | |
plot_cuts | 0.636 | 0.003 | 0.644 | |
plot_deletions | 0.669 | 0.118 | 0.405 | |
plot_height | 0.001 | 0.001 | 0.001 | |
plot_heterogeneity | 1.049 | 0.073 | 0.833 | |
plot_insertions | 0.337 | 0.002 | 0.346 | |
plot_mismatches | 0.325 | 0.002 | 0.337 | |
plot_variants | 1.765 | 0.050 | 1.498 | |
readCounts-set | 0.005 | 0.000 | 0.006 | |
readCounts | 0.005 | 0.000 | 0.006 | |
rveReads-set | 0.005 | 0.000 | 0.005 | |
rveReads | 0.119 | 0.006 | 0.130 | |
unassignedCount | 0.007 | 0.001 | 0.007 | |
unassignedData-set | 0.008 | 0.001 | 0.008 | |
unassignedData | 0.009 | 0.001 | 0.010 | |
writeAlignments | 0.022 | 0.004 | 0.027 | |