Patrick C.N. Martin
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ChIPanalyser |
| Branch: RELEASE_3_6 |
| Last Commit: 95cd8ed |
| Last Changed Date: 2017-10-30 12:41:41 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:39 -0400 (Thu, 12 Apr 2018).
| Package 215/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPanalyser 1.0.0 Patrick C.N. Martin
| 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: ChIPanalyser |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPanalyser_1.0.0.tar.gz |
| StartedAt: 2018-04-11 22:08:09 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:11:27 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 197.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPanalyser_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ChIPanalyser.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 ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.0.0’
* 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 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 ... 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
genomicProfileParameters-class 4.72 0.152 5.111
* 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
* installing *source* package ‘ChIPanalyser’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (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.
> 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, 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
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 -- Wed Apr 11 22:11:21 2018
***********************************************
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
12.452 0.220 12.688
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
| name | user | system | elapsed | |
| AllSitesAboveThreshold | 0.128 | 0.000 | 0.129 | |
| BPFrequency | 0.112 | 0.008 | 0.119 | |
| BPFrequency_- | 0.004 | 0.000 | 0.002 | |
| ChIPanalyser-package | 0 | 0 | 0 | |
| DNASequenceLength | 0.004 | 0.000 | 0.002 | |
| DNASequenceLength_- | 0.004 | 0.000 | 0.002 | |
| GRList-class | 0.000 | 0.000 | 0.001 | |
| NoAccess | 0.040 | 0.000 | 0.039 | |
| PFMFormat | 0.044 | 0.000 | 0.041 | |
| PFMFormat_ | 0.036 | 0.000 | 0.036 | |
| PWMThreshold | 0.040 | 0.000 | 0.039 | |
| PWMThreshold_- | 0.032 | 0.000 | 0.035 | |
| PWMpseudocount | 0.032 | 0.000 | 0.035 | |
| PWMpseudocount_- | 0.032 | 0.000 | 0.035 | |
| PositionFrequencyMatrix | 0.032 | 0.004 | 0.036 | |
| PositionFrequencyMatrix_- | 0.032 | 0.000 | 0.032 | |
| PositionWeightMatrix | 0.036 | 0.000 | 0.035 | |
| PositionWeightMatrix_- | 0.028 | 0.000 | 0.028 | |
| ScalingFactorPWM | 0.036 | 0.004 | 0.037 | |
| ScalingFactorPWM_- | 0.036 | 0.000 | 0.038 | |
| averageExpPWMScore | 0.036 | 0.000 | 0.040 | |
| backgroundSignal | 0.000 | 0.000 | 0.002 | |
| backgroundSignal_- | 0.004 | 0.000 | 0.004 | |
| boundMolecules | 0.000 | 0.004 | 0.003 | |
| boundMolecules_- | 0.008 | 0.000 | 0.010 | |
| chipMean | 0.004 | 0.000 | 0.003 | |
| chipMean_- | 0.004 | 0.000 | 0.003 | |
| chipSd | 0.000 | 0.000 | 0.003 | |
| chipSd_- | 0.004 | 0.000 | 0.003 | |
| chipSmooth | 0.000 | 0.000 | 0.003 | |
| chipSmooth_- | 0.000 | 0.000 | 0.004 | |
| computeChipProfile | 0.000 | 0.000 | 0.002 | |
| computeGenomeWidePWMScore | 0.000 | 0.000 | 0.002 | |
| computeOccupancy | 0.000 | 0.004 | 0.002 | |
| computeOptimal | 0.004 | 0.000 | 0.003 | |
| computePWMScore | 0.000 | 0.000 | 0.002 | |
| data | 0.000 | 0.000 | 0.001 | |
| genomicProfileParameters-class | 4.720 | 0.152 | 5.111 | |
| genomicProfileParameters | 2.344 | 0.076 | 2.423 | |
| maxPWMScore | 0.004 | 0.000 | 0.002 | |
| maxSignal | 0.004 | 0.000 | 0.005 | |
| maxSignal_- | 0.004 | 0.000 | 0.003 | |
| minPWMScore | 0.004 | 0.000 | 0.002 | |
| naturalLog | 0.036 | 0.000 | 0.035 | |
| naturalLog_- | 0.036 | 0.004 | 0.041 | |
| noOfSites | 0.032 | 0.000 | 0.035 | |
| noOfSites_- | 0.028 | 0.004 | 0.034 | |
| occupancyProfileParameters-class | 0.004 | 0.004 | 0.006 | |
| occupancyProfileParameters | 0.004 | 0.000 | 0.005 | |
| ploidy | 0.000 | 0.000 | 0.003 | |
| ploidy_- | 0.000 | 0.000 | 0.003 | |
| plotOccupancyProfile | 0.000 | 0.000 | 0.003 | |
| plotOptimalHeatMaps | 0.004 | 0.000 | 0.002 | |
| profileAccuracyEstimate | 0.004 | 0.000 | 0.002 | |
| removeBackground | 0.004 | 0.000 | 0.003 | |
| removeBackground_- | 0.004 | 0.000 | 0.004 | |
| searchSites | 0.004 | 0.000 | 0.002 | |
| stepSize | 0.004 | 0.000 | 0.004 | |
| stepSize_- | 0.004 | 0.000 | 0.003 | |
| strandRule | 0.032 | 0.000 | 0.032 | |
| strandRule_- | 0.036 | 0.000 | 0.035 | |
| thetaThreshold | 0.004 | 0.000 | 0.003 | |
| thetaThreshold_- | 0.004 | 0.000 | 0.003 | |
| whichstrand | 0.04 | 0.00 | 0.04 | |
| whichstrand_- | 0.032 | 0.004 | 0.035 | |