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BioC 3.5: CHECK report for GENESIS on veracruz2

This page was generated on 2017-10-18 14:33:03 -0400 (Wed, 18 Oct 2017).

Package 525/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.6.1
Matthew P. Conomos , Stephanie M. Gogarten
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GENESIS
Branch: RELEASE_3_5
Last Commit: 4fb1e02
Last Changed Date: 2017-06-27 16:52:25 -0400 (Tue, 27 Jun 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  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GENESIS
Version: 2.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GENESIS_2.6.1.tar.gz
StartedAt: 2017-10-18 04:01:34 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:08:43 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 429.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GENESIS_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GENESIS.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GENESIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENESIS’ version ‘2.6.1’
* 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 ‘GENESIS’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘survey:::saddle’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
assocTestMM 11.997  0.607  12.986
fitNullMM   10.859  0.499  11.674
pcrelate    10.380  0.473  11.166
admixMapMM  10.022  0.613  10.997
varCompCI    9.785  0.517  10.669
* 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/GENESIS.Rcheck/00check.log’
for details.


GENESIS.Rcheck/00install.out:

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

GENESIS.Rcheck/GENESIS-Ex.timings:

nameusersystemelapsed
admixMapMM10.022 0.61310.997
assocTestMM11.997 0.60712.986
assocTestSeq1.2130.0591.311
assocTestSeqWindow3.1320.0253.262
fitNullMM10.859 0.49911.674
king2mat0.4300.0040.439
pcair0.7210.1120.954
pcairPartition0.0930.0020.103
pcrelate10.380 0.47311.166
plot.pcair0.8150.0850.927
varCompCI 9.785 0.51710.669