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BioC 3.1: CHECK report for MMDiff on moscato2

This page was generated on 2015-10-09 09:30:20 -0700 (Fri, 09 Oct 2015).

Package 615/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff 1.8.0
Gabriele Schweikert
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MMDiff
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MMDiff
Version: 1.8.0
Command: E:\biocbld\bbs-3.1-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings MMDiff_1.8.0.tar.gz
StartedAt: 2015-10-09 03:56:58 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:24:27 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1648.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MMDiff.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbld\bbs-3.1-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings MMDiff_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/MMDiff.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MMDiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MMDiff' version '1.8.0'
* 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 whether package 'MMDiff' can be installed ... [27s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'GenomicRanges'
A package should be listed in only one of these fields.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [23m] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Cfp1Profiles    19.94   0.67  122.33
getPeakProfiles 11.36   0.28  229.09
Cfp1Dists        1.57   0.19  676.47
compHistDists    1.16   0.11  364.51
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/MMDiff.Rcheck/00check.log'
for details.


MMDiff.Rcheck/00install.out:

* installing *source* package 'MMDiff' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (MMDiff)

MMDiff.Rcheck/MMDiff-Ex.timings:

nameusersystemelapsed
Cfp1Dists 1.57 0.19676.47
Cfp1Profiles 19.94 0.67122.33
compHistDists 1.16 0.11364.51
detPeakPvals0.570.012.08
findOutliers0.190.020.20
getNormFactors0.250.030.28
getPeakProfiles 11.36 0.28229.09
plotHistDists0.340.020.36
plotPeak0.170.000.17