Package: flowQB

Version: 2.11.1

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_2.11.1.tar.gz

StartedAt: 2019-04-09 01:59:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:12:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 772.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: flowQB.Rcheck

Warnings: NA

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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_2.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.11.1’
* 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                327.380 22.172 348.471
fit_led                   16.534  5.516  21.581
qb_from_fits              15.820  5.421  21.119
calc_mean_sd_197           9.568  2.516   9.448
calc_mean_sd_capture_all   6.699  2.128   8.083
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  flowQB RUnit Tests - 19 test functions, 0 errors, 1 failure
  FAILURE in test_fit_beads: Error in checkTrue(apply(cbind(sum(beads_results$peak_clusters$cluster,  : 
    Test not TRUE
  
  
  Test files with failing tests
  
     test_fit_beads.R 
       test_fit_beads 
  
  
  Error in BiocGenerics:::testPackage("flowQB") : 
    unit tests failed for package flowQB
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck/00check.log’
for details.

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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/3.6/Resources/library’
* installing *source* package ‘flowQB’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowQB)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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")
Timing stopped at: 180.7 7.938 188.3
Error in checkTrue(apply(cbind(sum(beads_results$peak_clusters$cluster,  : 
  Test not TRUE

In addition: Warning message:
Quick-TRANSfer stage steps exceeded maximum (= 3762700) 


RUNIT TEST PROTOCOL -- Tue Apr  9 02:11:57 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
flowQB RUnit Tests - 19 test functions, 0 errors, 1 failure
FAILURE in test_fit_beads: Error in checkTrue(apply(cbind(sum(beads_results$peak_clusters$cluster,  : 
  Test not TRUE


Test files with failing tests

   test_fit_beads.R 
     test_fit_beads 


Error in BiocGenerics:::testPackage("flowQB") : 
  unit tests failed for package flowQB
Execution halted

name	user	system	elapsed
calc_mean_sd_197	9.568	2.516	9.448
calc_mean_sd_background	3.865	1.035	3.601
calc_mean_sd_capture	0.381	0.137	0.517
calc_mean_sd_capture_all	6.699	2.128	8.083
calc_mean_sd_duke	3.471	1.036	3.685
find_peak	0.002	0.000	0.002
fit_beads	327.380	22.172	348.471
fit_led	16.534	5.516	21.581
fitted_ellipse_gate	1.028	0.507	1.532
get_results_for_dyes	2.941	1.005	3.562
peak_gate-methods	0.922	0.438	1.356
pick_parameters-methods	0.760	0.423	1.180
qb_from_fits	15.820	5.421	21.119
split_in_two-methods	0.706	0.311	1.015