BioC 3.3: CHECK report for OmicsMarkeR on linux2.bioconductor.org

Package: OmicsMarkeR

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.3.0.tar.gz

StartedAt: 2015-10-27 06:26:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:30:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 222.7 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/OmicsMarkeR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 ... [7s/7s] 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’
Undefined global functions or variables:
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [79s/79s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          13.953  0.000  13.991
performance.metrics 13.122  0.012  13.211
fs.stability        12.396  0.012  12.469
feature.table       10.612  0.016  10.637
perm.features       10.336  0.008  10.410
predictNewClasses    9.827  0.000   9.832
fit.only.model       5.675  0.004   5.684
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [69s/69s]
 [69s/69s] 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
  ‘/home/biocbuild/bbs-3.3-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	0.003	0.000	0.003
aggregation	0.003	0.000	0.002
canberra	0.002	0.000	0.001
canberra_stability	0.001	0.000	0.002
create.corr.matrix	0.007	0.000	0.007
create.discr.matrix	0.002	0.004	0.006
create.random.matrix	0.009	0.000	0.009
denovo.grid	0.008	0.000	0.009
feature.table	10.612	0.016	10.637
fit.only.model	5.675	0.004	5.684
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	12.396	0.012	12.469
jaccard	0.001	0.000	0.002
kuncheva	0.003	0.000	0.002
modelList	0.002	0.000	0.003
ochiai	0.002	0.000	0.002
pairwise.model.stability	0.014	0.000	0.014
pairwise.stability	0.008	0.000	0.008
params	0.003	0.000	0.004
performance.metrics	13.122	0.012	13.211
perm.class	13.953	0.000	13.991
perm.features	10.336	0.008	10.410
pof	0.001	0.000	0.001
predictNewClasses	9.827	0.000	9.832
sorensen	0.001	0.000	0.001
spearman	0.001	0.000	0.000
svmrfeFeatureRanking	0.063	0.000	0.062
svmrfeFeatureRankingForMulticlass	0.123	0.000	0.123