BioC 3.5: CHECK report for GENESIS on veracruz2

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: 2017-08-16 03:15:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:22:39 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 428.0 seconds

RetCode: 0

Status:  OK

CheckDir: GENESIS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GENESIS_2.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GENESIS.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 10.619  0.611  11.612
admixMapMM  10.469  0.507  11.316
fitNullMM   10.159  0.481  10.932
varCompCI    9.747  0.481  10.554
pcrelate     9.330  0.405  10.006
* 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.

* 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)

name	user	system	elapsed
admixMapMM	10.469	0.507	11.316
assocTestMM	10.619	0.611	11.612
assocTestSeq	1.150	0.050	1.256
assocTestSeqWindow	2.967	0.012	3.074
fitNullMM	10.159	0.481	10.932
king2mat	0.392	0.003	0.406
pcair	0.619	0.084	0.720
pcairPartition	0.063	0.001	0.064
pcrelate	9.330	0.405	10.006
plot.pcair	0.823	0.109	0.970
varCompCI	9.747	0.481	10.554