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: 2015-10-27 06:15:30 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:20:01 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 270.5 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 3.2.2 (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 ‘1.2.0’
* 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 ... [93s/95s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          15.106  0.297  15.476
fs.stability        14.252  0.132  15.038
performance.metrics 13.794  0.207  14.350
predictNewClasses   13.022  0.256  13.358
perm.features       12.979  0.207  13.279
feature.table       12.231  0.296  12.590
fit.only.model       5.670  0.096   6.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [77s/77s]
 [78s/78s] 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	0.016
aggregation	0.004	0.001	0.004
canberra	0.003	0.000	0.003
canberra_stability	0.002	0.000	0.002
create.corr.matrix	0.010	0.001	0.012
create.discr.matrix	0.009	0.002	0.011
create.random.matrix	0.010	0.001	0.011
denovo.grid	0.014	0.002	0.015
feature.table	12.231	0.296	12.590
fit.only.model	5.670	0.096	6.514
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	14.252	0.132	15.038
jaccard	0.002	0.000	0.002
kuncheva	0.003	0.000	0.003
modelList	0.003	0.000	0.002
ochiai	0.001	0.001	0.001
pairwise.model.stability	0.014	0.000	0.014
pairwise.stability	0.008	0.000	0.008
params	0.003	0.000	0.002
performance.metrics	13.794	0.207	14.350
perm.class	15.106	0.297	15.476
perm.features	12.979	0.207	13.279
pof	0.002	0.000	0.002
predictNewClasses	13.022	0.256	13.358
sorensen	0.001	0.000	0.002
spearman	0.001	0.000	0.002
svmrfeFeatureRanking	0.109	0.001	0.139
svmrfeFeatureRankingForMulticlass	0.189	0.001	0.193