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This page was generated on 2019-03-19 12:52:53 -0400 (Tue, 19 Mar 2019).
Package 790/1676 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
InPAS 1.15.1 Jianhong Ou
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK |
Package: InPAS |
Version: 1.15.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_1.15.1.tar.gz |
StartedAt: 2019-03-19 01:26:44 -0400 (Tue, 19 Mar 2019) |
EndedAt: 2019-03-19 01:33:15 -0400 (Tue, 19 Mar 2019) |
EllapsedTime: 390.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: InPAS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/InPAS.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘InPAS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘InPAS’ version ‘1.15.1’ * 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 ‘InPAS’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed getUTR3eSet 11.304 0.170 11.556 filterRes 10.847 0.287 11.204 testUsage 8.418 0.092 8.541 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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
InPAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InPAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘InPAS’ ... ** R ** data ** 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 (InPAS)
InPAS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" 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. > require("BSgenome.Mmusculus.UCSC.mm10") || stop("can not load BSgenome.") Loading required package: BSgenome.Mmusculus.UCSC.mm10 Loading required package: BSgenome 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, 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: 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer [1] TRUE > require("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.") Loading required package: BSgenome.Hsapiens.UCSC.hg19 [1] TRUE > require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load TxDb") Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [1] TRUE > require("rtracklayer") || stop("can not load rtracklayer.") [1] TRUE > require("limma") || stop("can not load limma") Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA [1] TRUE > BiocGenerics:::testPackage("InPAS") seqlevelsStyle of genome is different from bedgraph file. RUNIT TEST PROTOCOL -- Tue Mar 19 01:33:09 2019 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 31.486 1.243 32.897
InPAS.Rcheck/InPAS-Ex.timings
name | user | system | elapsed | |
CPsites | 0.002 | 0.000 | 0.002 | |
coverageFromBedGraph | 0.002 | 0.000 | 0.002 | |
coverageRate | 0.003 | 0.001 | 0.004 | |
filterRes | 10.847 | 0.287 | 11.204 | |
fisher.exact.test | 0.078 | 0.008 | 0.087 | |
getUTR3eSet | 11.304 | 0.170 | 11.556 | |
inPAS | 0.003 | 0.001 | 0.003 | |
limmaAnalyze | 0.034 | 0.002 | 0.036 | |
prepare4GSEA | 0.112 | 0.002 | 0.115 | |
singleGroupAnalyze | 0.011 | 0.001 | 0.011 | |
singleSampleAnalyze | 0.004 | 0.001 | 0.005 | |
testUsage | 8.418 | 0.092 | 8.541 | |
usage4plot | 1.561 | 0.219 | 1.791 | |
utr3.danRer10 | 0.362 | 0.018 | 0.381 | |
utr3.hg19 | 0.669 | 0.023 | 0.697 | |
utr3.mm10 | 0.564 | 0.018 | 0.583 | |
utr3Annotation | 0.000 | 0.000 | 0.001 | |
utr3UsageEstimation | 0.002 | 0.000 | 0.002 | |