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BioC 3.2: CHECK report for PROPER on oaxaca

This page was generated on 2016-04-23 10:28:42 -0700 (Sat, 23 Apr 2016).

Package 804/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PROPER 1.2.0
Hao Wu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/PROPER
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PROPER
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.2.0.tar.gz
StartedAt: 2016-04-23 03:15:39 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:16:29 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 49.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PROPER.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PROPER.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PROPER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PROPER’ version ‘1.2.0’
* 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 ‘PROPER’ can be installed ... [2s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... WARNING
'library' or 'require' call not declared from: ‘edgeR’
'library' or 'require' call to ‘edgeR’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estParam: no visible global function definition for ‘exprs’
run.DESeq: no visible global function definition for ‘newCountDataSet’
run.DESeq: no visible global function definition for
  ‘estimateSizeFactors’
run.DESeq: no visible global function definition for
  ‘estimateDispersions’
run.DESeq: no visible global function definition for ‘nbinomTest’
run.DSS: no visible global function definition for ‘newSeqCountSet’
run.DSS: no visible global function definition for ‘estNormFactors’
run.DSS: no visible global function definition for ‘estDispersion’
run.DSS: no visible global function definition for ‘waldTest’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
  Code: function(X, type = 1)
  Docs: function(X, type = c(1, 2))
  Mismatches in argument default values:
    Name: 'type' Code: 1 Docs: c(1, 2)

* 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
runSims 15.898  0.813  16.739
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PROPER.Rcheck/00check.log’
for details.


PROPER.Rcheck/00install.out:

* installing *source* package ‘PROPER’ ...
** 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 (PROPER)

PROPER.Rcheck/PROPER-Ex.timings:

nameusersystemelapsed
RNAseq.SimOptions.2grp0.6020.0240.627
comparePower0.0020.0010.003
estParam0.0010.0000.000
plotPowerHist0.0000.0000.001
plots0.0010.0000.001
power.seqDepth000
runSims15.898 0.81316.739
simRNAseq0.3540.0240.379
summaryPower0.0000.0000.001