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This page was generated on 2021-11-29 15:05:08 -0500 (Mon, 29 Nov 2021).

CHECK results for scmeth on nebbiolo2

To the developers/maintainers of the scmeth package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scmeth.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 1731/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scmeth 1.14.0  (landing page)
Divy Kangeyan
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/scmeth
git_branch: RELEASE_3_14
git_last_commit: cb59e2c
git_last_commit_date: 2021-10-26 12:41:54 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: scmeth
Version: 1.14.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:scmeth.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings scmeth_1.14.0.tar.gz
StartedAt: 2021-11-28 10:52:05 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 10:57:27 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 321.7 seconds
RetCode: 0
Status:   OK  
CheckDir: scmeth.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:scmeth.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings scmeth_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/scmeth.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scmeth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scmeth’ version ‘1.14.0’
* 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 ‘scmeth’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
report  48.568   3.26  52.028
repMask  9.865   0.56  11.317
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/scmeth.Rcheck/00check.log’
for details.



Installation output

scmeth.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL scmeth
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘scmeth’ ...
** using staged installation
** R
** 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 (scmeth)

Tests output


Example timings

scmeth.Rcheck/scmeth-Ex.timings

nameusersystemelapsed
bsConversionPlot0.2180.0080.226
chromosomeCoverage0.3960.0120.407
coverage0.1230.0000.123
cpgDensity3.1550.2243.379
cpgDiscretization0.2090.0200.229
downsample0.3230.0120.335
featureCoverage3.0340.0643.585
mbiasplot0.0040.0040.008
methylationDist0.1580.0040.162
readmetrics0.0680.0200.088
repMask 9.865 0.56011.317
report48.568 3.26052.028