BioC 3.5: CHECK report for flowQB on oaxaca

Package: flowQB

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQB_2.3.1.tar.gz

StartedAt: 2017-03-04 02:55:50 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:08:18 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 748.8 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_2.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowQB.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘2.3.1’
* 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                271.095  8.345 279.060
fit_led                   10.809  1.939  11.900
qb_from_fits               9.876  1.942  11.773
calc_mean_sd_197           9.096  0.800  11.427
calc_mean_sd_capture_all   5.480  0.543   6.241
* 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	9.096	0.800	11.427
calc_mean_sd_background	3.115	0.262	2.601
calc_mean_sd_capture	0.362	0.052	0.424
calc_mean_sd_capture_all	5.480	0.543	6.241
calc_mean_sd_duke	2.552	0.197	2.243
find_peak	0.002	0.000	0.002
fit_beads	271.095	8.345	279.060
fit_led	10.809	1.939	11.900
fitted_ellipse_gate	0.695	0.146	0.837
get_results_for_dyes	1.869	0.237	1.922
peak_gate-methods	0.594	0.130	0.720
pick_parameters-methods	0.561	0.129	0.685
qb_from_fits	9.876	1.942	11.773
split_in_two-methods	0.659	0.135	0.793