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BioC 3.2: CHECK report for GenomicInteractions on perceval

This page was generated on 2015-11-10 14:49:11 -0800 (Tue, 10 Nov 2015).

Package 424/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.4.0
Malcolm Perry , Liz Ing-Simmons
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/GenomicInteractions
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  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicInteractions
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.4.0.tar.gz
StartedAt: 2015-11-10 05:15:03 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 05:20:52 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 349.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicInteractions.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicInteractions.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 ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicInteractions’ can be installed ... [28s/30s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicInteractions.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘GenomeInfoDb:::getDanglingSeqlevels’
  ‘GenomeInfoDb:::makeNewSeqnames’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  See the note in ?`:::` about the use of this operator.
* 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 ... [22s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [23s/23s]
 [23s/23s] 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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 by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’
Creating a generic function for ‘print’ from package ‘base’ in package ‘GenomicInteractions’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’
* DONE (GenomicInteractions)

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings:

nameusersystemelapsed
GenomicInteractions-class0.4060.0070.413
GenomicInteractions0.3380.0040.342
InteractionTrack1.2870.0441.331
annotateInteractions0.5800.0150.595
calculateDistances0.3430.0040.347
categoriseInteractions0.1310.0010.132
getters0.3590.0040.364
makeGenomicInteractionsFromFile2.0080.0322.041
plotCisTrans0.8580.0060.865
plotCounts0.3590.0160.375
plotDists0.2570.0350.292
plotInteractionAnnotations0.2830.0030.287
plotSummaryStats0.7640.0040.769
setters0.3270.0030.331
unique-GenomicInteractions-method0.2020.0080.209
viewPoint0.0010.0000.000