BioC 3.5: CHECK report for PSEA on veracruz2

Package: PSEA

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSEA_1.10.0.tar.gz

StartedAt: 2017-08-16 06:48:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:49:04 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 27.6 seconds

RetCode: 0

Status:  OK

CheckDir: PSEA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PSEA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PSEA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSEA/DESCRIPTION’ ... OK
* this is package ‘PSEA’ version ‘1.10.0’
* 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 ‘PSEA’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
crplot: no visible global function definition for ‘residuals’
crplot: no visible global function definition for ‘dev.new’
crplot: no visible global function definition for ‘plot’
crplot: no visible global function definition for ‘abline’
crplot: no visible global function definition for ‘points’
lmfitst : <anonymous>: no visible global function definition for
  ‘lm.fit’
swlm: no visible global function definition for ‘formula’
swlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline dev.new formula lm lm.fit plot points residuals
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "formula", "lm", "lm.fit", "residuals")
to your NAMESPACE file.
* 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 ... 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-3.5-bioc/meat/PSEA.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
coefmat	0.089	0.006	0.095
crplot	0.013	0.002	0.015
em_quantvg	0.056	0.001	0.057
fmm	0.030	0.001	0.032
lmfitst	0.075	0.001	0.078
marker	0.005	0.001	0.006
pvalmat	0.062	0.002	0.064
slt	0.003	0.000	0.003
swlm	0.042	0.001	0.043