Package: flowQB

Version: 2.10.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowQB_2.10.1.tar.gz

StartedAt: 2019-04-13 02:18:03 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:41:20 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 1397.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowQB.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowQB.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowQB_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowQB.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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                267.20  10.34  277.53
fit_led                   10.22   0.33   10.53
qb_from_fits               9.65   0.05    9.72
calc_mean_sd_197           3.97   0.22    5.36
calc_mean_sd_capture_all   3.26   0.20    8.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
fit_beads                278.00  10.94  288.77
qb_from_fits              11.99   0.26   12.28
fit_led                   11.14   0.34   11.27
calc_mean_sd_197           6.71   0.52    5.89
calc_mean_sd_capture_all   5.76   0.44    5.81
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowQB_2.10.1.tar.gz && rm -rf flowQB.buildbin-libdir && mkdir flowQB.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowQB.buildbin-libdir flowQB_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowQB_2.10.1.zip && rm flowQB_2.10.1.tar.gz flowQB_2.10.1.zip
###
##############################################################################
##############################################################################


  % 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 55578  100 55578    0     0   705k      0 --:--:-- --:--:-- --:--:--  743k

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_2.10.1.zip
* DONE (flowQB)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowQB' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
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")


RUNIT TEST PROTOCOL -- Sat Apr 13 02:36:52 2019 
*********************************************** 
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 
 332.10   11.34  346.25 

R version 3.5.3 (2019-03-11) -- "Great Truth"
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")


RUNIT TEST PROTOCOL -- Sat Apr 13 02:41:05 2019 
*********************************************** 
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 
 241.81   12.40  252.07