Nicolae Radu Zabet
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/DMRcaller |
| git_branch: master |
| git_last_commit: b5efd8f |
| git_last_commit_date: 2021-11-17 09:00:23 -0400 (Wed, 17 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:24 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 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. |
| Package 531/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DMRcaller 1.27.1 (landing page) Nicolae Radu Zabet
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DMRcaller |
| Version: 1.27.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcaller.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DMRcaller_1.27.1.tar.gz |
| StartedAt: 2022-03-17 18:57:53 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:01:35 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 221.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DMRcaller.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcaller.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DMRcaller_1.27.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DMRcaller.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.27.1'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readBismarkPool 14.27 0.73 15.00
computeDMRs 7.36 0.14 7.50
mergeDMRsIteratively 7.10 0.08 7.17
readBismark 6.61 0.32 6.94
saveBismark 6.56 0.13 6.69
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/DMRcaller.Rcheck/00check.log'
for details.
DMRcaller.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DMRcaller
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (DMRcaller)
Making 'packages.html' ... done
DMRcaller.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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: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 -- Thu Mar 17 19:01:23 2022
***********************************************
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
75.92 0.57 76.46
DMRcaller.Rcheck/DMRcaller-Ex.timings
| name | user | system | elapsed | |
| DMRcaller | 0.00 | 0.02 | 0.02 | |
| analyseReadsInsideRegionsForCondition | 0.62 | 0.11 | 0.73 | |
| computeDMRs | 7.36 | 0.14 | 7.50 | |
| computeDMRsReplicates | 0 | 0 | 0 | |
| computeMethylationDataCoverage | 0.28 | 0.09 | 0.37 | |
| computeMethylationDataSpatialCorrelation | 0.50 | 0.14 | 0.64 | |
| computeMethylationProfile | 0.64 | 0.14 | 0.78 | |
| computeOverlapProfile | 0.99 | 0.05 | 1.04 | |
| extractGC | 0 | 0 | 0 | |
| filterDMRs | 1.25 | 0.24 | 1.48 | |
| getWholeChromosomes | 0.10 | 0.06 | 0.17 | |
| joinReplicates | 0 | 0 | 0 | |
| mergeDMRsIteratively | 7.10 | 0.08 | 7.17 | |
| plotLocalMethylationProfile | 1.00 | 0.15 | 1.16 | |
| plotMethylationDataCoverage | 0.81 | 0.13 | 0.94 | |
| plotMethylationDataSpatialCorrelation | 0 | 0 | 0 | |
| plotMethylationProfile | 0.61 | 0.08 | 0.69 | |
| plotMethylationProfileFromData | 1.44 | 0.15 | 1.59 | |
| plotOverlapProfile | 1.01 | 0.06 | 1.08 | |
| poolMethylationDatasets | 0.71 | 0.16 | 0.86 | |
| poolTwoMethylationDatasets | 0.59 | 0.20 | 0.79 | |
| readBismark | 6.61 | 0.32 | 6.94 | |
| readBismarkPool | 14.27 | 0.73 | 15.00 | |
| saveBismark | 6.56 | 0.13 | 6.69 | |