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BioC 3.2: CHECK report for MMDiff on perceval

This page was generated on 2015-11-10 14:48:06 -0800 (Tue, 10 Nov 2015).

Package 661/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff 1.10.0
Gabriele Schweikert
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MMDiff
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MMDiff
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff_1.10.0.tar.gz
StartedAt: 2015-11-10 07:09:53 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 07:24:18 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 864.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MMDiff.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MMDiff.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff’ version ‘1.10.0’
* 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 ‘MMDiff’ can be installed ... [36s/37s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/526s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Cfp1Profiles    21.946  1.285  27.327
getPeakProfiles 12.693  0.422 117.709
Cfp1Dists        1.389  0.201 273.064
compHistDists    1.018  0.145  87.451
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MMDiff.Rcheck/00check.log’
for details.


MMDiff.Rcheck/00install.out:

* installing *source* package ‘MMDiff’ ...
** 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 (MMDiff)

MMDiff.Rcheck/MMDiff-Ex.timings:

nameusersystemelapsed
Cfp1Dists 1.389 0.201273.064
Cfp1Profiles21.946 1.28527.327
compHistDists 1.018 0.14587.451
detPeakPvals0.2710.0140.294
findOutliers0.1960.0190.224
getNormFactors0.2680.0200.298
getPeakProfiles 12.693 0.422117.709
plotHistDists0.3750.0310.453
plotPeak0.2300.0110.242