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CHECK report for MethPed on malbec2

This page was generated on 2018-10-17 08:28:36 -0400 (Wed, 17 Oct 2018).

Package 883/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethPed 1.8.0
Helena Carén
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MethPed
Branch: RELEASE_3_7
Last Commit: d7639ea
Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MethPed
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MethPed.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MethPed_1.8.0.tar.gz
StartedAt: 2018-10-16 01:53:05 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:56:04 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 179.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MethPed.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MethPed.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MethPed_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MethPed.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethPed/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethPed’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘MethPed’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   6.7Mb
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 3 marked Latin-1 strings
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
MethPed         74.236  0.156  74.451
plot.methped    25.068  0.028  25.111
summary.methped 24.740  0.024  24.786
probeMis        24.620  0.012  24.647
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/MethPed.Rcheck/00check.log’
for details.



Installation output

MethPed.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MethPed
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘MethPed’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MethPed)

Tests output


Example timings

MethPed.Rcheck/MethPed-Ex.timings

nameusersystemelapsed
MethPed74.236 0.15674.451
MethPed_900probes0.0080.0000.010
MethPed_sample1.6320.0161.647
checkNA1.5240.0281.553
plot.methped25.068 0.02825.111
probeMis24.620 0.01224.647
summary.methped24.740 0.02424.786