BioC 3.6: CHECK report for sevenbridges on veracruz1

Package: sevenbridges

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.7.0.tar.gz

StartedAt: 2017-08-16 08:28:02 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:31:08 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 185.8 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/sevenbridges.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Flow        51.928  0.133  53.764
Tool-class  13.724  0.059  14.177
link_what    7.977  0.019   8.229
link         7.139  0.011   7.351
convert_app  5.462  0.008   5.630
* 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

* installing *source* package ‘sevenbridges’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sevenbridges)

name	user	system	elapsed
App-class	0.001	0.000	0.001
Auth-class	0.009	0.000	0.019
Binding	0.050	0.005	0.057
CCBList	0.005	0.000	0.005
CWL	0.002	0.001	0.002
CommandInputParameter-class	0.045	0.003	0.050
CommandInputSchema-class	0.057	0.000	0.057
CommandLineBinding-class	0.008	0.000	0.008
CommandLineTool	0.021	0.000	0.021
CommandOutputBinding-class	0.009	0.000	0.009
CommandOutputParameter-class	0.017	0.000	0.019
CommandOutputSchema-class	0.025	0.000	0.026
DSCList	0.018	0.000	0.019
Enum	0.037	0.000	0.041
Expression-class	0.008	0.000	0.009
ExpressionTool-class	0.019	0.000	0.018
File-class	0.080	0.001	0.086
Files-class	0.008	0.000	0.008
Flow	51.928	0.133	53.764
Folders-class	0.052	0.001	0.053
Metadata	0.146	0.001	0.151
Parameter	0.03	0.00	0.03
Process	0.056	0.000	0.059
ProcessRequirement	0.052	0.001	0.053
Schema	0.013	0.000	0.013
TaskHook	0.002	0.000	0.002
Tool-class	13.724	0.059	14.177
ToolUI	0.000	0.001	0.000
Workflow	0.028	0.000	0.029
WorkflowStep	0.006	0.000	0.007
addIdNum	0.001	0.001	0.001
api	0.001	0.000	0.001
as-methods	0.116	0.001	0.119
batch	0.001	0.000	0.001
cli_list_projects	0	0	0
cli_list_tags	0.000	0.000	0.001
cli_upload	0.001	0.000	0.001
convert_app	5.462	0.008	5.630
cwl-utils	0.190	0.001	0.191
delete-methods	0.001	0.000	0.000
download-methods	0.001	0.000	0.000
get_token	0.000	0.001	0.000
get_uploader	0	0	0
input_output_matrix	0.217	0.002	0.228
link	7.139	0.011	7.351
link_what	7.977	0.019	8.229
project_details	0	0	0
project_members	0.001	0.000	0.000
requirements	0.049	0.000	0.049
response-methods	0.001	0.000	0.000
sbg_get_env	0.001	0.000	0.000
sbg_set_env	0.000	0.000	0.001
set_test_env	0.000	0.000	0.001
shorthand-cwl	0.02	0.00	0.02
tag-methods	0.001	0.000	0.001
test_tool_bunny	0.001	0.000	0.000
test_tool_cwlrun	0	0	0
test_tool_rabix	0.001	0.000	0.000
upload_complete_all	0.001	0.000	0.000
upload_complete_part	0.001	0.000	0.000
upload_delete	0	0	0
upload_info	0	0	0
upload_info_part	0	0	0
upload_init	0.000	0.000	0.001