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BioC 3.5: CHECK report for GenomicInteractions on toluca2

This page was generated on 2017-04-23 14:39:04 -0400 (Sun, 23 Apr 2017).

Package 540/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.9.2
Malcolm Perry
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicInteractions
Last Changed Rev: 126388 / Revision: 129046
Last Changed Date: 2017-02-01 08:01:40 -0500 (Wed, 01 Feb 2017)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicInteractions
Version: 1.9.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.9.2.tar.gz
StartedAt: 2017-04-23 04:28:00 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:34:54 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 414.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicInteractions.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.9.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.9.2’
* 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 ‘GenomicInteractions’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   7.9Mb
* 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 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
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.


GenomicInteractions.Rcheck/00install.out:

* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
* DONE (GenomicInteractions)

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings:

nameusersystemelapsed
GInteractions-subsetByFeatures-methods1.2580.0081.268
GenomicInteractions-class0.3650.0190.384
GenomicInteractions-package0.0010.0000.001
GenomicInteractions0.3940.0370.431
InteractionHelpers0.0620.0050.066
InteractionTrack1.3430.0071.354
annotateInteractions0.1780.0030.180
annotateRegions0.0400.0010.041
asBED-GInteractions-method0.3980.0080.406
availableDisplayPars0.0260.0010.027
calculateDistances0.0470.0010.048
categoriseInteractions0.3510.0030.355
export.bed123.3410.0193.363
export.bedpe0.1920.0060.199
export.chiasig0.1380.0050.142
export.igraph0.0920.0030.094
getters0.0890.0010.089
makeGenomicInteractionsFromFile1.7930.0531.849
plotAvgViewpoint0.2920.0040.297
plotCisTrans2.2720.0172.293
plotCounts1.3780.0051.388
plotDists0.3430.0030.347
plotInteractionAnnotations0.5710.0040.578
plotSummaryStats1.2150.0061.224
plotViewpoint0.6370.0040.644
resetAnnotations0.0400.0010.041
setters0.0500.0000.051
summariseByFeaturePairs1.0040.0051.011
summariseByFeatures0.4540.0040.460
viewPoint0.2350.0020.237