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CHECK report for mvGST on malbec2

This page was generated on 2017-12-05 07:07:09 -0500 (Tue, 05 Dec 2017).

Package 918/1469HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mvGST 1.13.0
John R. Stevens
Snapshot Date: 2017-12-04 17:00:16 -0500 (Mon, 04 Dec 2017)
URL: https://git.bioconductor.org/packages/mvGST
Branch: master
Last Commit: 7abbb11
Last Changed Date: 2017-10-30 12:53:49 -0500 (Mon, 30 Oct 2017)
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  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mvGST
Version: 1.13.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings mvGST_1.13.0.tar.gz
StartedAt: 2017-12-05 01:54:32 -0500 (Tue, 05 Dec 2017)
EndedAt: 2017-12-05 01:57:12 -0500 (Tue, 05 Dec 2017)
EllapsedTime: 159.9 seconds
RetCode: 0
Status:  OK 
CheckDir: mvGST.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings mvGST_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/mvGST.Rcheck’
* using R Under development (unstable) (2017-10-20 r73567)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mvGST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mvGST’ version ‘1.13.0’
* 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 ‘mvGST’ 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
combinePvalues: no visible global function definition for ‘pnorm’
combinePvalues: no visible global function definition for ‘qnorm’
distributeWeight: no visible global function definition for
  ‘flush.console’
hartung: no visible global function definition for ‘qnorm’
hartung: no visible global function definition for ‘pnorm’
interactiveGraph: no visible global function definition for ‘locator’
oneSideBYAdjust: no visible binding for global variable ‘p.adjust’
p.adjust.SFL: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console locator p.adjust pnorm qnorm
Consider adding
  importFrom("graphics", "locator")
  importFrom("stats", "p.adjust", "pnorm", "qnorm")
  importFrom("utils", "flush.console")
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
profileTable 35.716   0.02   35.75
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/mvGST.Rcheck/00check.log’
for details.



Installation output

mvGST.Rcheck/00install.out

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

Tests output


Example timings

mvGST.Rcheck/mvGST-Ex.timings

nameusersystemelapsed
go2Profile0.5560.0120.566
graphCell3.5600.0443.610
mvGST-package000
mvGSTsamples0.4400.0080.446
p.adjust.SFL0.7640.0160.806
pickOut0.9000.0080.910
profileTable35.716 0.02035.750