BioC 3.4: CHECK report for flowQB on morelia

Package: flowQB

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQB_2.2.0.tar.gz

StartedAt: 2017-04-15 02:13:03 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:26:26 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 802.9 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_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowQB.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.2.0’
* 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                296.130 11.231 307.189
fit_led                   16.328  2.440  19.190
qb_from_fits              13.740  2.245  15.927
calc_mean_sd_197          10.260  1.425  14.964
calc_mean_sd_capture_all   9.724  1.231  11.169
calc_mean_sd_duke          4.525  0.563   4.579
* 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	10.260	1.425	14.964
calc_mean_sd_background	2.942	0.256	2.451
calc_mean_sd_capture	0.558	0.094	0.663
calc_mean_sd_capture_all	9.724	1.231	11.169
calc_mean_sd_duke	4.525	0.563	4.579
find_peak	0.004	0.001	0.006
fit_beads	296.130	11.231	307.189
fit_led	16.328	2.440	19.190
fitted_ellipse_gate	1.480	0.344	1.804
get_results_for_dyes	4.386	0.597	4.655
peak_gate-methods	1.906	0.411	2.287
pick_parameters-methods	0.621	0.132	0.753
qb_from_fits	13.740	2.245	15.927
split_in_two-methods	0.892	0.203	1.086