BioC 3.6: CHECK report for sevenbridges on malbec1

Package: sevenbridges

Version: 1.7.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.7.0.tar.gz

StartedAt: 2017-08-16 02:23:23 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:25:50 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 146.9 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/sevenbridges.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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       42.712  0.028  42.762
Tool-class 11.404  0.012  11.423
link_what   6.804  0.000   6.808
link        5.648  0.000   5.650
* 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	0	0
Auth-class	0.004	0.004	0.007
Binding	0.032	0.000	0.035
CCBList	0.004	0.000	0.004
CWL	0.000	0.000	0.001
CommandInputParameter-class	0.036	0.000	0.033
CommandInputSchema-class	0.044	0.000	0.043
CommandLineBinding-class	0.004	0.000	0.006
CommandLineTool	0.016	0.000	0.016
CommandOutputBinding-class	0.008	0.000	0.006
CommandOutputParameter-class	0.012	0.000	0.010
CommandOutputSchema-class	0.024	0.000	0.023
DSCList	0.016	0.000	0.014
Enum	0.024	0.000	0.027
Expression-class	0.004	0.000	0.006
ExpressionTool-class	0.016	0.000	0.013
File-class	0.076	0.000	0.090
Files-class	0.004	0.000	0.007
Flow	42.712	0.028	42.762
Folders-class	0.032	0.000	0.033
Metadata	0.108	0.000	0.109
Parameter	0.024	0.004	0.026
Process	0.036	0.000	0.036
ProcessRequirement	0.040	0.000	0.041
Schema	0.012	0.000	0.013
TaskHook	0.004	0.000	0.001
Tool-class	11.404	0.012	11.423
ToolUI	0.000	0.000	0.001
Workflow	0.020	0.000	0.024
WorkflowStep	0.004	0.000	0.004
addIdNum	0.000	0.000	0.001
api	0.000	0.000	0.001
as-methods	0.088	0.000	0.089
batch	0.000	0.000	0.001
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	4.840	0.000	4.842
cwl-utils	0.168	0.000	0.167
delete-methods	0.004	0.000	0.000
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.168	0.000	0.169
link	5.648	0.000	5.650
link_what	6.804	0.000	6.808
project_details	0.004	0.000	0.000
project_members	0	0	0
requirements	0.044	0.000	0.043
response-methods	0.000	0.000	0.001
sbg_get_env	0.000	0.000	0.001
sbg_set_env	0	0	0
set_test_env	0	0	0
shorthand-cwl	0.020	0.000	0.018
tag-methods	0.000	0.000	0.001
test_tool_bunny	0.000	0.000	0.001
test_tool_cwlrun	0	0	0
test_tool_rabix	0	0	0
upload_complete_all	0	0	0
upload_complete_part	0	0	0
upload_delete	0	0	0
upload_info	0	0	0
upload_info_part	0	0	0
upload_init	0	0	0