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CHECK report for flowQB on tokay2

This page was generated on 2018-10-17 08:36:19 -0400 (Wed, 17 Oct 2018).

Package 515/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowQB 2.8.0
Josef Spidlen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowQB
Branch: RELEASE_3_7
Last Commit: 9b248f1
Last Changed Date: 2018-04-30 10:35:25 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowQB
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowQB_2.8.0.tar.gz
StartedAt: 2018-10-17 02:02:20 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:27:21 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1500.4 seconds
RetCode: 0
Status:  OK  
CheckDir: flowQB.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowQB_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowQB.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.8.0'
* 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 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                321.43  11.76  333.16
qb_from_fits              13.38   0.22   13.64
fit_led                   12.31   0.63   12.92
calc_mean_sd_197           5.46   0.51    6.45
calc_mean_sd_capture_all   4.78   0.27   10.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
fit_beads                330.15  13.05  344.99
fit_led                   12.94   0.58   13.29
qb_from_fits              11.81   0.33   12.14
calc_mean_sd_197           6.10   0.55    5.25
calc_mean_sd_capture_all   4.85   0.36    4.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowQB_2.8.0.tar.gz && rm -rf flowQB.buildbin-libdir && mkdir flowQB.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowQB.buildbin-libdir flowQB_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowQB_2.8.0.zip && rm flowQB_2.8.0.tar.gz flowQB_2.8.0.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 54491  100 54491    0     0   923k      0 --:--:-- --:--:-- --:--:-- 1064k

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
In R CMD INSTALL

install for x64

* installing *source* package 'flowQB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowQB' as flowQB_2.8.0.zip
* DONE (flowQB)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowQB' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

flowQB.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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")


RUNIT TEST PROTOCOL -- Wed Oct 17 02:22:24 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 
 326.53   13.07  349.73

flowQB.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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")


RUNIT TEST PROTOCOL -- Wed Oct 17 02:26:39 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 
 219.07   10.70  240.89

Example timings

flowQB.Rcheck/examples_i386/flowQB-Ex.timings

nameusersystemelapsed
calc_mean_sd_1975.460.516.45
calc_mean_sd_background1.870.112.37
calc_mean_sd_capture0.460.050.84
calc_mean_sd_capture_all 4.78 0.2710.08
calc_mean_sd_duke2.040.032.55
find_peak000
fit_beads321.43 11.76333.16
fit_led12.31 0.6312.92
fitted_ellipse_gate0.650.010.67
get_results_for_dyes1.480.031.50
peak_gate-methods0.630.020.65
pick_parameters-methods0.450.030.48
qb_from_fits13.38 0.2213.64
split_in_two-methods0.510.080.59

flowQB.Rcheck/examples_x64/flowQB-Ex.timings

nameusersystemelapsed
calc_mean_sd_1976.100.555.25
calc_mean_sd_background2.910.132.40
calc_mean_sd_capture0.360.040.40
calc_mean_sd_capture_all4.850.364.81
calc_mean_sd_duke1.760.051.60
find_peak0.020.000.01
fit_beads330.15 13.05344.99
fit_led12.94 0.5813.29
fitted_ellipse_gate0.800.150.96
get_results_for_dyes1.790.131.67
peak_gate-methods0.790.130.91
pick_parameters-methods0.640.110.75
qb_from_fits11.81 0.3312.14
split_in_two-methods0.730.060.79