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CHECK report for flowQB on malbec1

This page was generated on 2018-04-12 13:10:21 -0400 (Thu, 12 Apr 2018).

Package 490/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowQB 2.6.0
Josef Spidlen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/flowQB
Branch: RELEASE_3_6
Last Commit: 9ea8789
Last Changed Date: 2017-10-30 12:39:42 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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


Installation output

flowQB.Rcheck/00install.out

* 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)

Tests output

flowQB.Rcheck/tests/runTests.Rout


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 

Example timings

flowQB.Rcheck/flowQB-Ex.timings

nameusersystemelapsed
calc_mean_sd_1977.8560.3568.451
calc_mean_sd_background2.5160.0442.048
calc_mean_sd_capture0.3360.0120.369
calc_mean_sd_capture_all5.0800.1805.288
calc_mean_sd_duke2.3560.0762.085
find_peak0.0000.0000.001
fit_beads279.580 2.460282.232
fit_led12.444 0.40413.645
fitted_ellipse_gate0.4680.0201.551
get_results_for_dyes2.0560.0722.025
peak_gate-methods0.4920.0200.512
pick_parameters-methods0.2920.0160.308
qb_from_fits 9.872 0.25610.122
split_in_two-methods0.4120.0240.436