BioC 3.5: CHECK report for sevenbridges on malbec2

Package: sevenbridges

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.6.0.tar.gz

StartedAt: 2017-08-16 02:14:26 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:16:59 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 153.0 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.6.0’
* 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        43.236  0.020  43.280
Tool-class  11.836  0.004  11.847
link_what    6.740  0.000   6.742
link         6.072  0.000   6.073
convert_app  5.084  0.000   5.086
* 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	0.008	0.000	0.007
Binding	0.028	0.008	0.036
CCBList	0.000	0.004	0.004
CWL	0.000	0.004	0.001
CommandInputParameter-class	0.036	0.000	0.037
CommandInputSchema-class	0.044	0.000	0.045
CommandLineBinding-class	0.004	0.000	0.005
CommandLineTool	0.016	0.000	0.016
CommandOutputBinding-class	0.008	0.000	0.007
CommandOutputParameter-class	0.012	0.000	0.011
CommandOutputSchema-class	0.024	0.000	0.024
DSCList	0.016	0.000	0.015
Enum	0.028	0.000	0.029
Expression-class	0.008	0.000	0.006
ExpressionTool-class	0.012	0.000	0.014
File-class	0.076	0.000	0.094
Files-class	0.008	0.000	0.007
Flow	43.236	0.020	43.280
Folders-class	0.036	0.000	0.035
Metadata	0.116	0.000	0.117
Parameter	0.040	0.000	0.036
Process	0.036	0.000	0.038
ProcessRequirement	0.044	0.000	0.041
Schema	0.016	0.000	0.014
TaskHook	0.000	0.000	0.002
Tool-class	11.836	0.004	11.847
ToolUI	0.000	0.000	0.001
Workflow	0.032	0.000	0.031
WorkflowStep	0.004	0.000	0.005
addIdNum	0.004	0.000	0.000
api	0	0	0
as-methods	0.092	0.000	0.092
batch	0.000	0.000	0.001
cli_list_projects	0.000	0.000	0.001
cli_list_tags	0.000	0.000	0.001
cli_upload	0.000	0.000	0.001
convert_app	5.084	0.000	5.086
cwl-utils	0.168	0.004	0.173
delete-methods	0.000	0.000	0.001
download-methods	0.000	0.000	0.001
get_token	0.000	0.000	0.001
get_uploader	0.000	0.000	0.001
input_output_matrix	0.176	0.000	0.179
link	6.072	0.000	6.073
link_what	6.740	0.000	6.742
project_details	0.000	0.000	0.001
project_members	0.000	0.000	0.001
requirements	0.044	0.000	0.042
response-methods	0	0	0
sbg_get_env	0	0	0
sbg_set_env	0.004	0.000	0.001
set_test_env	0.000	0.000	0.001
shorthand-cwl	0.016	0.000	0.017
tag-methods	0.004	0.000	0.001
test_tool_bunny	0.000	0.000	0.001
test_tool_cwlrun	0.000	0.000	0.001
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	0.000	0.000	0.001
upload_init	0.000	0.000	0.001