Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:10:41 -0400 (Thu, 12 Apr 2018).
Package 1130/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Rcade 1.20.0 Jonathan Cairns
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | ![]() |
Package: Rcade |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.20.0.tar.gz |
StartedAt: 2018-04-12 02:11:32 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 02:14:28 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 175.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rcade.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Rcade.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 ‘Rcade/DESCRIPTION’ ... OK * this is package ‘Rcade’ version ‘1.20.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rcade’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: extdata 5.2Mb * 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 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 ... NOTE constructRcadeTable: no visible binding for global variable ‘p.DE’ constructRcadeTable: no visible binding for global variable ‘p.ChIP’ plotBBB,Rcade: no visible global function definition for ‘decorate3d’ Undefined global functions or variables: decorate3d p.ChIP p.DE * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed RcadeAnalysis 5.816 0.04 5.861 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.6-bioc/meat/Rcade.Rcheck/00check.log’ for details.
Rcade.Rcheck/00install.out
* installing *source* package ‘Rcade’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rcade)
Rcade.Rcheck/tests/runTests.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. > require("Rcade") || stop("unable to load Rcade") Loading required package: Rcade Loading required package: GenomicRanges Loading required package: stats4 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: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: baySeq Loading required package: abind Welcome to Rcade - version 1.20.0 If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade"). Attaching package: 'Rcade' The following object is masked from 'package:BiocGenerics': plotPCA [1] TRUE > BiocGenerics:::testPackage("Rcade") File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation. File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation. File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation. File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Found 24 chromosomes, of which 0 are present in the annotation. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation. File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Counting reads. File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Counting reads. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Counting reads. File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Counting reads. RUNIT TEST PROTOCOL -- Thu Apr 12 02:14:26 2018 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : Rcade RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 10.228 0.172 10.411
Rcade.Rcheck/Rcade-Ex.timings
name | user | system | elapsed | |
Rcade-class | 0.964 | 0.016 | 0.982 | |
RcadeAnalysis | 5.816 | 0.040 | 5.861 | |
RcadeSTAT1 | 0.012 | 0.000 | 0.009 | |
constructRcadeTable | 0.108 | 0.000 | 0.108 | |
countReads | 1.752 | 0.000 | 1.753 | |
defineBins | 0.008 | 0.000 | 0.011 | |
diffCountsBaySeq | 4.708 | 0.004 | 4.715 | |
exportRcade-methods | 0.000 | 0.004 | 0.002 | |