| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the ChIPanalyser package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 321/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPanalyser 1.21.0 (landing page) Patrick C.N. Martin
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: ChIPanalyser |
| Version: 1.21.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPanalyser_1.21.0.tar.gz |
| StartedAt: 2023-04-12 05:16:43 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:21:58 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 315.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPanalyser_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.21.0’
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getTestingData 5.312 0.136 5.449
* 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 ...
‘ChIPanalyser.Rmd’ using ‘UTF-8’... OK
‘GA_ChIPanalyser.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
ChIPanalyser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPanalyser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 ** 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)
ChIPanalyser.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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: '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.dm6
RUNIT TEST PROTOCOL -- Wed Apr 12 05:21:51 2023
***********************************************
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
58.482 4.053 62.562
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
| name | user | system | elapsed | |
| BPFrequency | 0.128 | 0.000 | 0.128 | |
| BPFrequency_- | 0.002 | 0.000 | 0.002 | |
| ChIPScore-class | 0.001 | 0.000 | 0.001 | |
| ChIPanalyser-package | 0 | 0 | 0 | |
| DNASequenceLength | 0.002 | 0.000 | 0.002 | |
| GRList-class | 0.001 | 0.000 | 0.001 | |
| PFMFormat | 0.135 | 0.024 | 0.159 | |
| PFMFormat_ | 0.044 | 0.004 | 0.048 | |
| PWMThreshold | 0.001 | 0.008 | 0.009 | |
| PWMThreshold_- | 0.012 | 0.008 | 0.020 | |
| PWMpseudocount | 0.002 | 0.008 | 0.010 | |
| PWMpseudocount_- | 0.009 | 0.000 | 0.010 | |
| PositionFrequencyMatrix | 0.040 | 0.008 | 0.047 | |
| PositionFrequencyMatrix_- | 0.023 | 0.004 | 0.027 | |
| PositionWeightMatrix | 0.041 | 0.008 | 0.049 | |
| PositionWeightMatrix_- | 0.014 | 0.000 | 0.014 | |
| averageExpPWMScore | 0.035 | 0.012 | 0.047 | |
| backgroundSignal | 0.008 | 0.000 | 0.008 | |
| backgroundSignal_- | 0.008 | 0.004 | 0.012 | |
| boundMolecules | 0.008 | 0.000 | 0.008 | |
| boundMolecules_- | 0.011 | 0.000 | 0.011 | |
| chipMean | 0.005 | 0.004 | 0.009 | |
| chipMean_- | 0.009 | 0.000 | 0.009 | |
| chipSd | 0.005 | 0.004 | 0.009 | |
| chipSd_- | 0.009 | 0.000 | 0.009 | |
| chipSmooth | 0.005 | 0.004 | 0.008 | |
| chipSmooth_- | 0.009 | 0.000 | 0.009 | |
| computeChIPProfile | 0.000 | 0.002 | 0.002 | |
| computeGenomeWideScores | 0 | 0 | 0 | |
| computeOccupancy | 0.001 | 0.001 | 0.001 | |
| computeOptimal | 0.002 | 0.000 | 0.002 | |
| computePWMScore | 0.001 | 0.001 | 0.002 | |
| data | 0.000 | 0.000 | 0.001 | |
| drop | 0.042 | 0.005 | 0.048 | |
| evolve | 0.001 | 0.000 | 0.001 | |
| generateStartingPopulation | 0.022 | 0.000 | 0.022 | |
| genomicProfiles-class | 0.001 | 0.000 | 0.001 | |
| genomicProfiles | 0.146 | 0.020 | 0.166 | |
| genomicProfilesInternal-class | 0.000 | 0.000 | 0.001 | |
| getHighestFitnessSolutions | 0.001 | 0.000 | 0.001 | |
| getTestingData | 5.312 | 0.136 | 5.449 | |
| getTrainingData | 1.342 | 0.040 | 1.382 | |
| lambdaPWM | 0.008 | 0.000 | 0.008 | |
| lambdaPWM_ | 0.008 | 0.000 | 0.008 | |
| loci-class | 0 | 0 | 0 | |
| loci | 1.318 | 0.112 | 1.429 | |
| lociWidth | 0.007 | 0.000 | 0.007 | |
| lociWidth_ | 0.007 | 0.000 | 0.007 | |
| maxPWMScore | 0.001 | 0.000 | 0.002 | |
| maxSignal | 0.006 | 0.000 | 0.006 | |
| maxSignal_- | 0.006 | 0.000 | 0.006 | |
| minPWMScore | 0.002 | 0.000 | 0.001 | |
| naturalLog | 0.007 | 0.000 | 0.007 | |
| naturalLog_- | 0.007 | 0.000 | 0.007 | |
| noOfSites | 0.007 | 0.000 | 0.007 | |
| noOfSites_- | 0.007 | 0.000 | 0.007 | |
| noiseFilter | 0.007 | 0.001 | 0.007 | |
| noiseFilter_ | 0.004 | 0.003 | 0.007 | |
| nos-class | 0.000 | 0.000 | 0.001 | |
| parameterOptions-class | 0.001 | 0.000 | 0.001 | |
| parameterOptions | 0.009 | 0.000 | 0.009 | |
| ploidy | 0.007 | 0.000 | 0.006 | |
| ploidy_- | 0.006 | 0.000 | 0.006 | |
| plotOccupancyProfile | 0.001 | 0.000 | 0.002 | |
| plotOptimalHeatMaps | 0.001 | 0.000 | 0.002 | |
| processingChIP | 1.357 | 0.152 | 1.510 | |
| profileAccuracyEstimate | 0.000 | 0.002 | 0.002 | |
| removeBackground | 0.005 | 0.001 | 0.007 | |
| removeBackground_- | 0.007 | 0.000 | 0.006 | |
| scores | 1.429 | 0.056 | 1.486 | |
| searchSites | 0.002 | 0.000 | 0.002 | |
| setChromatinStates | 1.871 | 0.012 | 1.882 | |
| singleRun | 0.001 | 0.000 | 0.001 | |
| splitData | 1.735 | 0.108 | 1.843 | |
| stepSize | 0.006 | 0.000 | 0.007 | |
| stepSize_- | 0.007 | 0.000 | 0.006 | |
| strandRule | 0.008 | 0.000 | 0.008 | |
| strandRule_- | 0.008 | 0.000 | 0.008 | |
| whichstrand | 0.008 | 0.000 | 0.007 | |
| whichstrand_- | 0.007 | 0.000 | 0.008 | |