BioC 3.2: CHECK report for OmicsMarkeR on oaxaca

Package: OmicsMarkeR

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.1.2.tar.gz

StartedAt: 2015-08-24 02:22:26 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:27:17 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 291.3 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_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/OmicsMarkeR.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 ‘OmicsMarkeR/DESCRIPTION’ ... OK
* this is package ‘OmicsMarkeR’ 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 ... 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/9s] 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 ... [102s/106s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          17.094  0.358  17.901
perm.features       15.267  0.382  15.901
fs.stability        14.818  0.313  15.465
performance.metrics 14.518  0.293  15.153
predictNewClasses   14.126  0.357  14.573
feature.table       13.874  0.253  14.804
fit.only.model       5.785  0.201   6.226
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [81s/81s]
 [81s/81s] 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
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	0.004	0.000	0.004
aggregation	0.004	0.001	0.003
canberra	0.002	0.000	0.002
canberra_stability	0.001	0.000	0.001
create.corr.matrix	0.009	0.001	0.010
create.discr.matrix	0.009	0.002	0.010
create.random.matrix	0.013	0.001	0.014
denovo.grid	0.014	0.002	0.016
feature.table	13.874	0.253	14.804
fit.only.model	5.785	0.201	6.226
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	14.818	0.313	15.465
jaccard	0.001	0.000	0.002
kuncheva	0.002	0.000	0.003
modelList	0.002	0.000	0.003
ochiai	0.002	0.000	0.002
pairwise.model.stability	0.011	0.000	0.011
pairwise.stability	0.006	0.000	0.006
params	0.003	0.000	0.003
performance.metrics	14.518	0.293	15.153
perm.class	17.094	0.358	17.901
perm.features	15.267	0.382	15.901
pof	0.001	0.000	0.002
predictNewClasses	14.126	0.357	14.573
sorensen	0.001	0.000	0.001
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.094	0.003	0.097
svmrfeFeatureRankingForMulticlass	0.206	0.001	0.208