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BioC 3.4: CHECK report for sevenbridges on zin1

This page was generated on 2016-09-21 03:40:10 -0700 (Wed, 21 Sep 2016).

Package 1104/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.3.8
Tengfei Yin
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sevenbridges
Last Changed Rev: 120873 / Revision: 121152
Last Changed Date: 2016-09-12 08:31:47 -0700 (Mon, 12 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: sevenbridges
Version: 1.3.8
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.3.8.tar.gz
StartedAt: 2016-09-20 12:30:15 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:32:50 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 154.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: sevenbridges.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sevenbridges_1.3.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sevenbridges.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.8’
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
* 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’
gen_list: no visible global function definition for ‘rdarg’
handle_url2: no visible global function definition for ‘is.url’
lift: no visible binding for global variable ‘tmp’
lift_docopt_from_function: no visible global function definition for
  ‘rdarg’
Undefined global functions or variables:
  gadgetTitleBar is.url miniCotentPanel miniPage rdarg
  stableColumnLayout textInput tmp 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 ... WARNING
Functions or methods with usage in documentation object 'test_tool' but not in code:
  test_tool

* 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        49.876  0.048  49.925
Tool-class  12.936  0.020  12.956
link_what    8.164  0.008   8.170
link         6.736  0.008   6.745
convert_app  5.792  0.004   5.795
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.


sevenbridges.Rcheck/00install.out:

* 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)

sevenbridges.Rcheck/sevenbridges-Ex.timings:

nameusersystemelapsed
App-class0.0000.0000.001
Auth-class0.0040.0000.005
Binding0.0120.0000.010
CCBList0.0040.0000.004
CWL0.0000.0000.001
CommandInputParameter-class0.0160.0000.016
CommandInputSchema-class0.0160.0000.016
CommandLineBinding-class0.0080.0000.007
CommandLineTool0.0120.0000.014
CommandOutputBinding-class0.0040.0000.007
CommandOutputParameter-class0.0120.0000.013
CommandOutputSchema-class0.0120.0000.013
DSCList0.0160.0000.016
Enum0.0160.0000.015
Expression-class0.0080.0000.007
ExpressionTool-class0.0200.0000.022
File-class0.1680.0000.170
Files-class0.0080.0000.008
Flow49.876 0.04849.925
Metadata0.0760.0000.075
Parameter0.0360.0040.037
Process0.0480.0000.048
ProcessRequirement0.0520.0000.051
Schema0.020.000.02
TaskHook0.0040.0000.002
Tool-class12.936 0.02012.956
Workflow0.0240.0000.024
WorkflowStep0.0040.0000.005
addIdNum0.0000.0000.001
api0.0040.0000.001
as-methods0.0680.0000.068
batch0.0000.0000.001
convert_app5.7920.0045.795
cwl-utils0.1400.0000.139
delete-methods0.0000.0000.001
download-methods000
lift_docopt000
link6.7360.0086.745
link_what8.1640.0088.170
misc_get_token0.0000.0000.001
misc_get_uploader000
misc_make_metadata000
misc_upload_cli000
project_details0.0040.0000.001
project_members000
requirements0.0520.0000.050
response-methods0.0000.0000.001
set_test_env000
shorthand-cwl0.020.000.02
tag-methods000
test_tool0.0000.0000.001
test_tool_bunny0.0000.0000.001
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part0.0040.0000.000
upload_delete000
upload_info0.0000.0000.001
upload_info_part0.0000.0000.001
upload_init0.0000.0000.001