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CHECK report for sevenbridges on tokay1

This page was generated on 2020-04-15 12:25:24 -0400 (Wed, 15 Apr 2020).

Package 1574/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.16.1
Nan Xiao
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/sevenbridges
Branch: RELEASE_3_10
Last Commit: fe93e09
Last Changed Date: 2020-03-26 16:04:53 -0400 (Thu, 26 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sevenbridges
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sevenbridges.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sevenbridges_1.16.1.tar.gz
StartedAt: 2020-04-15 06:34:18 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:40:52 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 393.7 seconds
RetCode: 0
Status:  OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sevenbridges.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sevenbridges_1.16.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/sevenbridges.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sevenbridges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sevenbridges' version '1.16.1'
* package encoding: UTF-8
* 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 'sevenbridges' 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
Flow        40.27   0.06   40.36
Tool-class  12.97   0.00   25.63
link_what   10.63   0.00   10.63
link         9.57   0.00    9.58
convert_app  6.13   0.01    6.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
Flow        62.86   0.03   62.92
Tool-class  15.93   0.02   15.95
link         8.53   0.00    8.54
link_what    8.19   0.00    8.18
convert_app  5.87   0.00    5.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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

sevenbridges.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sevenbridges_1.16.1.tar.gz && rm -rf sevenbridges.buildbin-libdir && mkdir sevenbridges.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sevenbridges.buildbin-libdir sevenbridges_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sevenbridges_1.16.1.zip && rm sevenbridges_1.16.1.tar.gz sevenbridges_1.16.1.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 1034k  100 1034k    0     0  19.2M      0 --:--:-- --:--:-- --:--:-- 20.6M

install for i386

* installing *source* package 'sevenbridges' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sevenbridges'
    finding HTML links ... done
    App-class                               html  
    Auth-class                              html  
    Binding                                 html  
    CCBList                                 html  
    CWL                                     html  
    CommandInputParameter-class             html  
    CommandInputSchema-class                html  
    CommandLineBinding-class                html  
    CommandLineTool                         html  
    CommandOutputBinding-class              html  
    CommandOutputParameter-class            html  
    CommandOutputSchema-class               html  
    DSCList                                 html  
    Enum                                    html  
    Expression-class                        html  
    ExpressionTool-class                    html  
    FS-class                                html  
    File-class                              html  
    Files-class                             html  
    Flow                                    html  
    Handler-class                           html  
    Item-class                              html  
    Metadata                                html  
    Parameter                               html  
    Process                                 html  
    ProcessRequirement                      html  
    Schema                                  html  
    TaskHook                                html  
    Tool-class                              html  
    Workflow                                html  
    WorkflowStep                            html  
    addIdNum                                html  
    api                                     html  
    as-methods                              html  
    batch                                   html  
    cli_list_projects                       html  
    cli_list_tags                           html  
    cli_upload                              html  
    convert_app                             html  
    cwl-utils                               html  
    delete-methods                          html  
    download-methods                        html  
    get_token                               html  
    get_uploader                            html  
    input_output_matrix                     html  
    link                                    html  
    link_what                               html  
    project_details                         html  
    project_members                         html  
    requirements                            html  
    response-methods                        html  
    sbg_get_env                             html  
    sbg_set_env                             html  
    setListClass                            html  
    set_test_env                            html  
    sevenbridges-package                    html  
    shorthand-cwl                           html  
    status_check                            html  
    tag-methods                             html  
    test_tool_bunny                         html  
    test_tool_cwlrun                        html  
    test_tool_rabix                         html  
    upload_complete_all                     html  
    upload_complete_part                    html  
    upload_delete                           html  
    upload_info                             html  
    upload_info_part                        html  
    upload_init                             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 'sevenbridges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sevenbridges' as sevenbridges_1.16.1.zip
* DONE (sevenbridges)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'sevenbridges' successfully unpacked and MD5 sums checked

Tests output

sevenbridges.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library("testthat")
> library("sevenbridges")
> test_check("sevenbridges")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.12    0.25    3.36 

sevenbridges.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library("testthat")
> library("sevenbridges")
> test_check("sevenbridges")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.14    0.18    3.32 

Example timings

sevenbridges.Rcheck/examples_i386/sevenbridges-Ex.timings

nameusersystemelapsed
App-class000
Auth-class000
Binding0.030.000.03
CCBList0.020.000.01
CWL000
CommandInputParameter-class0.010.000.02
CommandInputSchema-class0.020.000.01
CommandLineBinding-class0.010.000.02
CommandLineTool0.020.000.01
CommandOutputBinding-class000
CommandOutputParameter-class0.010.000.02
CommandOutputSchema-class0.020.000.02
DSCList0.020.000.01
Enum0.010.000.02
Expression-class0.020.000.01
ExpressionTool-class0.010.000.02
File-class0.070.000.06
Files-class0.010.000.02
Flow40.27 0.0640.36
Metadata0.040.000.04
Parameter0.030.000.03
Process0.040.000.04
ProcessRequirement0.030.000.03
Schema0.010.000.01
TaskHook000
Tool-class12.97 0.0025.63
Workflow0.050.000.04
WorkflowStep0.010.000.02
addIdNum000
api000
as-methods0.110.000.11
batch000
cli_list_projects000
cli_list_tags000
cli_upload000
convert_app6.130.016.14
cwl-utils0.140.020.17
delete-methods000
download-methods000
get_token000
get_uploader000
input_output_matrix0.160.020.17
link9.570.009.58
link_what10.63 0.0010.63
project_details000
project_members0.010.000.01
requirements0.070.000.06
response-methods000
sbg_get_env000
sbg_set_env000
set_test_env000
shorthand-cwl0.040.000.05
tag-methods000
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part000
upload_delete000
upload_info000
upload_info_part000
upload_init000

sevenbridges.Rcheck/examples_x64/sevenbridges-Ex.timings

nameusersystemelapsed
App-class000
Auth-class0.010.000.01
Binding0.050.000.05
CCBList0.020.000.02
CWL000
CommandInputParameter-class0.010.000.01
CommandInputSchema-class0.020.000.02
CommandLineBinding-class0.010.000.01
CommandLineTool0.020.000.02
CommandOutputBinding-class000
CommandOutputParameter-class0.010.000.01
CommandOutputSchema-class0.020.000.02
DSCList0.020.000.01
Enum0.010.000.02
Expression-class000
ExpressionTool-class0.010.000.01
File-class0.080.000.08
Files-class000
Flow62.86 0.0362.92
Metadata0.070.000.08
Parameter0.040.000.03
Process0.060.000.06
ProcessRequirement0.080.000.08
Schema0.030.000.03
TaskHook000
Tool-class15.93 0.0215.95
Workflow0.040.000.03
WorkflowStep0.010.000.02
addIdNum000
api000
as-methods0.080.000.08
batch000
cli_list_projects0.020.000.01
cli_list_tags000
cli_upload000
convert_app5.870.005.88
cwl-utils0.080.000.08
delete-methods000
download-methods000
get_token000
get_uploader000
input_output_matrix0.100.000.09
link8.530.008.54
link_what8.190.008.18
project_details000
project_members000
requirements0.060.000.07
response-methods000
sbg_get_env000
sbg_set_env000
set_test_env000
shorthand-cwl0.010.000.01
tag-methods000
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part000
upload_delete000
upload_info000
upload_info_part000
upload_init000