Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 588/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.38.0  (landing page)
Nicolae Radu Zabet
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/DMRcaller
git_branch: RELEASE_3_20
git_last_commit: c659d0b
git_last_commit_date: 2024-10-29 10:00:05 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for DMRcaller on teran2

To the developers/maintainers of the DMRcaller package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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: 1.38.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DMRcaller_1.38.0.tar.gz
StartedAt: 2024-11-20 02:02:07 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 02:07:54 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 347.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcaller.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DMRcaller_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/DMRcaller.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.38.0’
* 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 ‘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 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
computeDMRs          7.423  0.118   7.883
mergeDMRsIteratively 7.279  0.035   9.302
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.


Installation output

DMRcaller.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DMRcaller
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: '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, saveRDS, 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

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 -- Wed Nov 20 02:06:45 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 
111.592   0.737 136.640 

Example timings

DMRcaller.Rcheck/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller0.0000.0000.001
analyseReadsInsideRegionsForCondition0.6540.0620.877
computeDMRs7.4230.1187.883
computeDMRsReplicates000
computeMethylationDataCoverage0.2640.0410.305
computeMethylationDataSpatialCorrelation0.6040.0690.856
computeMethylationProfile0.6230.0200.714
computeOverlapProfile1.0260.0171.092
extractGC000
filterDMRs1.3490.0201.374
getWholeChromosomes0.1560.0170.174
joinReplicates000
mergeDMRsIteratively7.2790.0359.302
plotLocalMethylationProfile1.2530.0431.318
plotMethylationDataCoverage0.7910.0291.003
plotMethylationDataSpatialCorrelation000
plotMethylationProfile0.5920.0230.802
plotMethylationProfileFromData1.4890.0231.610
plotOverlapProfile1.1200.0151.171
poolMethylationDatasets0.6890.0300.771
poolTwoMethylationDatasets0.6990.0150.798
readBismark0.8270.0391.131
readBismarkPool2.8800.0713.059
saveBismark0.4640.0520.684