BioC 3.4: CHECK report for sevenbridges on morelia

Package: sevenbridges

Version: 1.4.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.4.9.tar.gz

StartedAt: 2017-04-15 08:02:16 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:06:14 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 238.1 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_1.4.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/sevenbridges.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.9’
* 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        75.386  0.162  75.625
Tool-class  19.453  0.038  19.509
link_what   12.048  0.018  12.078
link         9.681  0.012   9.702
convert_app  8.068  0.017   8.092
* 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	0.000	0.000	0.001
Auth-class	0.009	0.001	0.010
Binding	0.017	0.000	0.017
CCBList	0.009	0.000	0.008
CWL	0.001	0.000	0.002
CommandInputParameter-class	0.038	0.000	0.039
CommandInputSchema-class	0.027	0.000	0.028
CommandLineBinding-class	0.010	0.000	0.011
CommandLineTool	0.123	0.000	0.122
CommandOutputBinding-class	0.012	0.000	0.012
CommandOutputParameter-class	0.022	0.000	0.023
CommandOutputSchema-class	0.014	0.000	0.014
DSCList	0.025	0.000	0.026
Enum	0.024	0.002	0.027
Expression-class	0.011	0.001	0.013
ExpressionTool-class	0.019	0.002	0.021
File-class	0.088	0.003	0.092
Files-class	0.008	0.000	0.008
Flow	75.386	0.162	75.625
Folders-class	0.008	0.000	0.007
Metadata	0.115	0.001	0.115
Parameter	0.052	0.001	0.053
Process	0.082	0.000	0.083
ProcessRequirement	0.080	0.000	0.081
Schema	0.022	0.000	0.022
TaskHook	0.003	0.000	0.003
Tool-class	19.453	0.038	19.509
ToolUI	0.001	0.000	0.000
Workflow	0.048	0.001	0.048
WorkflowStep	0.01	0.00	0.01
addIdNum	0.001	0.000	0.001
api	0.001	0.000	0.001
as-methods	0.106	0.001	0.107
batch	0.001	0.000	0.001
cli_list_projects	0.000	0.000	0.001
cli_list_tags	0.001	0.000	0.000
cli_upload	0.001	0.000	0.000
convert_app	8.068	0.017	8.092
cwl-utils	0.090	0.001	0.091
delete-methods	0.000	0.000	0.001
download-methods	0	0	0
get_token	0	0	0
get_uploader	0.000	0.000	0.001
input_output_matrix	0.113	0.002	0.115
link	9.681	0.012	9.702
link_what	12.048	0.018	12.078
project_details	0.001	0.000	0.001
project_members	0.001	0.000	0.000
requirements	0.105	0.001	0.106
response-methods	0.000	0.000	0.001
sbg_get_env	0.001	0.000	0.001
sbg_set_env	0.001	0.001	0.001
set_test_env	0.001	0.000	0.000
shorthand-cwl	0.035	0.000	0.035
tag-methods	0.001	0.000	0.001
test_tool_bunny	0.001	0.000	0.000
test_tool_cwlrun	0.001	0.000	0.001
test_tool_rabix	0.001	0.001	0.001
upload_complete_all	0.001	0.000	0.001
upload_complete_part	0.001	0.000	0.000
upload_delete	0	0	0
upload_info	0.001	0.001	0.001
upload_info_part	0	0	0
upload_init	0.001	0.000	0.000