BioC 3.3: CHECK report for regionReport on morelia

Package: regionReport

Version: 1.5.49

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regionReport_1.5.49.tar.gz

StartedAt: 2016-04-21 06:45:33 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:53:30 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 477.0 seconds

RetCode: 0

Status:  OK

CheckDir: regionReport.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regionReport_1.5.49.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/regionReport.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regionReport’ version ‘1.5.49’
* 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 ‘regionReport’ can be installed ... [27s/34s] OK
* checking installed package size ... OK
* 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 object imported by a ':::' call: ‘DESeq2:::pvalueAdjustment’
  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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [213s/223s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
renderReport    96.015  3.965 106.635
DESeq2Report    39.085  1.205  41.695
derfinderReport 36.689  2.342  40.825
edgeReport      19.758  0.798  20.755
* 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-3.3-bioc/meat/regionReport.Rcheck/00check.log’
for details.

* installing *source* package ‘regionReport’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regionReport)

name	user	system	elapsed
DESeq2Report	39.085	1.205	41.695
derfinderReport	36.689	2.342	40.825
edgeReport	19.758	0.798	20.755
renderReport	96.015	3.965	106.635