BioC 3.2: CHECK report for gespeR on oaxaca

Package: gespeR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.2.0.tar.gz

StartedAt: 2016-04-23 00:38:11 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:42:26 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 255.2 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.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 gespeR_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gespeR.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 ‘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/18s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/82s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    5.569  0.282  50.866
gespeR-class      0.223  0.014  10.624
stability-methods 0.130  0.010  10.473
* 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	0.025	0.000	0.026
TargetRelations-class	0.010	0.001	0.011
annotate.gsp-methods	0.113	0.005	0.118
as.data.frame-Phenotypes-method	0.033	0.001	0.075
c-Phenotypes-method	0.040	0.001	0.042
concordance	0.773	0.009	0.794
gespeR-class	0.223	0.014	10.624
gespeR-package	5.569	0.282	50.866
gspssp-methods	0.150	0.010	0.161
join-methods	0.020	0.002	0.022
lasso.rand	0.013	0.001	0.039
na.rem-methods	0.029	0.000	0.029
path-methods	0.007	0.001	0.008
rbo	0.002	0.000	0.002
scores-methods	0.140	0.006	0.146
simData	0.018	0.001	0.019
stability-methods	0.130	0.010	10.473
stabilityfits	0.140	0.008	0.150
target-relations-methods	0.150	0.007	0.157
trmatrix-methods	0.135	0.006	0.141
values-methods	0.019	0.004	0.023