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BioC 3.5: CHECK report for genphen on toluca2

This page was generated on 2017-04-23 14:41:28 -0400 (Sun, 23 Apr 2017).

Package 547/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.3.0
Simo Kitanovski
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genphen
Last Changed Rev: 123157 / Revision: 129046
Last Changed Date: 2016-10-28 13:56:24 -0400 (Fri, 28 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genphen
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genphen_1.3.0.tar.gz
StartedAt: 2017-04-23 04:33:58 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:36:39 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 160.4 seconds
RetCode: 0
Status:  OK 
CheckDir: genphen.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genphen_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genphen.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genphen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genphen’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘randomForest’ ‘e1071’ ‘ggplot2’ ‘effsize’ ‘Biostrings’ ‘rjags’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘genphen’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getBayesianTtest : getDataList: no visible global function definition
  for ‘sd’
getBayesianTtest : getEss: no visible global function definition for
  ‘effectiveSize’
getBayesianTtest: no visible global function definition for ‘update’
getTTestScore: no visible global function definition for ‘t.test’
plotGenphenBayes: no visible binding for global variable ‘g.1’
plotGenphenBayes: no visible binding for global variable ‘site’
plotGenphenBayes: no visible binding for global variable ‘g.2’
plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.H’
plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.L’
plotGenphenRfSvm: no visible global function definition for
  ‘terrain.colors’
plotManhattan: no visible binding for global variable ‘t.test.pvalue’
Undefined global functions or variables:
  ca.hdi.H ca.hdi.L effectiveSize g.1 g.2 sd site t.test t.test.pvalue
  terrain.colors update
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("stats", "sd", "t.test", "update")
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 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotGenphenBayes 14.445  0.060  16.029
runGenphenRf     13.549  0.180  13.746
plotGenphenRfSvm 12.794  0.370  13.306
runGenphenBayes  10.616  0.030  10.668
plotManhattan     9.517  0.585  10.163
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/genphen.Rcheck/00check.log’
for details.


genphen.Rcheck/00install.out:

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

genphen.Rcheck/genphen-Ex.timings:

nameusersystemelapsed
genotype.saap0.0280.0030.034
genotype.saap.msa0.0030.0010.005
genotype.snp0.0050.0010.008
genotype.snp.msa0.0030.0010.005
phenotype.saap0.0020.0010.003
phenotype.snp0.0020.0010.003
plotGenphenBayes14.445 0.06016.029
plotGenphenRfSvm12.794 0.37013.306
plotManhattan 9.517 0.58510.163
plotSpecificGenotype0.9860.0071.000
runGenphenBayes10.616 0.03010.668
runGenphenRf13.549 0.18013.746
runGenphenSvm2.9750.0223.018