Package: MetaboSignal

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2018-10-16 22:29:04 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:34:31 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 327.1 seconds

RetCode: 0

Status:  OK

CheckDir: MetaboSignal.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MetaboSignal.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 ‘MetaboSignal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaboSignal’ version ‘1.10.0’
* 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-3.7-bioc/meat/MetaboSignal.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetaboSignal
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MetaboSignal’ ...
** 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
* DONE (MetaboSignal)

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.

> 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 -- Tue Oct 16 22:34:19 2018 
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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 
 16.245   0.927  18.049 

name	user	system	elapsed
MS2_mergeNetworks	0.061	0.007	0.070
MS2_ppiNetwork	1.443	0.048	1.512
MS_changeNames	0.001	0.000	0.001
MS_convertGene	0.052	0.009	0.739
MS_distances	0.145	0.010	0.159
MS_exportCytoscape	0.001	0.000	0.000
MS_findMappedNodes	0.003	0.001	0.004
MS_getPathIds	0	0	0
MS_keggFinder	0.381	0.012	4.197
MS_keggNetwork	0.001	0.000	0.001
MS_nodeBW	0.042	0.006	0.049
MS_removeDrugs	0.006	0.001	0.007
MS_removeNode	0.011	0.002	0.013
MS_replaceNode	0.007	0.002	0.008
MS_shortestPaths	0.028	0.004	0.032
MS_shortestPathsNetwork	0.001	0.000	0.001
MS_tissueFilter	0.001	0.001	0.001
MS_topologyFilter	0.302	0.023	0.330