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BioC 3.5: CHECK report for RPA on oaxaca

This page was generated on 2017-03-04 16:38:08 -0500 (Sat, 04 Mar 2017).

Package 1105/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.31.0
Leo Lahti
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RPA
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: RPA
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RPA_1.31.0.tar.gz
StartedAt: 2017-03-04 08:29:40 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 08:32:20 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 159.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RPA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RPA_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RPA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.31.0’
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RPA.Rcheck/00check.log’
for details.


RPA.Rcheck/00install.out:

* 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)

RPA.Rcheck/RPA-Ex.timings:

nameusersystemelapsed
RPA-package000
RPA.iteration0.0000.0000.001
RPA.preprocess0.0010.0000.000
collect.hyperparameters0.0000.0000.001
d.update.fast0.0000.0000.001
estimate.affinities000
estimate.hyperparameters000
frpa000
get.batches000
get.probe.matrix0.0000.0000.001
get.probe.parameters0.0000.0000.001
get.probeset000
hyperparameter.update0.0010.0000.001
online.quantile0.0010.0000.000
probe.parameters.tolist0.0010.0000.000
probe.performance0.0010.0000.000
probeplot0.0000.0000.001
probetable000
retrieve.probesets000
rpa000
rpa.complete000
rpa.fit0.0000.0000.001
rpa.online0.0000.0000.001
rpa.plot000
rpa.summarize000
rpaplot000
sample.probeset0.0000.0000.001
summarize.batch0.0000.0000.001
summarize.batches000
summarize_probedata0.0010.0000.000
updating.hyperparameters0.0010.0000.000