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BioC 3.2: CHECK report for FRGEpistasis on zin1

This page was generated on 2015-08-24 10:49:51 -0700 (Mon, 24 Aug 2015).

Package 369/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FRGEpistasis 1.5.0
Futao Zhang
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FRGEpistasis
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / 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 UNNEEDED, same version exists in internal repository

Summary

Package: FRGEpistasis
Version: 1.5.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings FRGEpistasis_1.5.0.tar.gz
StartedAt: 2015-08-23 23:55:25 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:58:02 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 157.3 seconds
RetCode: 0
Status:  OK 
CheckDir: FRGEpistasis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings FRGEpistasis_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/FRGEpistasis.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 ‘FRGEpistasis’ can be installed ... [3s/3s] 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 ... [119s/119s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
pCAPiontwiseEpistasis 107.746   0.04 108.156
* 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-3.2-bioc/meat/FRGEpistasis.Rcheck/00check.log’
for details.


FRGEpistasis.Rcheck/00install.out:

* 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)

FRGEpistasis.Rcheck/FRGEpistasis-Ex.timings:

nameusersystemelapsed
fRGEpistasis3.3580.0203.385
fRGInteraction0.0060.0000.007
fourierExpansion0.1130.0000.113
frgEpistasisTest1.9540.0121.986
innerEpi0.0710.0000.071
innerSnpListInteraction0.0310.0000.031
logTransPheno0.0000.0000.001
outerEpi0.6210.0000.621
outerSnpListInteraction0.0380.0040.041
pCAInteraction1.5010.0001.503
pCAPiontwiseEpistasis107.746 0.040108.156
pointwiseInteraction1.2250.0001.224
rankTransPheno0.0010.0000.001
reduceGeno0.5640.0080.578
snpPairInteraction0.0030.0000.003