BioC 3.2: CHECK report for OmicsMarkeR on windows1.bioconductor.org

Package: OmicsMarkeR

Version: 1.2.0

Command: rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && C:\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 && C:\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: 2015-10-27 04:10:30 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:16:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 381.7 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 && C:\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  && C:\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 'C:/biocbld/bbs-3.2-bioc/meat/OmicsMarkeR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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' ... [76s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          12.34   0.00   12.35
perm.features       11.51   0.01   11.53
feature.table       10.97   0.08   11.04
performance.metrics 10.99   0.00   10.98
fs.stability        10.86   0.00   10.86
predictNewClasses   10.78   0.03   10.82
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          15.83   0.05   16.05
feature.table       12.51   0.03   12.55
predictNewClasses   12.49   0.01   12.51
perm.features       12.06   0.02   12.10
performance.metrics 11.25   0.03   11.28
fs.stability        11.05   0.04   11.10
fit.only.model       5.00   0.02    5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [59s]
 [59s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [67s]
 [67s] 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
  'C:/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
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.

install for x64

* installing *source* package 'OmicsMarkeR' ...
** 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.
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.2.0.zip
* DONE (OmicsMarkeR)

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	0.02	0.00	0.02
denovo.grid	0	0	0
feature.table	10.97	0.08	11.04
fit.only.model	4.55	0.03	4.58
fs.ensembl.stability	0.01	0.00	0.02
fs.stability	10.86	0.00	10.86
jaccard	0	0	0
kuncheva	0	0	0
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0	0	0
pairwise.stability	0	0	0
params	0.01	0.00	0.02
performance.metrics	10.99	0.00	10.98
perm.class	12.34	0.00	12.35
perm.features	11.51	0.01	11.53
pof	0	0	0
predictNewClasses	10.78	0.03	10.82
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.06	0.00	0.06
svmrfeFeatureRankingForMulticlass	0.13	0.00	0.13

name	user	system	elapsed
RPT	0.02	0.00	0.02
aggregation	0	0	0
canberra	0	0	0
canberra_stability	0	0	0
create.corr.matrix	0.02	0.00	0.01
create.discr.matrix	0	0	0
create.random.matrix	0.01	0.00	0.02
denovo.grid	0.02	0.00	0.01
feature.table	12.51	0.03	12.55
fit.only.model	5.00	0.02	5.01
fs.ensembl.stability	0	0	0
fs.stability	11.05	0.04	11.10
jaccard	0	0	0
kuncheva	0	0	0
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0.02	0.00	0.02
pairwise.stability	0.01	0.00	0.01
params	0	0	0
performance.metrics	11.25	0.03	11.28
perm.class	15.83	0.05	16.05
perm.features	12.06	0.02	12.10
pof	0	0	0
predictNewClasses	12.49	0.01	12.51
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.07	0.00	0.06
svmrfeFeatureRankingForMulticlass	0.14	0.00	0.14