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BioC 3.2: CHECK report for RPA on perceval

This page was generated on 2015-11-10 14:46:25 -0800 (Tue, 10 Nov 2015).

Package 909/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.26.0
Leo Lahti
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RPA
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RPA
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RPA_1.26.0.tar.gz
StartedAt: 2015-11-10 09:06:14 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 09:07:13 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 59.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RPA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RPA_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RPA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.26.0’
* 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 ... [3s/3s] 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 ... NOTE
Package in Depends field not imported from: ‘parallel’
  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
estimate.hyperparameters: no visible global function definition for
  ‘mclapply’
get.affinities: no visible global function definition for ‘mclapply’
RPA.preprocess: no visible global function definition for ‘normalize’
summarize.batch: no visible global function definition for ‘mclapply’
updating.hyperparameters: no visible global function definition for
  ‘mclapply’
* 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’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rpa.R’ [20s/20s]
 [20s/20s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-package0.0010.0000.000
RPA.iteration0.0000.0000.001
RPA.preprocess0.0010.0000.000
collect.hyperparameters000
d.update.fast000
estimate.affinities0.0010.0000.000
estimate.hyperparameters0.0010.0000.000
frpa0.0000.0000.001
get.batches0.0000.0010.001
get.probe.matrix0.0010.0000.001
get.probe.parameters0.0010.0000.001
hyperparameter.update0.0010.0000.002
online.quantile0.0010.0000.001
probe.parameters.tolist0.0010.0000.000
probe.performance0.0010.0000.000
probeplot0.0000.0010.001
probetable0.0000.0000.001
rpa0.0010.0000.001
rpa.complete0.0010.0000.001
rpa.fit0.0000.0000.001
rpa.online000
rpa.plot0.0010.0000.001
rpa.summarize0.0010.0000.000
rpaplot0.0010.0000.000
sample.probeset0.0000.0000.001
summarize.batch0.0000.0000.001
summarize.batches0.0010.0000.001
updating.hyperparameters0.0000.0000.001