BioC 3.2: CHECK report for GenomicInteractions on oaxaca

Package: GenomicInteractions

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.4.2.tar.gz

StartedAt: 2016-04-23 00:32:22 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:38:27 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 365.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicInteractions.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.2’
* 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 ... [31s/32s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ 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 10.3Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [22s/22s]
 [22s/22s] 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.

* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘S4Vectors::Position’ by ‘ggplot2::Position’ 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 ‘S4Vectors::Position’ by ‘ggplot2::Position’ when loading ‘GenomicInteractions’
* DONE (GenomicInteractions)

name	user	system	elapsed
GenomicInteractions-class	0.302	0.023	0.324
GenomicInteractions	0.244	0.011	0.256
InteractionTrack	1.093	0.015	1.109
annotateInteractions	0.491	0.014	0.674
calculateDistances	0.237	0.005	0.241
categoriseInteractions	0.110	0.003	0.114
getters	0.253	0.005	0.258
makeGenomicInteractionsFromFile	2.086	0.037	2.126
plotCisTrans	0.257	0.005	0.418
plotCounts	0.374	0.004	0.378
plotDists	0.300	0.005	0.305
plotInteractionAnnotations	0.287	0.003	0.291
plotSummaryStats	0.872	0.018	0.893
setters	0.221	0.018	0.239
unique-GenomicInteractions-method	0.230	0.008	0.238
viewPoint	0.001	0.000	0.000