BioC 3.4: CHECK report for sevenbridges on malbec1

Package: sevenbridges

Version: 1.4.9

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.4.9.tar.gz

StartedAt: 2017-04-15 01:14:01 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:16:49 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 167.6 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.4.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sevenbridges.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.9’
* 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        51.052  0.008  51.099
Tool-class  13.012  0.000  13.022
link_what    9.668  0.000   9.678
link         7.372  0.004   7.381
convert_app  6.180  0.004   6.186
* 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	0.004	0.000	0.000
Auth-class	0.016	0.000	0.015
Binding	0.012	0.000	0.011
CCBList	0.004	0.000	0.005
CWL	0.000	0.000	0.001
CommandInputParameter-class	0.016	0.000	0.015
CommandInputSchema-class	0.012	0.000	0.015
CommandLineBinding-class	0.108	0.000	0.112
CommandLineTool	0.012	0.000	0.014
CommandOutputBinding-class	0.008	0.000	0.007
CommandOutputParameter-class	0.016	0.000	0.013
CommandOutputSchema-class	0.012	0.000	0.012
DSCList	0.012	0.004	0.017
Enum	0.012	0.000	0.015
Expression-class	0.000	0.008	0.008
ExpressionTool-class	0.012	0.004	0.018
File-class	0.068	0.000	0.068
Files-class	0.008	0.000	0.007
Flow	51.052	0.008	51.099
Folders-class	0.004	0.000	0.005
Metadata	0.068	0.000	0.070
Parameter	0.032	0.000	0.031
Process	0.048	0.000	0.050
ProcessRequirement	0.052	0.000	0.049
Schema	0.016	0.000	0.016
TaskHook	0.000	0.000	0.001
Tool-class	13.012	0.000	13.022
ToolUI	0.004	0.000	0.001
Workflow	0.024	0.000	0.026
WorkflowStep	0.008	0.000	0.005
addIdNum	0	0	0
api	0	0	0
as-methods	0.068	0.000	0.066
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	6.180	0.004	6.186
cwl-utils	0.096	0.000	0.098
delete-methods	0	0	0
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.084	0.000	0.083
link	7.372	0.004	7.381
link_what	9.668	0.000	9.678
project_details	0.004	0.000	0.000
project_members	0	0	0
requirements	0.080	0.000	0.078
response-methods	0	0	0
sbg_get_env	0.000	0.000	0.001
sbg_set_env	0.000	0.000	0.001
set_test_env	0.000	0.000	0.001
shorthand-cwl	0.036	0.000	0.035
tag-methods	0.000	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	0.004	0.000	0.001
upload_complete_all	0	0	0
upload_complete_part	0.000	0.000	0.001
upload_delete	0.000	0.000	0.001
upload_info	0.000	0.000	0.001
upload_info_part	0	0	0
upload_init	0	0	0