BioC 3.5: CHECK report for sevenbridges on oaxaca

Package: sevenbridges

Version: 1.5.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.5.9.tar.gz

StartedAt: 2017-03-04 09:01:52 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:05:15 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 203.4 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_1.5.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sevenbridges.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.9’
* 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        58.759  0.151  58.935
Tool-class  16.772  0.041  16.820
link_what    9.475  0.014   9.493
link         7.789  0.007   7.796
convert_app  6.872  0.012   6.886
* 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	0.001	0.001
Auth-class	0.01	0.00	0.01
Binding	0.042	0.005	0.107
CCBList	0.006	0.000	0.006
CWL	0.002	0.000	0.002
CommandInputParameter-class	0.055	0.000	0.055
CommandInputSchema-class	0.056	0.001	0.056
CommandLineBinding-class	0.007	0.000	0.007
CommandLineTool	0.018	0.001	0.019
CommandOutputBinding-class	0.009	0.000	0.009
CommandOutputParameter-class	0.015	0.000	0.016
CommandOutputSchema-class	0.029	0.001	0.029
DSCList	0.019	0.000	0.020
Enum	0.045	0.001	0.045
Expression-class	0.009	0.000	0.009
ExpressionTool-class	0.022	0.000	0.023
File-class	0.103	0.001	0.140
Files-class	0.010	0.000	0.011
Flow	58.759	0.151	58.935
Folders-class	0.053	0.000	0.052
Metadata	0.203	0.004	0.207
Parameter	0.046	0.000	0.047
Process	0.075	0.002	0.078
ProcessRequirement	0.067	0.000	0.068
Schema	0.023	0.001	0.023
TaskHook	0.002	0.000	0.002
Tool-class	16.772	0.041	16.820
ToolUI	0	0	0
Workflow	0.023	0.000	0.023
WorkflowStep	0.006	0.000	0.005
addIdNum	0.000	0.000	0.001
api	0	0	0
as-methods	0.129	0.001	0.131
batch	0.001	0.001	0.002
cli_list_projects	0.001	0.000	0.001
cli_list_tags	0.001	0.000	0.001
cli_upload	0.000	0.000	0.001
convert_app	6.872	0.012	6.886
cwl-utils	0.259	0.001	0.260
delete-methods	0.001	0.000	0.000
download-methods	0.000	0.000	0.001
get_token	0	0	0
get_uploader	0.001	0.000	0.000
input_output_matrix	0.259	0.003	0.261
link	7.789	0.007	7.796
link_what	9.475	0.014	9.493
project_details	0.001	0.000	0.001
project_members	0.001	0.000	0.001
requirements	0.055	0.000	0.055
response-methods	0.000	0.000	0.001
sbg_get_env	0.001	0.000	0.000
sbg_set_env	0.001	0.000	0.001
set_test_env	0.001	0.000	0.001
shorthand-cwl	0.036	0.000	0.036
tag-methods	0.001	0.000	0.001
test_tool_bunny	0.001	0.000	0.001
test_tool_cwlrun	0	0	0
test_tool_rabix	0.000	0.000	0.001
upload_complete_all	0.000	0.000	0.001
upload_complete_part	0	0	0
upload_delete	0.000	0.000	0.001
upload_info	0.000	0.000	0.001
upload_info_part	0.000	0.000	0.001
upload_init	0	0	0