BioC 3.2: CHECK report for FRGEpistasis on oaxaca

Package: FRGEpistasis

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FRGEpistasis_1.6.0.tar.gz

StartedAt: 2016-04-23 00:15:17 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:18:47 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 210.3 seconds

RetCode: 0

Status:  OK

CheckDir: FRGEpistasis.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 FRGEpistasis_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/FRGEpistasis.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FRGEpistasis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FRGEpistasis’ version ‘1.6.0’
* 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 ‘FRGEpistasis’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [155s/156s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
pCAPiontwiseEpistasis 140.364  0.465 141.199
* 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-3.2-bioc/meat/FRGEpistasis.Rcheck/00check.log’
for details.

* installing *source* package ‘FRGEpistasis’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FRGEpistasis)

name	user	system	elapsed
fRGEpistasis	4.432	0.045	4.484
fRGInteraction	0.008	0.000	0.009
fourierExpansion	0.174	0.031	0.206
frgEpistasisTest	2.186	0.021	2.212
innerEpi	0.089	0.001	0.091
innerSnpListInteraction	0.038	0.001	0.038
logTransPheno	0.001	0.000	0.001
outerEpi	0.755	0.005	0.762
outerSnpListInteraction	0.046	0.000	0.047
pCAInteraction	1.742	0.011	1.753
pCAPiontwiseEpistasis	140.364	0.465	141.199
pointwiseInteraction	1.625	0.008	1.635
rankTransPheno	0.001	0.000	0.001
reduceGeno	0.994	0.033	1.029
snpPairInteraction	0.005	0.000	0.004