Package: flowQB

Version: 2.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowQB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowQB_2.10.1.tar.gz

StartedAt: 2019-04-15 23:59:15 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:12:47 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 812.0 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 --install=check:flowQB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowQB_2.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowQB.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.10.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
fit_beads                324.580 12.656 339.375
fit_led                   13.860  2.338  15.972
qb_from_fits              11.953  2.053  14.021
calc_mean_sd_197           7.864  0.860   6.822
calc_mean_sd_capture_all   5.856  0.702   6.144
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowQB
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowQB’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowQB)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("flowQB")


RUNIT TEST PROTOCOL -- Tue Apr 16 00:12:42 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
flowQB RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: Quick-TRANSfer stage steps exceeded maximum (= 3762700) 
2: Quick-TRANSfer stage steps exceeded maximum (= 3762700) 
3: Quick-TRANSfer stage steps exceeded maximum (= 3762700) 
4: Quick-TRANSfer stage steps exceeded maximum (= 3762700) 
5: Quick-TRANSfer stage steps exceeded maximum (= 3709000) 
> 
> proc.time()
   user  system elapsed 
324.487  17.001 339.919 

name	user	system	elapsed
calc_mean_sd_197	7.864	0.860	6.822
calc_mean_sd_background	3.166	0.371	2.538
calc_mean_sd_capture	0.329	0.059	0.389
calc_mean_sd_capture_all	5.856	0.702	6.144
calc_mean_sd_duke	2.573	0.273	2.369
find_peak	0.001	0.000	0.001
fit_beads	324.580	12.656	339.375
fit_led	13.860	2.338	15.972
fitted_ellipse_gate	0.710	0.214	0.923
get_results_for_dyes	2.193	0.318	2.281
peak_gate-methods	0.706	0.208	0.909
pick_parameters-methods	0.485	0.140	0.627
qb_from_fits	11.953	2.053	14.021
split_in_two-methods	0.494	0.127	0.629