BioC 3.1: CHECK report for gespeR on morelia

Package: gespeR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.0.0.tar.gz

StartedAt: 2015-10-09 02:24:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:28:59 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 247.9 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gespeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [16s/17s] 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 ... NOTE
gespeR,Phenotypes-TargetRelations : .local: warning in
  Phenotypes(phenotype = gsp, ids = names(gsp), type = "GSP"): partial
  argument match of 'phenotype' to 'phenotypes'
* 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 ... [17s/77s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    5.415  0.573  46.923
gespeR-class      0.169  0.016  10.056
stability-methods 0.114  0.014   9.764
* 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-3.1-bioc/meat/gespeR.Rcheck/00check.log’
for details.

* installing *source* package ‘gespeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (gespeR)

name	user	system	elapsed
Phenotypes-class	0.009	0.003	0.012
TargetRelations-class	0.009	0.003	0.011
annotate.gsp-methods	0.269	0.070	0.339
as.data.frame-Phenotypes-method	0.035	0.005	0.039
c-Phenotypes-method	0.017	0.000	0.018
concordance	0.794	0.022	0.816
gespeR-class	0.169	0.016	10.056
gespeR-package	5.415	0.573	46.923
gspssp-methods	0.225	0.017	0.242
join-methods	0.012	0.001	0.013
lasso.rand	0.004	0.001	0.014
na.rem-methods	0.008	0.000	0.008
path-methods	0.005	0.001	0.006
rbo	0.002	0.000	0.002
scores-methods	0.216	0.022	0.239
simData	0.014	0.001	0.015
stability-methods	0.114	0.014	9.764
stabilityfits	0.236	0.052	0.287
target-relations-methods	0.503	0.050	0.553
trmatrix-methods	0.179	0.009	0.188
values-methods	0.009	0.001	0.009