Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for sevenbridges on merida2

This page was generated on 2018-10-17 08:55:16 -0400 (Wed, 17 Oct 2018).

Package 1356/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.10.5
Nan Xiao
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/sevenbridges
Branch: RELEASE_3_7
Last Commit: ba1fba3
Last Changed Date: 2018-10-10 17:11:01 -0400 (Wed, 10 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sevenbridges
Version: 1.10.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.10.5.tar.gz
StartedAt: 2018-10-17 00:02:14 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:05:42 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 207.7 seconds
RetCode: 0
Status:  OK 
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/sevenbridges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.5’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Flow        67.641  0.204  68.453
Tool-class  16.863  0.056  17.045
link_what   10.379  0.021  10.474
link         8.092  0.015   8.147
convert_app  7.211  0.016   7.318
* 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


Installation output

sevenbridges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘sevenbridges’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sevenbridges)

Tests output

sevenbridges.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("sevenbridges")
> test_check("sevenbridges")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.483   0.235   3.727 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0020.0000.002
Auth-class0.0080.0000.009
Binding0.0650.0010.067
CCBList0.0200.0000.021
CWL0.0030.0000.004
CommandInputParameter-class0.0910.0010.094
CommandInputSchema-class0.0260.0000.027
CommandLineBinding-class0.0110.0000.011
CommandLineTool0.0260.0000.027
CommandOutputBinding-class0.0130.0010.013
CommandOutputParameter-class0.0150.0000.015
CommandOutputSchema-class0.1780.0010.181
DSCList0.0190.0000.020
Enum0.0320.0000.035
Expression-class0.0120.0000.012
ExpressionTool-class0.0280.0000.028
File-class0.0880.0050.097
Files-class0.0110.0000.011
Flow67.641 0.20468.453
Folders-class0.0080.0000.008
Metadata0.1080.0020.109
Parameter0.0490.0010.049
Process0.0700.0010.071
ProcessRequirement0.0630.0000.064
Schema0.0230.0000.023
TaskHook0.0040.0000.004
Tool-class16.863 0.05617.045
ToolUI0.0010.0000.001
Workflow0.0410.0000.042
WorkflowStep0.0060.0000.005
addIdNum0.0010.0000.001
api0.0010.0000.001
as-methods0.0870.0010.087
batch0.0020.0010.001
cli_list_projects0.0010.0000.001
cli_list_tags0.0010.0000.001
cli_upload0.0010.0000.002
convert_app7.2110.0167.318
cwl-utils0.1450.0020.148
delete-methods0.0010.0000.001
download-methods0.0010.0000.001
get_token0.0010.0000.001
get_uploader0.0010.0000.001
input_output_matrix0.1320.0030.135
link8.0920.0158.147
link_what10.379 0.02110.474
project_details0.0010.0000.001
project_members0.0010.0000.002
requirements0.0520.0010.053
response-methods0.0010.0000.002
sbg_get_env0.0020.0000.002
sbg_set_env0.0020.0000.002
set_test_env0.0010.0000.002
shorthand-cwl0.0390.0000.039
tag-methods0.0020.0010.002
test_tool_bunny0.0020.0000.002
test_tool_cwlrun0.0020.0010.002
test_tool_rabix0.0010.0000.002
upload_complete_all0.0020.0000.002
upload_complete_part0.0020.0000.002
upload_delete0.0020.0000.002
upload_info0.0010.0000.001
upload_info_part0.0020.0000.001
upload_init0.0020.0000.002