BioC 3.2: CHECK report for CexoR on perceval

Package: CexoR

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CexoR_1.7.4.tar.gz

StartedAt: 2015-08-23 22:56:08 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:01:18 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 310.0 seconds

RetCode: 0

Status:  OK

CheckDir: CexoR.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 CexoR_1.7.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CexoR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CexoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CexoR’ version ‘1.7.4’
* 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 ‘CexoR’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cexor: no visible global function definition for ‘start<-’
cexor: no visible global function definition for ‘end<-’
plotcexor: no visible global function definition for ‘start<-’
plotcexor: no visible global function definition for ‘end<-’
plotcexor: no visible global function definition for ‘reduce’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
CexoR-package 18.942  0.262  19.247
plotcexor     18.119  0.170  18.389
cexor         18.120  0.139  18.308
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [27s/27s]
 [27s/28s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CexoR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CexoR-package	18.942	0.262	19.247
cexor	18.120	0.139	18.308
plotcexor	18.119	0.170	18.389