Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:13 -0400 (Wed, 22 Sep 2021).

CHECK results for DMRcaller on tokay2

To the developers/maintainers of the DMRcaller package:
- Please 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 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.

raw results

Package 516/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.24.0  (landing page)
Nicolae Radu Zabet
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/DMRcaller
git_branch: RELEASE_3_13
git_last_commit: 828312c
git_last_commit_date: 2021-05-19 12:12:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DMRcaller
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DMRcaller_1.24.0.tar.gz
StartedAt: 2021-09-21 22:02:46 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 22:10:55 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 488.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcaller.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DMRcaller_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DMRcaller.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRcaller/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DMRcaller' version '1.24.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
mergeDMRsIteratively 17.05   0.05   17.09
computeDMRs          15.11   0.08   15.19
readBismarkPool       9.19   0.25    9.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
mergeDMRsIteratively 17.67   0.00   17.67
computeDMRs          15.62   0.09   15.72
readBismarkPool       9.75   0.27   10.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DMRcaller.Rcheck/00check.log'
for details.



Installation output

DMRcaller.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DMRcaller_1.24.0.tar.gz && rm -rf DMRcaller.buildbin-libdir && mkdir DMRcaller.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRcaller.buildbin-libdir DMRcaller_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DMRcaller_1.24.0.zip && rm DMRcaller_1.24.0.tar.gz DMRcaller_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 31 1127k   31  358k    0     0  1287k      0 --:--:-- --:--:-- --:--:-- 1289k
100 1127k  100 1127k    0     0  2636k      0 --:--:-- --:--:-- --:--:-- 2634k

install for i386

* installing *source* package 'DMRcaller' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRcaller'
    finding HTML links ... done
    DMRcaller                               html  
    finding level-2 HTML links ... done

    DMRsNoiseFilterCG                       html  
    GEs                                     html  
    analyseReadsInsideRegionsForCondition   html  
    computeDMRs                             html  
    computeDMRsReplicates                   html  
    computeMethylationDataCoverage          html  
    computeMethylationDataSpatialCorrelation
                                            html  
    computeMethylationProfile               html  
    computeOverlapProfile                   html  
    extractGC                               html  
    filterDMRs                              html  
    getWholeChromosomes                     html  
    joinReplicates                          html  
    mergeDMRsIteratively                    html  
    methylationDataList                     html  
    plotLocalMethylationProfile             html  
    plotMethylationDataCoverage             html  
    plotMethylationDataSpatialCorrelation   html  
    plotMethylationProfile                  html  
    plotMethylationProfileFromData          html  
    plotOverlapProfile                      html  
    poolMethylationDatasets                 html  
    poolTwoMethylationDatasets              html  
    readBismark                             html  
    readBismarkPool                         html  
    saveBismark                             html  
    syntheticDataReplicates                 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

install for x64

* installing *source* package 'DMRcaller' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRcaller' as DMRcaller_1.24.0.zip
* DONE (DMRcaller)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DMRcaller' successfully unpacked and MD5 sums checked

Tests output

DMRcaller.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("DMRcaller")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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 Sep 21 22:08:55 2021 
*********************************************** 
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 
 102.76    0.39  103.12 

DMRcaller.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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("DMRcaller")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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 Sep 21 22:10:44 2021 
*********************************************** 
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 
 108.62    0.32  108.93 

Example timings

DMRcaller.Rcheck/examples_i386/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller000
analyseReadsInsideRegionsForCondition1.080.031.11
computeDMRs15.11 0.0815.19
computeDMRsReplicates000
computeMethylationDataCoverage0.720.050.77
computeMethylationDataSpatialCorrelation0.560.010.58
computeMethylationProfile1.700.071.76
computeOverlapProfile2.220.002.22
extractGC000
filterDMRs3.250.093.34
getWholeChromosomes0.550.000.55
joinReplicates000
mergeDMRsIteratively17.05 0.0517.09
plotLocalMethylationProfile1.500.111.61
plotMethylationDataCoverage1.170.061.24
plotMethylationDataSpatialCorrelation000
plotMethylationProfile1.390.051.44
plotMethylationProfileFromData3.090.043.14
plotOverlapProfile2.50.02.5
poolMethylationDatasets1.070.031.09
poolTwoMethylationDatasets0.930.071.00
readBismark4.490.074.56
readBismarkPool9.190.259.44
saveBismark3.560.073.62

DMRcaller.Rcheck/examples_x64/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller000
analyseReadsInsideRegionsForCondition0.900.050.95
computeDMRs15.62 0.0915.72
computeDMRsReplicates000
computeMethylationDataCoverage0.670.100.76
computeMethylationDataSpatialCorrelation0.460.080.53
computeMethylationProfile1.830.011.85
computeOverlapProfile1.980.022.00
extractGC000
filterDMRs3.520.133.64
getWholeChromosomes0.180.010.21
joinReplicates000
mergeDMRsIteratively17.67 0.0017.67
plotLocalMethylationProfile1.470.071.54
plotMethylationDataCoverage1.020.061.07
plotMethylationDataSpatialCorrelation000
plotMethylationProfile1.590.011.61
plotMethylationProfileFromData2.720.072.78
plotOverlapProfile2.540.042.60
poolMethylationDatasets0.680.020.69
poolTwoMethylationDatasets0.840.030.87
readBismark4.610.144.75
readBismarkPool 9.75 0.2710.02
saveBismark3.620.043.67