BioC 3.2: CHECK report for OmicsMarkeR on moscato1

Package: OmicsMarkeR

Version: 1.2.0

Command: rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.2.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz

StartedAt: 2016-04-23 05:35:53 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:46:45 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 652.5 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.2.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/OmicsMarkeR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'OmicsMarkeR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [115s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
predictNewClasses   19.32   0.03   19.34
perm.class          17.80   0.05   17.84
feature.table       17.58   0.04   18.39
perm.features       17.38   0.01   17.39
fs.stability        14.59   0.01   14.60
performance.metrics 14.50   0.00   14.49
fit.only.model       7.99   0.00    8.16
** running examples for arch 'x64' ... [139s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          23.26   0.01   23.31
feature.table       21.09   0.02   21.21
performance.metrics 20.48   0.05   20.59
fs.stability        20.23   0.00   20.26
perm.features       18.98   0.02   19.37
predictNewClasses   18.56   0.06   18.62
fit.only.model       8.61   0.03    8.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [90s]
 [90s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [101s]
 [101s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/OmicsMarkeR.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'OmicsMarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.2.0.zip
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.00	0.00	0.26
aggregation	0	0	0
canberra	0	0	0
canberra_stability	0	0	0
create.corr.matrix	0.01	0.00	0.02
create.discr.matrix	0	0	0
create.random.matrix	0.02	0.00	0.01
denovo.grid	0.01	0.00	0.02
feature.table	17.58	0.04	18.39
fit.only.model	7.99	0.00	8.16
fs.ensembl.stability	0	0	0
fs.stability	14.59	0.01	14.60
jaccard	0.01	0.00	0.02
kuncheva	0	0	0
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0.02	0.00	0.01
pairwise.stability	0	0	0
params	0	0	0
performance.metrics	14.50	0.00	14.49
perm.class	17.80	0.05	17.84
perm.features	17.38	0.01	17.39
pof	0	0	0
predictNewClasses	19.32	0.03	19.34
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.11	0.00	0.11
svmrfeFeatureRankingForMulticlass	0.28	0.00	0.28

name	user	system	elapsed
RPT	0	0	0
aggregation	0.02	0.00	0.02
canberra	0	0	0
canberra_stability	0	0	0
create.corr.matrix	0.01	0.00	0.01
create.discr.matrix	0	0	0
create.random.matrix	0.01	0.00	0.02
denovo.grid	0.03	0.00	0.03
feature.table	21.09	0.02	21.21
fit.only.model	8.61	0.03	8.67
fs.ensembl.stability	0	0	0
fs.stability	20.23	0.00	20.26
jaccard	0	0	0
kuncheva	0.01	0.00	0.02
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0.04	0.00	0.03
pairwise.stability	0	0	0
params	0	0	0
performance.metrics	20.48	0.05	20.59
perm.class	23.26	0.01	23.31
perm.features	18.98	0.02	19.37
pof	0	0	0
predictNewClasses	18.56	0.06	18.62
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.13	0.00	0.12
svmrfeFeatureRankingForMulticlass	0.28	0.00	0.29