Package: flowQB

Version: 2.11.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowQB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowQB_2.11.1.tar.gz

StartedAt: 2019-04-09 00:33:04 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:43:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 640.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: flowQB.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowQB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowQB_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.11.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
fit_beads        316.052  3.079 319.042
fit_led           11.800  0.590  12.100
qb_from_fits      10.501  0.449  10.873
calc_mean_sd_197   6.919  0.518   6.169
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowQB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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")
Timing stopped at: 183.9 1.708 185.4
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 00:43:41 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	6.919	0.518	6.169
calc_mean_sd_background	2.599	0.108	2.079
calc_mean_sd_capture	0.271	0.032	0.319
calc_mean_sd_capture_all	4.586	0.241	4.501
calc_mean_sd_duke	2.348	0.162	2.156
find_peak	0.001	0.000	0.002
fit_beads	316.052	3.079	319.042
fit_led	11.80	0.59	12.10
fitted_ellipse_gate	0.685	0.052	0.736
get_results_for_dyes	1.768	0.109	1.655
peak_gate-methods	0.564	0.048	0.614
pick_parameters-methods	0.401	0.020	0.422
qb_from_fits	10.501	0.449	10.873
split_in_two-methods	0.346	0.009	0.353