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BioC 3.6: CHECK report for genphen on malbec1

This page was generated on 2017-08-16 13:24:21 -0400 (Wed, 16 Aug 2017).

Package 556/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.5.0
Simo Kitanovski
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genphen
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genphen
Version: 1.5.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genphen_1.5.0.tar.gz
StartedAt: 2017-08-15 23:33:02 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:35:10 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 128.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genphen.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genphen_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/genphen.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runGenphenRf     12.332  0.088  12.429
plotGenphenBayes 11.764  0.028  11.864
plotGenphenRfSvm 10.236  0.016  10.264
runGenphenBayes  10.180  0.004  10.190
plotManhattan     7.292  0.008   7.308
* 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
  ‘/home/biocbuild/bbs-3.6-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.saap0.0200.0000.018
genotype.saap.msa0.0040.0000.002
genotype.snp0.0040.0000.003
genotype.snp.msa0.0040.0000.002
phenotype.saap0.0000.0040.002
phenotype.snp0.0000.0000.001
plotGenphenBayes11.764 0.02811.864
plotGenphenRfSvm10.236 0.01610.264
plotManhattan7.2920.0087.308
plotSpecificGenotype0.6720.0000.672
runGenphenBayes10.180 0.00410.190
runGenphenRf12.332 0.08812.429
runGenphenSvm1.9640.0001.964