Package: sevenbridges

Version: 1.10.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.10.5.tar.gz

StartedAt: 2018-10-17 00:02:14 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:05:42 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 207.7 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.10.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/sevenbridges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.10.5’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Flow        67.641  0.204  68.453
Tool-class  16.863  0.056  17.045
link_what   10.379  0.021  10.474
link         8.092  0.015   8.147
convert_app  7.211  0.016   7.318
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sevenbridges
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘sevenbridges’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sevenbridges)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.483   0.235   3.727 

name	user	system	elapsed
App-class	0.002	0.000	0.002
Auth-class	0.008	0.000	0.009
Binding	0.065	0.001	0.067
CCBList	0.020	0.000	0.021
CWL	0.003	0.000	0.004
CommandInputParameter-class	0.091	0.001	0.094
CommandInputSchema-class	0.026	0.000	0.027
CommandLineBinding-class	0.011	0.000	0.011
CommandLineTool	0.026	0.000	0.027
CommandOutputBinding-class	0.013	0.001	0.013
CommandOutputParameter-class	0.015	0.000	0.015
CommandOutputSchema-class	0.178	0.001	0.181
DSCList	0.019	0.000	0.020
Enum	0.032	0.000	0.035
Expression-class	0.012	0.000	0.012
ExpressionTool-class	0.028	0.000	0.028
File-class	0.088	0.005	0.097
Files-class	0.011	0.000	0.011
Flow	67.641	0.204	68.453
Folders-class	0.008	0.000	0.008
Metadata	0.108	0.002	0.109
Parameter	0.049	0.001	0.049
Process	0.070	0.001	0.071
ProcessRequirement	0.063	0.000	0.064
Schema	0.023	0.000	0.023
TaskHook	0.004	0.000	0.004
Tool-class	16.863	0.056	17.045
ToolUI	0.001	0.000	0.001
Workflow	0.041	0.000	0.042
WorkflowStep	0.006	0.000	0.005
addIdNum	0.001	0.000	0.001
api	0.001	0.000	0.001
as-methods	0.087	0.001	0.087
batch	0.002	0.001	0.001
cli_list_projects	0.001	0.000	0.001
cli_list_tags	0.001	0.000	0.001
cli_upload	0.001	0.000	0.002
convert_app	7.211	0.016	7.318
cwl-utils	0.145	0.002	0.148
delete-methods	0.001	0.000	0.001
download-methods	0.001	0.000	0.001
get_token	0.001	0.000	0.001
get_uploader	0.001	0.000	0.001
input_output_matrix	0.132	0.003	0.135
link	8.092	0.015	8.147
link_what	10.379	0.021	10.474
project_details	0.001	0.000	0.001
project_members	0.001	0.000	0.002
requirements	0.052	0.001	0.053
response-methods	0.001	0.000	0.002
sbg_get_env	0.002	0.000	0.002
sbg_set_env	0.002	0.000	0.002
set_test_env	0.001	0.000	0.002
shorthand-cwl	0.039	0.000	0.039
tag-methods	0.002	0.001	0.002
test_tool_bunny	0.002	0.000	0.002
test_tool_cwlrun	0.002	0.001	0.002
test_tool_rabix	0.001	0.000	0.002
upload_complete_all	0.002	0.000	0.002
upload_complete_part	0.002	0.000	0.002
upload_delete	0.002	0.000	0.002
upload_info	0.001	0.000	0.001
upload_info_part	0.002	0.000	0.001
upload_init	0.002	0.000	0.002