Patrick C.N. Martin
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ChIPanalyser |
| Branch: RELEASE_3_8 |
| Last Commit: b5a2283 |
| Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:00 -0400 (Tue, 16 Apr 2019).
| Package 242/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPanalyser 1.4.0 Patrick C.N. Martin
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ChIPanalyser |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz |
| StartedAt: 2019-04-15 22:48:24 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:52:19 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 234.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ChIPanalyser.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPanalyser’ version ‘1.4.0’ * package encoding: UTF-8 * 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 ‘ChIPanalyser’ 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 * 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
ChIPanalyser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ChIPanalyser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘ChIPanalyser’ ... ** R ** data *** moving datasets to lazyload DB ** 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 (ChIPanalyser)
ChIPanalyser.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("ChIPanalyser")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BSgenome.Dmelanogaster.UCSC.dm3
RUNIT TEST PROTOCOL -- Mon Apr 15 22:52:13 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
14.724 0.524 15.296
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
| name | user | system | elapsed | |
| AllSitesAboveThreshold | 0.196 | 0.000 | 0.203 | |
| BPFrequency | 0.144 | 0.012 | 0.158 | |
| BPFrequency_- | 0.004 | 0.000 | 0.003 | |
| ChIPanalyser-package | 0.000 | 0.000 | 0.001 | |
| DNASequenceLength | 0.000 | 0.000 | 0.003 | |
| DNASequenceLength_- | 0.000 | 0.004 | 0.003 | |
| GRList-class | 0.004 | 0.000 | 0.001 | |
| NoAccess | 0.052 | 0.004 | 0.056 | |
| PFMFormat | 0.056 | 0.000 | 0.057 | |
| PFMFormat_ | 0.052 | 0.004 | 0.058 | |
| PWMThreshold | 0.052 | 0.008 | 0.056 | |
| PWMThreshold_- | 0.052 | 0.004 | 0.058 | |
| PWMpseudocount | 0.052 | 0.004 | 0.057 | |
| PWMpseudocount_- | 0.060 | 0.000 | 0.058 | |
| PositionFrequencyMatrix | 0.044 | 0.012 | 0.058 | |
| PositionFrequencyMatrix_- | 0.028 | 0.020 | 0.046 | |
| PositionWeightMatrix | 0.052 | 0.008 | 0.058 | |
| PositionWeightMatrix_- | 0.040 | 0.004 | 0.043 | |
| ScalingFactorPWM | 0.060 | 0.000 | 0.059 | |
| ScalingFactorPWM_- | 0.056 | 0.004 | 0.060 | |
| averageExpPWMScore | 0.056 | 0.004 | 0.057 | |
| backgroundSignal | 0.004 | 0.000 | 0.005 | |
| backgroundSignal_- | 0.004 | 0.000 | 0.005 | |
| boundMolecules | 0.000 | 0.004 | 0.004 | |
| boundMolecules_- | 0.004 | 0.000 | 0.004 | |
| chipMean | 0.004 | 0.000 | 0.002 | |
| chipMean_- | 0.004 | 0.000 | 0.002 | |
| chipSd | 0.000 | 0.000 | 0.002 | |
| chipSd_- | 0.000 | 0.000 | 0.002 | |
| chipSmooth | 0.004 | 0.000 | 0.002 | |
| chipSmooth_- | 0.000 | 0.004 | 0.004 | |
| computeChipProfile | 0.000 | 0.000 | 0.002 | |
| computeGenomeWidePWMScore | 0.000 | 0.000 | 0.001 | |
| computeOccupancy | 0.004 | 0.000 | 0.002 | |
| computeOptimal | 0.000 | 0.000 | 0.002 | |
| computePWMScore | 0.000 | 0.004 | 0.002 | |
| data | 0.000 | 0.000 | 0.001 | |
| genomicProfileParameters-class | 4.092 | 0.112 | 4.395 | |
| genomicProfileParameters | 2.860 | 0.068 | 2.933 | |
| maxPWMScore | 0.004 | 0.000 | 0.003 | |
| maxSignal | 0.004 | 0.000 | 0.003 | |
| maxSignal_- | 0.000 | 0.004 | 0.004 | |
| minPWMScore | 0.004 | 0.000 | 0.002 | |
| naturalLog | 0.056 | 0.000 | 0.054 | |
| naturalLog_- | 0.048 | 0.004 | 0.054 | |
| noOfSites | 0.032 | 0.000 | 0.034 | |
| noOfSites_- | 0.048 | 0.000 | 0.049 | |
| occupancyProfileParameters-class | 0.004 | 0.000 | 0.007 | |
| occupancyProfileParameters | 0.004 | 0.000 | 0.007 | |
| ploidy | 0.004 | 0.000 | 0.002 | |
| ploidy_- | 0.004 | 0.000 | 0.002 | |
| plotOccupancyProfile | 0.000 | 0.000 | 0.002 | |
| plotOptimalHeatMaps | 0.004 | 0.000 | 0.002 | |
| processingChIPseq | 0.048 | 0.004 | 0.054 | |
| profileAccuracyEstimate | 0.004 | 0.000 | 0.002 | |
| removeBackground | 0.000 | 0.000 | 0.002 | |
| removeBackground_- | 0.004 | 0.000 | 0.003 | |
| searchSites | 0.004 | 0.000 | 0.002 | |
| stepSize | 0.000 | 0.000 | 0.002 | |
| stepSize_- | 0.000 | 0.000 | 0.002 | |
| strandRule | 0.036 | 0.000 | 0.035 | |
| strandRule_- | 0.032 | 0.000 | 0.031 | |
| whichstrand | 0.032 | 0.000 | 0.031 | |
| whichstrand_- | 0.028 | 0.004 | 0.032 | |