BioC 3.4: CHECK report for flowQB on morelia

Package: flowQB

Version: 2.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQB_2.1.2.tar.gz

StartedAt: 2016-09-20 06:36:00 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:46:53 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 653.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowQB.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 flowQB_2.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowQB.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQB’ version ‘2.1.2’
* 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 ‘flowQB’ 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 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
fit_beads                245.738  9.834 255.394
fit_led                   11.576  1.893  13.709
qb_from_fits              10.196  1.709  11.862
calc_mean_sd_197           8.772  1.248  10.935
calc_mean_sd_capture_all   7.084  0.968   8.135
* 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 ‘flowQB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowQB)

name	user	system	elapsed
calc_mean_sd_197	8.772	1.248	10.935
calc_mean_sd_background	2.374	0.224	2.631
calc_mean_sd_capture	0.388	0.076	0.458
calc_mean_sd_capture_all	7.084	0.968	8.135
calc_mean_sd_duke	3.457	0.474	3.594
find_peak	0.003	0.001	0.004
fit_beads	245.738	9.834	255.394
fit_led	11.576	1.893	13.709
fitted_ellipse_gate	1.06	0.28	1.32
get_results_for_dyes	3.039	0.467	3.361
peak_gate-methods	1.161	0.252	1.389
pick_parameters-methods	0.403	0.085	0.487
qb_from_fits	10.196	1.709	11.862
split_in_two-methods	0.773	0.151	0.919