BioC 3.5: CHECK report for DMRScan on malbec2
This page was generated on 2017-10-18 14:18:20 -0400 (Wed, 18 Oct 2017).
DMRScan 1.0.0 Christian M Page
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/DMRScan | Branch: RELEASE_3_5 | Last Commit: 5042a5e | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: DMRScan |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DMRScan_1.0.0.tar.gz |
StartedAt: 2017-10-17 22:45:27 -0400 (Tue, 17 Oct 2017) |
EndedAt: 2017-10-17 22:50:41 -0400 (Tue, 17 Oct 2017) |
EllapsedTime: 314.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DMRScan.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DMRScan_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DMRScan.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRScan/DESCRIPTION’ ... OK
* this is package ‘DMRScan’ version ‘1.0.0’
* 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 ‘DMRScan’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 4.9Mb
* 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 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 ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DMRScan_slidingWindow 72.456 0.032 72.585
DMRScan_package 63.752 0.112 63.941
makeCpGgenes 59.760 0.108 59.946
makeCpGregions 55.692 0.016 55.772
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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
‘/home/biocbuild/bbs-3.5-bioc/meat/DMRScan.Rcheck/00check.log’
for details.
DMRScan.Rcheck/00install.out:
* installing *source* package ‘DMRScan’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DMRScan)
DMRScan.Rcheck/DMRScan-Ex.timings:
name | user | system | elapsed
|
DMRScan.methylationData | 0.564 | 0.128 | 0.690 |
|
DMRScan.phenotypes | 0.004 | 0.000 | 0.004 |
|
DMRScan_package | 63.752 | 0.112 | 63.941 |
|
DMRScan_slidingWindow | 72.456 | 0.032 | 72.585 |
|
Region-class_init | 0.000 | 0.000 | 0.001 |
|
RegionList-class_init | 0 | 0 | 0 |
|
Rt-methods | 0 | 0 | 0 |
|
St-methods | 0 | 0 | 0 |
|
estimateThreshold | 0.044 | 0.000 | 0.042 |
|
getRegions | 0 | 0 | 0 |
|
makeCpGgenes | 59.760 | 0.108 | 59.946 |
|
makeCpGregions | 55.692 | 0.016 | 55.772 |
|
nCpG | 0.000 | 0.000 | 0.001 |
|
pVal | 0.000 | 0.000 | 0.002 |
|
pos | 0.004 | 0.000 | 0.002 |
|
setRegion | 0.004 | 0.000 | 0.001 |
|
tVal | 0.000 | 0.000 | 0.001 |
|