BioC 3.5: CHECK report for sevenbridges on toluca2

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: 2017-04-23 09:50:21 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:53:59 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 217.5 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 r72187)
* 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        67.087  0.191  67.705
Tool-class  16.977  0.049  17.207
link_what   10.675  0.019  10.760
link         8.779  0.017   8.913
convert_app  7.374  0.018   7.726
* 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	0.011	0.000	0.011
Binding	0.062	0.006	0.069
CCBList	0.006	0.000	0.007
CWL	0.002	0.000	0.002
CommandInputParameter-class	0.055	0.002	0.057
CommandInputSchema-class	0.072	0.000	0.072
CommandLineBinding-class	0.011	0.000	0.012
CommandLineTool	0.019	0.000	0.020
CommandOutputBinding-class	0.01	0.00	0.01
CommandOutputParameter-class	0.017	0.001	0.018
CommandOutputSchema-class	0.04	0.00	0.04
DSCList	0.021	0.001	0.022
Enum	0.040	0.000	0.042
Expression-class	0.009	0.001	0.010
ExpressionTool-class	0.022	0.000	0.022
File-class	0.117	0.002	0.120
Files-class	0.01	0.00	0.01
Flow	67.087	0.191	67.705
Folders-class	0.059	0.003	0.062
Metadata	0.186	0.002	0.188
Parameter	0.044	0.002	0.045
Process	0.066	0.000	0.068
ProcessRequirement	0.062	0.000	0.063
Schema	0.028	0.001	0.028
TaskHook	0.003	0.000	0.003
Tool-class	16.977	0.049	17.207
ToolUI	0.001	0.000	0.001
Workflow	0.03	0.00	0.03
WorkflowStep	0.007	0.000	0.007
addIdNum	0.001	0.000	0.001
api	0.001	0.000	0.001
as-methods	0.115	0.001	0.116
batch	0.002	0.000	0.001
cli_list_projects	0	0	0
cli_list_tags	0.001	0.000	0.001
cli_upload	0.001	0.000	0.001
convert_app	7.374	0.018	7.726
cwl-utils	0.284	0.002	0.301
delete-methods	0.000	0.000	0.001
download-methods	0.000	0.000	0.001
get_token	0.001	0.000	0.000
get_uploader	0	0	0
input_output_matrix	0.278	0.003	0.294
link	8.779	0.017	8.913
link_what	10.675	0.019	10.760
project_details	0.001	0.000	0.000
project_members	0.001	0.000	0.000
requirements	0.076	0.001	0.077
response-methods	0	0	0
sbg_get_env	0.000	0.000	0.001
sbg_set_env	0.000	0.001	0.001
set_test_env	0.000	0.000	0.001
shorthand-cwl	0.027	0.000	0.027
tag-methods	0.000	0.000	0.001
test_tool_bunny	0.001	0.000	0.001
test_tool_cwlrun	0.001	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	0	0
upload_init	0.001	0.000	0.000