| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| 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 | ||||
| Package 333/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPanalyser 1.26.0 (landing page) Patrick C.N. Martin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ChIPanalyser |
| Version: 1.26.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPanalyser_1.26.0.tar.gz |
| StartedAt: 2024-06-13 01:41:02 -0400 (Thu, 13 Jun 2024) |
| EndedAt: 2024-06-13 01:48:21 -0400 (Thu, 13 Jun 2024) |
| EllapsedTime: 439.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPanalyser.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPanalyser_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ChIPanalyser.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPanalyser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPanalyser' version '1.26.0'
* 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 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 code 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 ... NOTE
checkRd: (-1) data.Rd:24-25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:26-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:28-31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:32-33: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:34-35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) evolve.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:93-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateStartingPopulation.Rd:31-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) generateStartingPopulation.Rd:40-44: Lost braces in \enumerate; meant \describe ?
* 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 sizes of PDF files under 'inst/doc' ... 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 ... 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
'F:/biocbuild/bbs-3.19-bioc/meat/ChIPanalyser.Rcheck/00check.log'
for details.
ChIPanalyser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-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 ** 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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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, table, tapply,
union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
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 -- Thu Jun 13 01:48:01 2024
***********************************************
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
86.50 35.45 123.87
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
| name | user | system | elapsed | |
| BPFrequency | 0.36 | 0.02 | 0.38 | |
| BPFrequency_- | 0.00 | 0.01 | 0.01 | |
| ChIPScore-class | 0 | 0 | 0 | |
| ChIPanalyser-package | 0 | 0 | 0 | |
| DNASequenceLength | 0 | 0 | 0 | |
| GRList-class | 0 | 0 | 0 | |
| PFMFormat | 0.21 | 0.05 | 0.26 | |
| PFMFormat_ | 0.04 | 0.08 | 0.11 | |
| PWMThreshold | 0.01 | 0.01 | 0.03 | |
| PWMThreshold_- | 0.00 | 0.03 | 0.04 | |
| PWMpseudocount | 0.02 | 0.00 | 0.01 | |
| PWMpseudocount_- | 0.01 | 0.02 | 0.03 | |
| PositionFrequencyMatrix | 0.08 | 0.01 | 0.10 | |
| PositionFrequencyMatrix_- | 0.03 | 0.03 | 0.06 | |
| PositionWeightMatrix | 0.03 | 0.04 | 0.06 | |
| PositionWeightMatrix_- | 0.00 | 0.01 | 0.01 | |
| averageExpPWMScore | 0.06 | 0.03 | 0.10 | |
| backgroundSignal | 0.02 | 0.00 | 0.01 | |
| backgroundSignal_- | 0.01 | 0.00 | 0.02 | |
| boundMolecules | 0.00 | 0.02 | 0.01 | |
| boundMolecules_- | 0.02 | 0.01 | 0.03 | |
| chipMean | 0.01 | 0.00 | 0.02 | |
| chipMean_- | 0.02 | 0.00 | 0.02 | |
| chipSd | 0.01 | 0.00 | 0.01 | |
| chipSd_- | 0.02 | 0.00 | 0.02 | |
| chipSmooth | 0.02 | 0.00 | 0.01 | |
| chipSmooth_- | 0.01 | 0.00 | 0.02 | |
| computeChIPProfile | 0.02 | 0.00 | 0.01 | |
| computeGenomeWideScores | 0 | 0 | 0 | |
| computeOccupancy | 0.02 | 0.00 | 0.01 | |
| computeOptimal | 0 | 0 | 0 | |
| computePWMScore | 0.01 | 0.00 | 0.02 | |
| data | 0.00 | 0.02 | 0.02 | |
| drop | 0.05 | 0.02 | 0.06 | |
| evolve | 0 | 0 | 0 | |
| generateStartingPopulation | 0.02 | 0.01 | 0.03 | |
| genomicProfiles-class | 0 | 0 | 0 | |
| genomicProfiles | 0.84 | 0.02 | 0.86 | |
| genomicProfilesInternal-class | 0 | 0 | 0 | |
| getHighestFitnessSolutions | 0.02 | 0.00 | 0.01 | |
| getTestingData | 4.03 | 0.18 | 4.25 | |
| getTrainingData | 1.48 | 0.18 | 1.71 | |
| lambdaPWM | 0.00 | 0.01 | 0.01 | |
| lambdaPWM_ | 0.02 | 0.00 | 0.02 | |
| loci-class | 0 | 0 | 0 | |
| loci | 1.51 | 0.14 | 1.69 | |
| lociWidth | 0.02 | 0.02 | 0.03 | |
| lociWidth_ | 0.01 | 0.01 | 0.03 | |
| maxPWMScore | 0.02 | 0.00 | 0.01 | |
| maxSignal | 0.02 | 0.00 | 0.02 | |
| maxSignal_- | 0 | 0 | 0 | |
| minPWMScore | 0.01 | 0.00 | 0.02 | |
| naturalLog | 0.01 | 0.00 | 0.02 | |
| naturalLog_- | 0.02 | 0.02 | 0.03 | |
| noOfSites | 0.01 | 0.00 | 0.01 | |
| noOfSites_- | 0.02 | 0.01 | 0.04 | |
| noiseFilter | 0.01 | 0.00 | 0.01 | |
| noiseFilter_ | 0.02 | 0.00 | 0.02 | |
| nos-class | 0 | 0 | 0 | |
| parameterOptions-class | 0 | 0 | 0 | |
| parameterOptions | 0.00 | 0.02 | 0.02 | |
| ploidy | 0 | 0 | 0 | |
| ploidy_- | 0.03 | 0.00 | 0.03 | |
| plotOccupancyProfile | 0 | 0 | 0 | |
| plotOptimalHeatMaps | 0 | 0 | 0 | |
| processingChIP | 1.26 | 0.17 | 1.45 | |
| profileAccuracyEstimate | 0.00 | 0.02 | 0.02 | |
| removeBackground | 0.02 | 0.00 | 0.01 | |
| removeBackground_- | 0.01 | 0.00 | 0.02 | |
| scores | 1.36 | 0.12 | 1.53 | |
| searchSites | 0.02 | 0.00 | 0.02 | |
| setChromatinStates | 1.61 | 0.02 | 1.62 | |
| singleRun | 0.00 | 0.01 | 0.02 | |
| splitData | 1.20 | 0.14 | 1.40 | |
| stepSize | 0.02 | 0.00 | 0.02 | |
| stepSize_- | 0 | 0 | 0 | |
| strandRule | 0.00 | 0.02 | 0.01 | |
| strandRule_- | 0.01 | 0.00 | 0.02 | |
| whichstrand | 0.00 | 0.01 | 0.01 | |
| whichstrand_- | 0.00 | 0.02 | 0.02 | |