BioC 3.1: CHECK report for RefPlus on zin2

Package: RefPlus

Version: 1.38.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RefPlus_1.38.0.tar.gz

StartedAt: 2015-10-09 04:49:46 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:51:16 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 90.9 seconds

RetCode: 0

Status:  OK

CheckDir: RefPlus.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RefPlus_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RefPlus.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RefPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefPlus’ version ‘1.38.0’
* 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 ‘RefPlus’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘affyPLM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rma.para: no visible global function definition for ‘rmaPLM’
rma.para: no visible global function definition for ‘coefs.probe’
rma.para: no visible global function definition for ‘coefs’
* checking Rd files ... NOTE
prepare_Rd: colMedians.Rd:19: Dropping empty section \references
prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples
* 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 ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RefPlus-package 12.554  0.172  12.737
rmaplus         10.578  0.112  10.726
rma.para         6.565  0.056   6.616
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/RefPlus.Rcheck/00check.log’
for details.

* installing *source* package ‘RefPlus’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RefPlus)

name	user	system	elapsed
RefPlus-package	12.554	0.172	12.737
colMedians	0.001	0.000	0.001
normalize.quantiles2	0.001	0.000	0.002
rma.para	6.565	0.056	6.616
rmaplus	10.578	0.112	10.726