BioC 3.5: CHECK report for sevenbridges on veracruz2

Package: sevenbridges

Version: 1.6.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.6.4.tar.gz

StartedAt: 2017-10-18 08:59:39 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:02:50 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 190.7 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 --no-vignettes --timings sevenbridges_1.6.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sevenbridges.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.4’
* 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 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        56.662  0.348  58.798
Tool-class  15.503  0.103  16.076
link_what    9.364  0.049   9.738
link         7.552  0.042   7.806
convert_app  6.344  0.034   6.537
* 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	0.008	0.000	0.009
Binding	0.045	0.005	0.052
CCBList	0.004	0.001	0.005
CWL	0.002	0.000	0.002
CommandInputParameter-class	0.045	0.002	0.049
CommandInputSchema-class	0.059	0.000	0.060
CommandLineBinding-class	0.007	0.000	0.007
CommandLineTool	0.022	0.001	0.023
CommandOutputBinding-class	0.007	0.000	0.008
CommandOutputParameter-class	0.013	0.001	0.013
CommandOutputSchema-class	0.028	0.000	0.028
DSCList	0.019	0.001	0.020
Enum	0.037	0.000	0.039
Expression-class	0.01	0.00	0.01
ExpressionTool-class	0.017	0.000	0.017
File-class	0.106	0.002	0.111
Files-class	0.008	0.000	0.008
Flow	56.662	0.348	58.798
Folders-class	0.046	0.001	0.051
Metadata	0.137	0.002	0.140
Parameter	0.037	0.000	0.042
Process	0.049	0.000	0.050
ProcessRequirement	0.059	0.001	0.060
Schema	0.018	0.001	0.018
TaskHook	0.002	0.000	0.003
Tool-class	15.503	0.103	16.076
ToolUI	0	0	0
Workflow	0.030	0.001	0.030
WorkflowStep	0.007	0.000	0.007
addIdNum	0	0	0
api	0.000	0.001	0.001
as-methods	0.116	0.001	0.119
batch	0.001	0.001	0.001
cli_list_projects	0.001	0.000	0.001
cli_list_tags	0.000	0.000	0.001
cli_upload	0	0	0
convert_app	6.344	0.034	6.537
cwl-utils	0.242	0.002	0.248
delete-methods	0.001	0.000	0.000
download-methods	0.001	0.000	0.001
get_token	0.000	0.000	0.001
get_uploader	0	0	0
input_output_matrix	0.257	0.004	0.272
link	7.552	0.042	7.806
link_what	9.364	0.049	9.738
project_details	0.001	0.000	0.001
project_members	0.001	0.000	0.001
requirements	0.052	0.001	0.056
response-methods	0	0	0
sbg_get_env	0.001	0.000	0.001
sbg_set_env	0.001	0.000	0.001
set_test_env	0	0	0
shorthand-cwl	0.025	0.000	0.025
tag-methods	0.001	0.000	0.001
test_tool_bunny	0.001	0.000	0.001
test_tool_cwlrun	0.000	0.000	0.001
test_tool_rabix	0.001	0.000	0.001
upload_complete_all	0.000	0.000	0.001
upload_complete_part	0.000	0.000	0.001
upload_delete	0.001	0.000	0.001
upload_info	0.001	0.000	0.001
upload_info_part	0.000	0.001	0.001
upload_init	0	0	0