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BioC 3.1: CHECK report for HybridMTest on petty

This page was generated on 2015-10-09 09:35:00 -0700 (Fri, 09 Oct 2015).

Package 475/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HybridMTest 1.12.0
Demba Fofana
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/HybridMTest
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HybridMTest
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HybridMTest_1.12.0.tar.gz
StartedAt: 2015-10-08 23:44:43 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:45:35 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 51.9 seconds
RetCode: 0
Status:  OK 
CheckDir: HybridMTest.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HybridMTest_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HybridMTest.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HybridMTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HybridMTest’ version ‘1.12.0’
* 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 ‘HybridMTest’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘fdrtool’ ‘MASS’ ‘survival’
  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
grenander: no visible global function definition for ‘gcmlcm’
hybrid.test: no visible global function definition for ‘exprs’
hybrid.test: no visible global function definition for ‘pData’
row.cox: no visible global function definition for ‘Surv’
row.cox: no visible global function definition for ‘coxph’
row.cox: no visible global function definition for ‘cox.zph’
row.slr.resids: no visible global function definition for ‘ginv’
* 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 ... [2s/2s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/HybridMTest.Rcheck/00check.log’
for details.


HybridMTest.Rcheck/00install.out:

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

HybridMTest.Rcheck/HybridMTest-Ex.timings:

nameusersystemelapsed
GroupComp.data0.0350.0030.039
HybridMTest-package0.0090.0040.013
correlation.data0.0020.0000.003
grenander.ebp0.0060.0000.024
hybrid.test0.2850.0090.298
row.kgrp.shapiro0.0880.0060.094
row.kruskal.wallis0.0400.0060.046
row.oneway.anova0.0240.0060.030
row.pearson0.0150.0020.017
row.slr.shapiro0.0430.0020.045
row.spearman0.0250.0030.028