BioC 3.2: CHECK report for OmicsMarkeR on zin1

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: 2016-04-23 03:32:51 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:36:31 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 219.3 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 3.2.4 Revised (2016-03-16 r70336)
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [82s/82s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
perm.class          13.965  0.012  14.109
feature.table       12.424  0.032  12.464
perm.features       11.754  0.000  11.875
predictNewClasses   11.702  0.000  11.747
performance.metrics 11.653  0.007  12.133
fs.stability        11.542  0.039  11.595
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [65s/65s]
 [66s/66s] 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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.004	0.000	0.009
aggregation	0.003	0.000	0.003
canberra	0.002	0.000	0.002
canberra_stability	0.001	0.000	0.002
create.corr.matrix	0.008	0.000	0.008
create.discr.matrix	0.008	0.000	0.007
create.random.matrix	0.01	0.00	0.01
denovo.grid	0.011	0.000	0.011
feature.table	12.424	0.032	12.464
fit.only.model	4.914	0.016	4.927
fs.ensembl.stability	0.000	0.000	0.001
fs.stability	11.542	0.039	11.595
jaccard	0.001	0.000	0.001
kuncheva	0.002	0.000	0.002
modelList	0.002	0.000	0.002
ochiai	0.001	0.000	0.001
pairwise.model.stability	0.012	0.000	0.012
pairwise.stability	0.007	0.000	0.007
params	0.003	0.000	0.003
performance.metrics	11.653	0.007	12.133
perm.class	13.965	0.012	14.109
perm.features	11.754	0.000	11.875
pof	0.001	0.000	0.001
predictNewClasses	11.702	0.000	11.747
sorensen	0.001	0.000	0.001
spearman	0.002	0.000	0.002
svmrfeFeatureRanking	0.088	0.000	0.087
svmrfeFeatureRankingForMulticlass	0.182	0.000	0.182