BioC 3.3: CHECK report for sevenbridges on morelia

Package: sevenbridges

Version: 1.1.17

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sevenbridges_1.1.17.tar.gz

StartedAt: 2016-04-21 07:30:00 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:31:18 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 78.3 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_1.1.17.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/sevenbridges.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.17’
* 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 ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.9Mb
* 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 ... NOTE
Missing or unexported object: ‘liftr::parse_rmd’
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::new_SimpleList_from_list’ ‘httr:::body_config’
  ‘httr:::compact’ ‘httr:::is.url’ ‘httr:::named’
  ‘httr:::request_build’ ‘httr:::request_perform’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ToolUI: no visible global function definition for ‘miniPage’
ToolUI: no visible global function definition for ‘gadgetTitleBar’
ToolUI: no visible global function definition for ‘miniCotentPanel’
ToolUI: no visible global function definition for ‘stableColumnLayout’
ToolUI: no visible global function definition for ‘textInput’
ToolUI: no visible global function definition for ‘uiOutput’
handle_url2: no visible global function definition for ‘is.url’
Undefined global functions or variables:
  gadgetTitleBar is.url miniCotentPanel miniPage stableColumnLayout
  textInput uiOutput
* 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 ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [2s/2s]
 [2s/2s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.

* 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
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Binding	0.010	0.002	0.020
CCBList	0.006	0.000	0.007
CWL	0.001	0.000	0.002
CommandInputParameter-class	0.023	0.003	0.024
CommandInputSchema-class	0.024	0.001	0.025
CommandLineBinding-class	0.006	0.000	0.006
CommandLineTool	0.017	0.001	0.018
CommandOutputBinding-class	0.012	0.000	0.011
CommandOutputParameter-class	0.020	0.001	0.020
CommandOutputSchema-class	0.018	0.000	0.019
DSCList	0.030	0.001	0.030
Enum	0.025	0.000	0.025
Expression-class	0.011	0.000	0.011
ExpressionTool-class	0.018	0.000	0.019
File-class	0.104	0.002	0.105
Parameter	0.053	0.001	0.054
Process	0.075	0.000	0.075
ProcessRequirement	0.079	0.000	0.079
Schema	0.014	0.001	0.015
TaskHook	0.001	0.000	0.001
Workflow	0.03	0.00	0.03
WorkflowStep	0.005	0.000	0.005
addIdNum	0.000	0.001	0.000
api	0.000	0.000	0.001
as-methods	0.070	0.001	0.072
delete-methods	0	0	0
download-methods	0.001	0.000	0.000
misc_get_token	0.001	0.000	0.001
misc_get_uploader	0.001	0.000	0.001
misc_make_metadata	0.001	0.001	0.000
misc_upload_cli	0.001	0.000	0.000
project_details	0.001	0.000	0.000
project_members	0.000	0.000	0.001
requirements	0.077	0.001	0.079
response-methods	0.000	0.000	0.001
shorthand-cwl	0.031	0.000	0.031
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	0.001	0.000	0.001
upload_info_part	0.001	0.000	0.000
upload_init	0	0	0