BioC 3.3: CHECK report for pbcmc on morelia

Package: pbcmc

Version: 0.99.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pbcmc_0.99.5.tar.gz

StartedAt: 2016-04-21 05:54:06 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:56:55 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 169.3 seconds

RetCode: 0

Status:  OK

CheckDir: pbcmc.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pbcmc_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pbcmc.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pbcmc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pbcmc’ version ‘0.99.5’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pbcmc’ can be installed ... [9s/10s] 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [64s/34s]
 [65s/34s] 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: OK

* installing *source* package ‘pbcmc’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: unlist
Creating a generic function for ‘summary’ from package ‘base’ in package ‘pbcmc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist
* DONE (pbcmc)

name	user	system	elapsed
MolecularPermutationClassifierConstructor	0.641	0.044	0.764
MolecularPermutationClassifierGenerics	0.164	0.103	2.345
MolecularPermutationClassifierGetseters	0.049	0.009	0.057
MolecularPermutationClassifierShow	0.055	0.008	0.063
PAM50-class	2.422	0.252	4.605
PAM50Classify	0.065	0.007	0.073
PAM50Constructor	0.468	0.035	0.503
PAM50Filtrate	0.911	0.045	0.957
PAM50Permutate	0.103	0.086	2.277
PAM50SubjectReport	2.304	0.110	2.416
PAM50Subtype	0.069	0.008	0.077