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BioC 3.5: CHECK report for hierGWAS on oaxaca

This page was generated on 2017-03-04 16:49:59 -0500 (Sat, 04 Mar 2017).

Package 605/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hierGWAS 1.5.0
Laura Buzdugan
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hierGWAS
Last Changed Rev: 123157 / Revision: 127142
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 UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: hierGWAS
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hierGWAS_1.5.0.tar.gz
StartedAt: 2017-03-04 04:21:07 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:22:11 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 64.0 seconds
RetCode: 0
Status:  OK 
CheckDir: hierGWAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hierGWAS_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/hierGWAS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hierGWAS/DESCRIPTION’ ... OK
* this is package ‘hierGWAS’ version ‘1.5.0’
* 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 ‘hierGWAS’ 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
MEL: no visible global function definition for ‘glm’
MEL: no visible binding for global variable ‘binomial’
MEL: no visible global function definition for ‘glm.control’
MEL: no visible global function definition for ‘coef’
adj.pval: no visible global function definition for ‘quantile’
cluster.snp: no visible global function definition for ‘cor’
cluster.snp: no visible global function definition for ‘as.dist’
cluster.snp: no visible global function definition for ‘as.dendrogram’
return.r2: no visible global function definition for ‘lm’
test.hierarchy: no visible global function definition for
  ‘order.dendrogram’
test.snp: no visible global function definition for ‘anova’
test.snp: no visible global function definition for ‘lm’
Undefined global functions or variables:
  anova as.dendrogram as.dist binomial coef cor glm glm.control lm
  order.dendrogram quantile
Consider adding
  importFrom("stats", "anova", "as.dendrogram", "as.dist", "binomial",
             "coef", "cor", "glm", "glm.control", "lm",
             "order.dendrogram", "quantile")
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/hierGWAS.Rcheck/00check.log’
for details.


hierGWAS.Rcheck/00install.out:

* installing *source* package ‘hierGWAS’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hierGWAS)

hierGWAS.Rcheck/hierGWAS-Ex.timings:

nameusersystemelapsed
cluster.snp0.0860.0100.121
compute.r20.6280.0130.656
multisplit0.4940.0120.506
simGWAS0.0030.0010.004
test.hierarchy4.3600.0294.393