Package: flowQB

Version: 2.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowQB_2.6.0.tar.gz

StartedAt: 2018-04-11 23:31:38 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:43:06 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 687.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowQB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowQB_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/flowQB.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘2.6.0’
* 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 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 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                279.580  2.460 282.232
fit_led                   12.444  0.404  13.645
qb_from_fits               9.872  0.256  10.122
calc_mean_sd_197           7.856  0.356   8.451
calc_mean_sd_capture_all   5.080  0.180   5.288
* 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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")

Attaching package: 'flowCore'

The following object is masked from 'package:base':

    sort

Loading required package: rJava
Loading required package: xlsxjars


RUNIT TEST PROTOCOL -- Wed Apr 11 23:43:03 2018 
*********************************************** 
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 
294.292   3.616 296.157 

name	user	system	elapsed
calc_mean_sd_197	7.856	0.356	8.451
calc_mean_sd_background	2.516	0.044	2.048
calc_mean_sd_capture	0.336	0.012	0.369
calc_mean_sd_capture_all	5.080	0.180	5.288
calc_mean_sd_duke	2.356	0.076	2.085
find_peak	0.000	0.000	0.001
fit_beads	279.580	2.460	282.232
fit_led	12.444	0.404	13.645
fitted_ellipse_gate	0.468	0.020	1.551
get_results_for_dyes	2.056	0.072	2.025
peak_gate-methods	0.492	0.020	0.512
pick_parameters-methods	0.292	0.016	0.308
qb_from_fits	9.872	0.256	10.122
split_in_two-methods	0.412	0.024	0.436