BioC 3.5: CHECK report for RPA on malbec2

Package: RPA

Version: 1.32.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.32.0.tar.gz

StartedAt: 2017-08-16 02:00:19 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:02:43 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 143.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RPA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RPA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RPA’ version ‘1.32.0’
* 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 ‘RPA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
RPA.iteration: no visible global function definition for ‘sd’
levelmap: no visible global function definition for ‘na.omit’
plot.rpa.list: no visible global function definition for ‘par’
probeplot: no visible global function definition for ‘plot’
probeplot: no visible global function definition for ‘lines’
rpa.fit : <anonymous>: no visible global function definition for
  ‘rnorm’
rpa.fit : <anonymous>: no visible global function definition for ‘sd’
rpa.impute : <anonymous>: no visible global function definition for
  ‘rnorm’
rpa.impute : <anonymous>: no visible global function definition for
  ‘sd’
rpa.online: no visible global function definition for ‘rnorm’
rpa.online: no visible global function definition for ‘sessionInfo’
rpaplot: no visible global function definition for ‘par’
rpaplot: no visible global function definition for ‘lines’
s2.neglogp: no visible global function definition for ‘dchisq’
s2.neglogp: no visible global function definition for ‘dgamma’
s2.update: no visible global function definition for ‘optim’
sample.probeset: no visible global function definition for ‘rgamma’
sample.probeset: no visible global function definition for ‘rnorm’
summarize_probedata: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dchisq dgamma lines na.omit optim par plot read.csv rgamma rnorm sd
  sessionInfo
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "dchisq", "dgamma", "na.omit", "optim", "rgamma",
             "rnorm", "sd")
  importFrom("utils", "read.csv", "sessionInfo")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘RPA.Rmd’, ‘RPA.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rpa.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/RPA.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RPA-package	0	0	0
RPA.iteration	0	0	0
RPA.preprocess	0	0	0
collect.hyperparameters	0	0	0
d.update.fast	0	0	0
estimate.affinities	0	0	0
estimate.hyperparameters	0.000	0.000	0.001
frpa	0.000	0.000	0.001
get.batches	0.000	0.000	0.001
get.probe.matrix	0	0	0
get.probe.parameters	0.004	0.000	0.000
get.probeset	0	0	0
hyperparameter.update	0.000	0.000	0.001
online.quantile	0.004	0.000	0.000
probe.parameters.tolist	0	0	0
probe.performance	0.000	0.000	0.001
probeplot	0.000	0.000	0.001
probetable	0	0	0
retrieve.probesets	0	0	0
rpa	0	0	0
rpa.complete	0	0	0
rpa.fit	0	0	0
rpa.online	0	0	0
rpa.plot	0	0	0
rpa.summarize	0	0	0
rpaplot	0	0	0
sample.probeset	0	0	0
summarize.batch	0	0	0
summarize.batches	0.000	0.000	0.001
summarize_probedata	0.004	0.000	0.001
updating.hyperparameters	0	0	0