BioC 3.6: CHECK report for zinbwave on veracruz1

Package: zinbwave

Version: 0.99.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings zinbwave_0.99.6.tar.gz

StartedAt: 2017-08-16 09:40:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:43:15 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 172.8 seconds

RetCode: 0

Status:  OK

CheckDir: zinbwave.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 zinbwave_0.99.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/zinbwave.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zinbwave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zinbwave’ version ‘0.99.6’
* 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 ‘zinbwave’ 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 ‘zinbwave’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zinbwave)

name	user	system	elapsed
getAlpha_mu	0.092	0.000	0.097
getAlpha_pi	0.101	0.005	0.109
getBeta_mu	0.003	0.001	0.004
getBeta_pi	0.002	0.001	0.003
getEpsilon_W	0.043	0.000	0.043
getEpsilon_alpha	0.003	0.000	0.003
getEpsilon_beta_mu	0.002	0.000	0.002
getEpsilon_beta_pi	0.002	0.000	0.002
getEpsilon_gamma_mu	0.002	0.000	0.002
getEpsilon_gamma_pi	0.003	0.001	0.003
getEpsilon_zeta	0.003	0.000	0.006
getGamma_mu	0.004	0.000	0.004
getGamma_pi	0.002	0.000	0.002
getLogMu	0.003	0.000	0.004
getLogitPi	0.002	0.000	0.002
getMu	0.003	0.001	0.003
getPhi	0.003	0.000	0.004
getPi	0.003	0.000	0.003
getTheta	0.004	0.000	0.004
getV_mu	0.002	0.000	0.003
getV_pi	0.002	0.000	0.002
getW	0.002	0.000	0.002
getX_mu	0.004	0.000	0.003
getX_pi	0.002	0.000	0.002
getZeta	0.002	0.000	0.002
loglik	0.004	0.000	0.004
orthogonalizeTraceNorm	0.002	0.000	0.002
penalty	0.003	0.000	0.004
zinb.loglik	0.001	0.000	0.001
zinb.loglik.dispersion	0.001	0.000	0.002
zinbFit	1.403	0.775	3.190
zinbInitialize	0.190	0.240	0.656
zinbModel	0.002	0.001	0.002
zinbOptimize	2.157	2.794	0.920
zinbOptimizeDispersion	0.176	0.227	0.616
zinbSim	0.028	0.006	0.034
zinbwave	0.352	0.350	1.221