| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:10 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the ChIPanalyser package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPanalyser.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 296/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPanalyser 1.17.1 (landing page) Patrick C.N. Martin
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChIPanalyser |
| Version: 1.17.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPanalyser_1.17.1.tar.gz |
| StartedAt: 2022-03-17 18:42:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:46:07 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 211.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPanalyser_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChIPanalyser.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChIPanalyser/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPanalyser' version '1.17.1' * 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 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 ... NOTE .methodSwitchGoF: no visible global function definition for 'ks' Undefined global functions or variables: ks * 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 LazyData ... 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: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/ChIPanalyser.Rcheck/00check.log' for details.
ChIPanalyser.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ChIPanalyser' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'drop' in package 'ChIPanalyser'
** help
*** installing help indices
converting help for package 'ChIPanalyser'
finding HTML links ... done
BPFrequency-methods html
BPFrequency html
BPFrequency_--methods html
BPFrequency_- html
ChIPScore-class html
ChIPanalyser-package html
DNASequenceLength-methods html
DNASequenceLength html
GRList-class html
PFMFormat-methods html
PFMFormat html
PFMFormat_--methods html
PFMFormat_ html
PWMThreshold-methods html
PWMThreshold html
PWMThreshold_--methods html
PWMThreshold_- html
PWMpseudocount-methods html
PWMpseudocount html
PWMpseudocount_--methods html
PWMpseudocount_- html
PositionFrequencyMatrix-methods html
PositionFrequencyMatrix html
PositionFrequencyMatrix_--methods html
PositionFrequencyMatrix_- html
PositionWeightMatrix-methods html
PositionWeightMatrix html
PositionWeightMatrix_--methods html
PositionWeightMatrix_- html
averageExpPWMScore-methods html
averageExpPWMScore html
backgroundSignal-methods html
backgroundSignal html
backgroundSignal_--methods html
backgroundSignal_- html
boundMolecules-methods html
boundMolecules html
boundMolecules_--methods html
boundMolecules_- html
chipMean-methods html
chipMean html
chipMean_--methods html
chipMean_- html
chipSd-methods html
chipSd html
chipSd_--methods html
chipSd_- html
chipSmooth-methods html
chipSmooth html
chipSmooth_--methods html
chipSmooth_- html
computeChIPProfile html
finding level-2 HTML links ... done
computeGenomeWideScores html
computeOccupancy html
computeOptimal html
computePWMScore html
data html
drop-methods html
drop html
genomicProfiles-class html
genomicProfiles html
genomicProfilesInternal-class html
initialize-methods html
lambdaPWM-methods html
lambdaPWM html
lambdaPWM_--methods html
lambdaPWM_ html
loci-class html
loci-methods html
loci html
lociWidth-methods html
lociWidth html
lociWidth_--methods html
lociWidth_ html
maxPWMScore-methods html
maxPWMScore html
maxSignal-methods html
maxSignal html
maxSignal_--methods html
maxSignal_- html
minPWMScore-methods html
minPWMScore html
naturalLog-methods html
naturalLog html
naturalLog_--methods html
naturalLog_- html
noOfSites-methods html
noOfSites html
noOfSites_--methods html
noOfSites_- html
noiseFilter-methods html
noiseFilter html
noiseFilter_--methods html
noiseFilter_ html
nos-class html
parameterOptions-class html
parameterOptions html
ploidy-methods html
ploidy html
ploidy_--methods html
ploidy_- html
plotOccupancyProfile html
plotOptimalHeatMaps html
processingChIP html
profileAccuracyEstimate html
profiles-methods html
removeBackground-methods html
removeBackground html
removeBackground_--methods html
removeBackground_- html
scores-methods html
scores html
searchSites html
show-methods html
stepSize-methods html
stepSize html
stepSize_--methods html
stepSize_- html
strandRule-methods html
strandRule html
strandRule_--methods html
strandRule_- html
whichstrand-methods html
whichstrand html
whichstrand_--methods html
whichstrand_- html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPanalyser)
Making 'packages.html' ... done
ChIPanalyser.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ChIPanalyser'
The following object is masked from 'package:IRanges':
drop
The following object is masked from 'package:base':
drop
Loading required package: BSgenome.Dmelanogaster.UCSC.dm3
RUNIT TEST PROTOCOL -- Thu Mar 17 18:45:50 2022
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPanalyser RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.84 1.20 14.03
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
| name | user | system | elapsed | |
| BPFrequency | 0.11 | 0.00 | 0.11 | |
| BPFrequency_- | 0.01 | 0.00 | 0.01 | |
| ChIPScore-class | 0.00 | 0.02 | 0.02 | |
| ChIPanalyser-package | 0 | 0 | 0 | |
| DNASequenceLength | 0 | 0 | 0 | |
| GRList-class | 0 | 0 | 0 | |
| PFMFormat | 0.10 | 0.06 | 0.15 | |
| PFMFormat_ | 0.04 | 0.01 | 0.07 | |
| PWMThreshold | 0.02 | 0.00 | 0.01 | |
| PWMThreshold_- | 0.02 | 0.00 | 0.02 | |
| PWMpseudocount | 0.01 | 0.00 | 0.01 | |
| PWMpseudocount_- | 0.02 | 0.00 | 0.02 | |
| PositionFrequencyMatrix | 0.04 | 0.00 | 0.05 | |
| PositionFrequencyMatrix_- | 0.02 | 0.00 | 0.01 | |
| PositionWeightMatrix | 0.02 | 0.05 | 0.06 | |
| PositionWeightMatrix_- | 0.01 | 0.00 | 0.02 | |
| averageExpPWMScore | 0.05 | 0.00 | 0.05 | |
| backgroundSignal | 0.01 | 0.00 | 0.01 | |
| backgroundSignal_- | 0.00 | 0.02 | 0.02 | |
| boundMolecules | 0.00 | 0.01 | 0.01 | |
| boundMolecules_- | 0.02 | 0.00 | 0.02 | |
| chipMean | 0 | 0 | 0 | |
| chipMean_- | 0 | 0 | 0 | |
| chipSd | 0.01 | 0.00 | 0.01 | |
| chipSd_- | 0.02 | 0.00 | 0.02 | |
| chipSmooth | 0 | 0 | 0 | |
| chipSmooth_- | 0 | 0 | 0 | |
| computeChIPProfile | 0.00 | 0.01 | 0.01 | |
| computeGenomeWideScores | 0 | 0 | 0 | |
| computeOccupancy | 0 | 0 | 0 | |
| computeOptimal | 0 | 0 | 0 | |
| computePWMScore | 0 | 0 | 0 | |
| data | 0 | 0 | 0 | |
| drop | 0.03 | 0.00 | 0.03 | |
| genomicProfiles-class | 0 | 0 | 0 | |
| genomicProfiles | 0.04 | 0.00 | 0.05 | |
| genomicProfilesInternal-class | 0 | 0 | 0 | |
| lambdaPWM | 0.02 | 0.00 | 0.01 | |
| lambdaPWM_ | 0.02 | 0.00 | 0.02 | |
| loci-class | 0 | 0 | 0 | |
| loci | 1.37 | 0.07 | 1.43 | |
| lociWidth | 0.02 | 0.00 | 0.02 | |
| lociWidth_ | 0 | 0 | 0 | |
| maxPWMScore | 0.00 | 0.01 | 0.02 | |
| maxSignal | 0 | 0 | 0 | |
| maxSignal_- | 0.01 | 0.00 | 0.01 | |
| minPWMScore | 0 | 0 | 0 | |
| naturalLog | 0.02 | 0.00 | 0.02 | |
| naturalLog_- | 0 | 0 | 0 | |
| noOfSites | 0.00 | 0.02 | 0.01 | |
| noOfSites_- | 0.01 | 0.00 | 0.02 | |
| noiseFilter | 0 | 0 | 0 | |
| noiseFilter_ | 0.02 | 0.00 | 0.01 | |
| nos-class | 0 | 0 | 0 | |
| parameterOptions-class | 0 | 0 | 0 | |
| parameterOptions | 0.01 | 0.00 | 0.02 | |
| ploidy | 0 | 0 | 0 | |
| ploidy_- | 0 | 0 | 0 | |
| plotOccupancyProfile | 0.02 | 0.00 | 0.02 | |
| plotOptimalHeatMaps | 0 | 0 | 0 | |
| processingChIP | 0.69 | 0.08 | 0.76 | |
| profileAccuracyEstimate | 0 | 0 | 0 | |
| removeBackground | 0.01 | 0.00 | 0.02 | |
| removeBackground_- | 0 | 0 | 0 | |
| scores | 0.71 | 0.06 | 0.76 | |
| searchSites | 0.00 | 0.01 | 0.02 | |
| stepSize | 0 | 0 | 0 | |
| stepSize_- | 0 | 0 | 0 | |
| strandRule | 0.00 | 0.02 | 0.01 | |
| strandRule_- | 0.01 | 0.00 | 0.02 | |
| whichstrand | 0 | 0 | 0 | |
| whichstrand_- | 0.00 | 0.02 | 0.01 | |