BioC 3.1: CHECK report for OmicsMarkeR on zin2

Package: OmicsMarkeR

Version: 1.0.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.0.1.tar.gz

StartedAt: 2015-10-06 03:57:41 -0700 (Tue, 06 Oct 2015)

EndedAt: 2015-10-06 04:00:15 -0700 (Tue, 06 Oct 2015)

EllapsedTime: 154.8 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/OmicsMarkeR.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 ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ version ‘1.0.1’
* 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 ‘OmicsMarkeR’ can be installed ... [6s/6s] 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
perm.class: no visible binding for global variable ‘outIndex’
* 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 ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          13.234  0.000  13.234
performance.metrics 11.997  0.024  12.250
feature.table       11.948  0.031  12.211
fs.stability        11.928  0.000  11.967
perm.features       11.861  0.004  11.904
predictNewClasses   11.754  0.020  11.764
fit.only.model       4.971  0.004   5.255
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [3s/3s] OK
* 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-3.1-bioc/meat/OmicsMarkeR.Rcheck/00check.log’
for details.

* installing *source* package ‘OmicsMarkeR’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.003	0.000	0.003
aggregation	0.003	0.000	0.003
canberra	0.001	0.000	0.000
create.corr.matrix	0.022	0.000	0.023
create.discr.matrix	0.015	0.003	0.020
create.random.matrix	0.022	0.001	0.022
denovo.grid	0.023	0.000	0.022
feature.table	11.948	0.031	12.211
fit.only.model	4.971	0.004	5.255
fs.ensembl.stability	0.001	0.000	0.000
fs.stability	11.928	0.000	11.967
jaccard	0.001	0.000	0.001
kuncheva	0.001	0.000	0.001
ochiai	0.001	0.000	0.000
pairwise.model.stability	0.005	0.000	0.005
pairwise.stability	0.002	0.000	0.002
params	0.002	0.000	0.002
performance.metrics	11.997	0.024	12.250
perm.class	13.234	0.000	13.234
perm.features	11.861	0.004	11.904
pof	0.000	0.000	0.001
predictNewClasses	11.754	0.020	11.764
sorensen	0.001	0.000	0.000
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.107	0.000	0.107
svmrfeFeatureRankingForMulticlass	0.184	0.000	0.184