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This page was generated on 2024-12-11 11:46 -0500 (Wed, 11 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4752
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4464
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4414
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4369
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4277
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 581/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.39.0  (landing page)
Nicolae Radu Zabet
Snapshot Date: 2024-12-10 13:40 -0500 (Tue, 10 Dec 2024)
git_url: https://git.bioconductor.org/packages/DMRcaller
git_branch: devel
git_last_commit: 13a82ad
git_last_commit_date: 2024-10-29 10:00:05 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for DMRcaller on kjohnson3

To the developers/maintainers of the DMRcaller package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/DMRcaller.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.

raw results


Summary

Package: DMRcaller
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcaller_1.39.0.tar.gz
StartedAt: 2024-12-10 21:12:13 -0500 (Tue, 10 Dec 2024)
EndedAt: 2024-12-10 21:17:22 -0500 (Tue, 10 Dec 2024)
EllapsedTime: 309.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcaller.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcaller_1.39.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DMRcaller.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘DMRcaller’ 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 ... NOTE
extractGC: no visible global function definition for ‘getSeq’
extractGC: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  getSeq seqlevels
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DMRcaller.Rd: GRanges
  DMRsNoiseFilterCG.Rd: GRanges
  analyseReadsInsideRegionsForCondition.Rd: GRanges
  computeDMRs.Rd: GRanges
  computeDMRsReplicates.Rd: GRanges
  computeMethylationDataCoverage.Rd: GRanges
  computeMethylationDataSpatialCorrelation.Rd: GRanges
  computeMethylationProfile.Rd: GRanges
  computeOverlapProfile.Rd: GRanges
  extractGC.Rd: GRanges
  filterDMRs.Rd: GRanges
  getWholeChromosomes.Rd: GRanges
  joinReplicates.Rd: GRanges
  mergeDMRsIteratively.Rd: GRanges
  plotLocalMethylationProfile.Rd: GRanges, GRangesList
  plotMethylationDataCoverage.Rd: GRanges
  plotMethylationDataSpatialCorrelation.Rd: GRanges
  plotMethylationProfile.Rd: GRanges
  plotMethylationProfileFromData.Rd: GRanges
  plotOverlapProfile.Rd: GRanges
  poolMethylationDatasets.Rd: GRangesList, GRanges
  poolTwoMethylationDatasets.Rd: GRanges
  readBismark.Rd: GRanges
  readBismarkPool.Rd: GRanges
  saveBismark.Rd: GRanges
  syntheticDataReplicates.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.


Installation output

DMRcaller.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcaller
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘DMRcaller’ ...
** using staged installation
** R
** data
** 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 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 (DMRcaller)

Tests output

DMRcaller.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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("DMRcaller")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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

Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs 
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Selecting data...
Identifying DMRs...
Validating objects 
Finding overlaps 
Joining objects 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Merge DMRs iteratively ...


RUNIT TEST PROTOCOL -- Tue Dec 10 21:17:18 2024 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
  'x' has been rounded to integer: Mean relative difference: 0.002857143
> 
> proc.time()
   user  system elapsed 
 39.269   0.117  39.385 

Example timings

DMRcaller.Rcheck/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller0.0000.0010.001
analyseReadsInsideRegionsForCondition0.2850.0080.293
computeDMRs2.3800.0272.408
computeDMRsReplicates000
computeMethylationDataCoverage0.2630.0110.274
computeMethylationDataSpatialCorrelation0.1740.0070.182
computeMethylationProfile0.4080.0100.418
computeOverlapProfile0.4450.0100.454
extractGC000
filterDMRs0.5750.0160.591
getWholeChromosomes0.2060.0080.214
joinReplicates000
mergeDMRsIteratively2.6090.0152.625
plotLocalMethylationProfile0.5200.0250.545
plotMethylationDataCoverage0.2860.0080.296
plotMethylationDataSpatialCorrelation0.0000.0010.000
plotMethylationProfile0.4050.0170.422
plotMethylationProfileFromData0.5470.0190.566
plotOverlapProfile0.4770.0080.484
poolMethylationDatasets0.3740.0250.400
poolTwoMethylationDatasets0.3570.0270.384
readBismark0.6430.0370.682
readBismarkPool1.5600.0911.652
saveBismark0.5090.0220.531