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CHECK report for flowQB on tokay2

This page was generated on 2019-04-09 12:00:42 -0400 (Tue, 09 Apr 2019).

Package 567/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowQB 2.11.1
Josef Spidlen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flowQB
Branch: master
Last Commit: 5aea5b8
Last Changed Date: 2019-01-04 13:09:36 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: flowQB
Version: 2.11.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowQB_2.11.1.tar.gz
StartedAt: 2019-04-09 02:47:30 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:10:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1361.3 seconds
RetCode: 1
Status:  ERROR  
CheckDir: flowQB.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowQB_2.11.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
fit_beads                292.91  10.55  303.45
fit_led                   13.11   0.28   13.39
qb_from_fits              11.55   0.21   11.78
calc_mean_sd_197           5.00   0.39    5.51
calc_mean_sd_capture_all   4.64   0.06    6.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fit_beads        312.63  11.54  326.16
fit_led           10.70   0.38   10.81
qb_from_fits       9.87   0.19   10.08
calc_mean_sd_197   6.47   0.50    5.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowQB.Rcheck/00check.log'
for details.

Installation output

flowQB.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowQB_2.11.1.tar.gz && rm -rf flowQB.buildbin-libdir && mkdir flowQB.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowQB.buildbin-libdir flowQB_2.11.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowQB_2.11.1.zip && rm flowQB_2.11.1.tar.gz flowQB_2.11.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 54540  100 54540    0     0   147k      0 --:--:-- --:--:-- --:--:--  150k

install for i386

* installing *source* package 'flowQB' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowQB'
    finding HTML links ... done
    calc_mean_sd_197                        html  
    calc_mean_sd_background                 html  
    calc_mean_sd_capture                    html  
    calc_mean_sd_capture_all                html  
    calc_mean_sd_duke                       html  
    find_peak                               html  
    fit_beads                               html  
    fit_led                                 html  
    fitted_ellipse_gate                     html  
    get_results_for_dyes                    html  
    peak_gate-methods                       html  
    finding level-2 HTML links ... done

    pick_parameters-methods                 html  
    qb_from_fits                            html  
    split_in_two-methods                    html  
** 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

install for x64

* installing *source* package 'flowQB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowQB' as flowQB_2.11.1.zip
* DONE (flowQB)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flowQB' successfully unpacked and MD5 sums checked

Tests output

flowQB.Rcheck/tests_i386/runTests.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 187.2 5.8 194.4
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 09 03:04:31 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

flowQB.Rcheck/tests_x64/runTests.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 170.5 6.77 177.6
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 09 03:07:53 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

Example timings

flowQB.Rcheck/examples_i386/flowQB-Ex.timings

nameusersystemelapsed
calc_mean_sd_1975.000.395.51
calc_mean_sd_background2.060.102.85
calc_mean_sd_capture0.330.010.64
calc_mean_sd_capture_all4.640.066.26
calc_mean_sd_duke2.020.052.30
find_peak000
fit_beads292.91 10.55303.45
fit_led13.11 0.2813.39
fitted_ellipse_gate0.790.120.92
get_results_for_dyes1.820.071.85
peak_gate-methods0.890.060.95
pick_parameters-methods0.560.120.69
qb_from_fits11.55 0.2111.78
split_in_two-methods0.560.040.61

flowQB.Rcheck/examples_x64/flowQB-Ex.timings

nameusersystemelapsed
calc_mean_sd_1976.470.505.52
calc_mean_sd_background2.520.031.80
calc_mean_sd_capture0.290.000.28
calc_mean_sd_capture_all4.280.364.12
calc_mean_sd_duke1.590.031.41
find_peak000
fit_beads312.63 11.54326.16
fit_led10.70 0.3810.81
fitted_ellipse_gate0.560.010.58
get_results_for_dyes1.740.101.51
peak_gate-methods0.700.080.78
pick_parameters-methods0.700.070.78
qb_from_fits 9.87 0.1910.08
split_in_two-methods0.460.030.48