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BioC 3.5: CHECK report for GenomicInteractions on oaxaca

This page was generated on 2017-03-04 16:48:16 -0500 (Sat, 04 Mar 2017).

Package 522/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.9.2
Malcolm Perry
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicInteractions
Last Changed Rev: 126388 / Revision: 127142
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 UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

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: 2017-03-04 03:30:41 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 03:37:21 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 399.9 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 r72177)
* 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-methods0.6880.0130.702
GenomicInteractions-class0.8380.0030.840
GenomicInteractions-package0.0010.0000.001
GenomicInteractions0.3360.0100.346
InteractionHelpers0.0450.0050.050
InteractionTrack1.1030.0451.234
annotateInteractions0.1520.0020.874
annotateRegions0.0290.0010.041
asBED-GInteractions-method0.3320.0070.613
availableDisplayPars0.0200.0010.046
calculateDistances0.0640.0000.064
categoriseInteractions0.2990.0060.305
export.bed122.4130.0223.852
export.bedpe0.1820.0050.187
export.chiasig0.1040.0050.109
export.igraph0.0890.0030.161
getters0.0890.0010.090
makeGenomicInteractionsFromFile1.6470.0681.739
plotAvgViewpoint0.3640.0070.395
plotCisTrans1.5460.0161.576
plotCounts1.3750.0051.393
plotDists0.3330.0030.343
plotInteractionAnnotations0.6200.0040.625
plotSummaryStats1.3690.0101.396
plotViewpoint0.6420.0030.677
resetAnnotations0.0360.0010.037
setters0.0460.0010.046
summariseByFeaturePairs0.9780.0060.985
summariseByFeatures0.4750.0040.486
viewPoint0.2690.0030.272