Back to Multiple platform build/check report for BioC 3.6
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MMDiff2 on veracruz1

This page was generated on 2018-04-12 13:42:57 -0400 (Thu, 12 Apr 2018).

Package 879/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.6.0
Gabriele Schweikert
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MMDiff2
Branch: RELEASE_3_6
Last Commit: d9bdacb
Last Changed Date: 2017-10-30 12:41:16 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MMDiff2
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff2_1.6.0.tar.gz
StartedAt: 2018-04-12 06:35:06 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:39:58 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 291.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MMDiff2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff2_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MMDiff2.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MMDiff2’ 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: ‘methods’
  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 ... NOTE
DBAmmd: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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
compDists 49.582  8.365  58.963
plotPeak   7.404  0.552   8.107
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MMDiff2.Rcheck/00check.log’
for details.



Installation output

MMDiff2.Rcheck/00install.out

* installing *source* package ‘MMDiff2’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MMDiff2)

Tests output


Example timings

MMDiff2.Rcheck/MMDiff2-Ex.timings

nameusersystemelapsed
Cfp1-Peaks0.0010.0000.001
DBAmmd-Accessors4.2180.5414.871
DBAmmd-class0.1050.0100.121
MMD0.0020.0000.002
compDists49.582 8.36558.963
compHists4.0250.3724.479
compPvals2.5070.2612.794
estimateFragmentCenters1.8490.1552.053
getPeakReads0.8810.0450.971
mm9-Genes0.0010.0000.001
plotDISTS4Peak1.2540.1501.421
plotDists1.3480.1631.525
plotPeak7.4040.5528.107
reportResults1.3970.1501.568
runShinyMMDiff20.0010.0000.001
server.MMDiff20.0010.0000.001
ui.MMDiff20.0000.0010.001