BioC 3.2: CHECK report for OmicsMarkeR on linux1.bioconductor.org

Package: OmicsMarkeR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz

StartedAt: 2015-10-27 06:24:40 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:28:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 227.1 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.2.0’
* 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 ... [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’
* 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 ... [81s/81s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.features       13.558  0.016  13.589
fs.stability        13.199  0.004  13.302
perm.class          13.002  0.008  13.031
performance.metrics 12.695  0.008  12.773
feature.table       10.541  0.004  10.562
predictNewClasses   10.067  0.004  10.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [68s/68s]
 [68s/68s] 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-3.2-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	0.003	0.000	0.004
aggregation	0.003	0.000	0.003
canberra	0.001	0.000	0.001
canberra_stability	0.001	0.000	0.001
create.corr.matrix	0.007	0.000	0.007
create.discr.matrix	0.006	0.000	0.006
create.random.matrix	0.009	0.000	0.009
denovo.grid	0.01	0.00	0.01
feature.table	10.541	0.004	10.562
fit.only.model	4.123	0.020	4.142
fs.ensembl.stability	0.001	0.000	0.001
fs.stability	13.199	0.004	13.302
jaccard	0.002	0.000	0.001
kuncheva	0.002	0.000	0.002
modelList	0.002	0.000	0.002
ochiai	0.002	0.000	0.001
pairwise.model.stability	0.014	0.000	0.014
pairwise.stability	0.008	0.000	0.008
params	0.004	0.000	0.003
performance.metrics	12.695	0.008	12.773
perm.class	13.002	0.008	13.031
perm.features	13.558	0.016	13.589
pof	0.001	0.000	0.001
predictNewClasses	10.067	0.004	10.140
sorensen	0.001	0.000	0.001
spearman	0.001	0.000	0.001
svmrfeFeatureRanking	0.058	0.004	0.061
svmrfeFeatureRankingForMulticlass	0.121	0.000	0.121