BioC 3.2: CHECK report for OmicsMarkeR on oaxaca

Package: OmicsMarkeR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz

StartedAt: 2016-04-23 02:45:40 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:50:07 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 266.5 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.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 OmicsMarkeR_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/OmicsMarkeR.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 ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmicsMarkeR’ can be installed ... [9s/10s] 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 ... [94s/96s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          15.515  0.289  16.234
performance.metrics 14.354  0.167  16.137
feature.table       13.661  0.208  13.920
fs.stability        12.795  0.376  13.220
predictNewClasses   12.746  0.421  13.226
perm.features       12.479  0.293  12.827
fit.only.model       5.521  0.216   5.748
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [79s/79s]
 [79s/80s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/OmicsMarkeR.Rcheck/00check.log’
for details.

* installing *source* package ‘OmicsMarkeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.005	0.001	0.026
aggregation	0.003	0.000	0.004
canberra	0.003	0.000	0.003
canberra_stability	0.003	0.000	0.003
create.corr.matrix	0.009	0.002	0.010
create.discr.matrix	0.010	0.002	0.011
create.random.matrix	0.013	0.002	0.015
denovo.grid	0.016	0.000	0.017
feature.table	13.661	0.208	13.920
fit.only.model	5.521	0.216	5.748
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	12.795	0.376	13.220
jaccard	0.001	0.001	0.002
kuncheva	0.002	0.000	0.002
modelList	0.003	0.000	0.003
ochiai	0.001	0.000	0.002
pairwise.model.stability	0.015	0.000	0.016
pairwise.stability	0.008	0.001	0.009
params	0.003	0.000	0.004
performance.metrics	14.354	0.167	16.137
perm.class	15.515	0.289	16.234
perm.features	12.479	0.293	12.827
pof	0.001	0.000	0.001
predictNewClasses	12.746	0.421	13.226
sorensen	0.001	0.000	0.002
spearman	0.001	0.001	0.001
svmrfeFeatureRanking	0.089	0.000	0.089
svmrfeFeatureRankingForMulticlass	0.167	0.001	0.168