Package: MetaboSignal

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaboSignal_1.16.0.tar.gz

StartedAt: 2020-04-15 03:41:18 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:47:17 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 359.4 seconds

RetCode: 0

Status:  OK

CheckDir: MetaboSignal.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaboSignal_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MetaboSignal.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboSignal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaboSignal’ version ‘1.16.0’
* 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 ‘MetaboSignal’ 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 ... NOTE
MS_tissueFilter: no visible binding for global variable
  'hpaNormalTissue'
get_molecule_type: no visible binding for global variable
  'regulatory_interactions'
Undefined global functions or variables:
  hpaNormalTissue regulatory_interactions
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/MetaboSignal.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MetaboSignal’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MetaboSignal.Rmd’ using ‘UTF-8’ 
   ‘MetaboSignal2.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetaboSignal)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("MetaboSignal")

Note: some source_nodes or target_nodes were not mapped onto the network
Calculating distances

Building shortest path network

Note that all source_nodes and target_nodes were successfully mapped onto the network

Calculating distances

Building shortest path network

Note that all source_nodes and target_nodes were successfully mapped onto the network

Calculating distances

Building shortest path network

Note that all source_nodes and target_nodes were successfully mapped onto the network

Network features:
Number of nodes:59
Number of edges:100

Network features:
Number of nodes:59
Number of edges:100



RUNIT TEST PROTOCOL -- Wed Apr 15 03:47:07 2020 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MetaboSignal RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.961   0.957  19.533 

name	user	system	elapsed
MS2_mergeNetworks	0.073	0.008	0.081
MS2_ppiNetwork	2.314	0.033	2.358
MS_changeNames	0.000	0.000	0.001
MS_convertGene	0.055	0.003	0.609
MS_distances	0.084	0.006	0.089
MS_exportCytoscape	0.000	0.000	0.001
MS_findMappedNodes	0.003	0.001	0.004
MS_getPathIds	0	0	0
MS_keggFinder	0.445	0.010	4.353
MS_keggNetwork	0	0	0
MS_nodeBW	0.040	0.005	0.049
MS_reactionNetwork	0	0	0
MS_removeDrugs	0.004	0.001	0.005
MS_removeNode	0.011	0.001	0.012
MS_replaceNode	0.011	0.001	0.013
MS_shortestPaths	0.023	0.003	0.026
MS_shortestPathsNetwork	0.001	0.000	0.000
MS_tissueFilter	0	0	0
MS_topologyFilter	0.264	0.030	0.299