BioC 3.5: CHECK report for pbcmc on toluca2

Package: pbcmc

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pbcmc_1.3.2.tar.gz

StartedAt: 2017-04-23 07:48:22 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:52:00 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 217.9 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_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pbcmc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.3.2’
* 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 ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
PAM50-class 6.36  0.298       9
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
** 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	0.743	0.049	0.801
MolecularPermutationClassifierGenerics	0.336	0.124	3.530
MolecularPermutationClassifierGetseters	0.059	0.010	0.069
MolecularPermutationClassifierShow	0.054	0.008	0.062
PAM50-class	6.360	0.298	9.000
PAM50Classify	0.066	0.005	0.072
PAM50Constructor	0.797	0.081	0.886
PAM50Filtrate	0.978	0.050	1.091
PAM50Permutate	0.129	0.097	2.654
PAM50SubjectReport	4.642	0.160	4.850
PAM50Subtype	0.069	0.012	0.081