BioC 3.2: CHECK report for gespeR on linux1.bioconductor.org

Package: gespeR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.2.0.tar.gz

StartedAt: 2015-10-27 04:02:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:06:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 231.7 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/gespeR.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 ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.2.0’
* 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 ‘gespeR’ can be installed ... [15s/15s] 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 ... 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 ... [14s/87s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    5.943  0.314  55.477
gespeR-class      0.477  0.016  11.677
stability-methods 0.117  0.035  12.425
* 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: OK

* installing *source* package ‘gespeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘gespeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gespeR)

name	user	system	elapsed
Phenotypes-class	0.022	0.000	0.023
TargetRelations-class	0.011	0.000	0.011
annotate.gsp-methods	0.159	0.004	0.163
as.data.frame-Phenotypes-method	0.022	0.008	0.029
c-Phenotypes-method	0.030	0.001	0.030
concordance	0.399	0.011	0.411
gespeR-class	0.477	0.016	11.677
gespeR-package	5.943	0.314	55.477
gspssp-methods	0.180	0.004	0.184
join-methods	0.020	0.000	0.021
lasso.rand	0.006	0.000	0.007
na.rem-methods	0.022	0.000	0.022
path-methods	0.008	0.000	0.008
rbo	0.002	0.000	0.002
scores-methods	0.16	0.00	0.16
simData	0.011	0.004	0.015
stability-methods	0.117	0.035	12.425
stabilityfits	0.116	0.000	0.117
target-relations-methods	0.148	0.000	0.148
trmatrix-methods	0.162	0.000	0.162
values-methods	0.023	0.008	0.030