BioC 3.2: CHECK report for gespeR on zin1

Package: gespeR

Version: 1.1.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.1.2.tar.gz

StartedAt: 2015-08-24 00:16:21 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:20:02 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 220.5 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gespeR_1.1.2.tar.gz
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* 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 ‘1.1.2’
* 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 ... [13s/13s] 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 ... [15s/85s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    5.451  0.355  52.635
gespeR-class      0.459  0.025  12.004
stability-methods 0.113  0.025  11.924
* 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	0.017	0.000	0.017
TargetRelations-class	0.009	0.000	0.009
annotate.gsp-methods	0.12	0.00	0.12
as.data.frame-Phenotypes-method	0.02	0.00	0.02
c-Phenotypes-method	0.023	0.000	0.023
concordance	0.433	0.000	0.433
gespeR-class	0.459	0.025	12.004
gespeR-package	5.451	0.355	52.635
gspssp-methods	0.127	0.004	0.131
join-methods	0.013	0.004	0.016
lasso.rand	0.005	0.000	0.005
na.rem-methods	0.017	0.000	0.017
path-methods	0.006	0.000	0.006
rbo	0.002	0.000	0.002
scores-methods	0.117	0.008	0.125
simData	0.012	0.000	0.012
stability-methods	0.113	0.025	11.924
stabilityfits	0.111	0.004	0.116
target-relations-methods	0.117	0.000	0.120
trmatrix-methods	0.112	0.004	0.116
values-methods	0.019	0.004	0.022