BioC 3.5: CHECK report for sevenbridges on malbec2

Package: sevenbridges

Version: 1.6.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.6.4.tar.gz

StartedAt: 2017-10-18 02:27:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:30:01 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 159.9 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.6.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/sevenbridges.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.4’
* package encoding: UTF-8
* 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        43.420  0.028  43.476
Tool-class  11.728  0.008  11.744
link_what    6.928  0.000   6.929
link         5.848  0.000   5.850
convert_app  5.116  0.000   5.117
* 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	0.000	0.001
Auth-class	0.008	0.000	0.008
Binding	0.032	0.004	0.036
CCBList	0.004	0.000	0.004
CWL	0.004	0.000	0.002
CommandInputParameter-class	0.024	0.008	0.034
CommandInputSchema-class	0.044	0.000	0.045
CommandLineBinding-class	0.008	0.000	0.005
CommandLineTool	0.016	0.000	0.017
CommandOutputBinding-class	0.008	0.000	0.007
CommandOutputParameter-class	0.012	0.000	0.012
CommandOutputSchema-class	0.028	0.000	0.026
DSCList	0.024	0.000	0.022
Enum	0.048	0.000	0.048
Expression-class	0.008	0.000	0.006
ExpressionTool-class	0.012	0.004	0.015
File-class	0.080	0.000	0.098
Files-class	0.008	0.000	0.007
Flow	43.420	0.028	43.476
Folders-class	0.032	0.000	0.032
Metadata	0.112	0.000	0.113
Parameter	0.032	0.000	0.028
Process	0.04	0.00	0.04
ProcessRequirement	0.044	0.000	0.044
Schema	0.012	0.004	0.014
TaskHook	0.000	0.000	0.001
Tool-class	11.728	0.008	11.744
ToolUI	0	0	0
Workflow	0.024	0.000	0.024
WorkflowStep	0.004	0.004	0.006
addIdNum	0	0	0
api	0	0	0
as-methods	0.096	0.000	0.095
batch	0.004	0.000	0.001
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	5.116	0.000	5.117
cwl-utils	0.180	0.000	0.179
delete-methods	0	0	0
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.196	0.000	0.196
link	5.848	0.000	5.850
link_what	6.928	0.000	6.929
project_details	0	0	0
project_members	0	0	0
requirements	0.044	0.000	0.045
response-methods	0	0	0
sbg_get_env	0	0	0
sbg_set_env	0	0	0
set_test_env	0	0	0
shorthand-cwl	0.016	0.000	0.017
tag-methods	0	0	0
test_tool_bunny	0.004	0.000	0.000
test_tool_cwlrun	0.000	0.000	0.001
test_tool_rabix	0.000	0.000	0.001
upload_complete_all	0.000	0.000	0.001
upload_complete_part	0.000	0.000	0.001
upload_delete	0.000	0.000	0.001
upload_info	0.000	0.000	0.001
upload_info_part	0.000	0.000	0.001
upload_init	0.000	0.000	0.001