Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:14 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MetaboSignal on merida1


To the developers/maintainers of the MetaboSignal package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaboSignal.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1124/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaboSignal 1.26.2  (landing page)
Andrea Rodriguez-Martinez
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MetaboSignal
git_branch: RELEASE_3_15
git_last_commit: 54eefda
git_last_commit_date: 2022-07-27 03:44:19 -0400 (Wed, 27 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaboSignal
Version: 1.26.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaboSignal_1.26.2.tar.gz
StartedAt: 2022-10-19 04:25:19 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:34:27 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 547.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaboSignal.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaboSignal_1.26.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MetaboSignal.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.2’
* 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 LazyData ... 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-3.15-bioc/meat/MetaboSignal.Rcheck/00check.log’
for details.



Installation output

MetaboSignal.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
** 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)

Tests output

MetaboSignal.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 Oct 19 04:34:16 2022 
*********************************************** 
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 
Warning messages:
1: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
2: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
3: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
4: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
5: In betweenness(network_i, all_nodes, directed = FALSE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
6: In betweenness(network_i, nodes, directed = FALSE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
7: In betweenness(network_i, nodes, directed = FALSE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
8: In betweenness(network_i, all_nodes, directed = FALSE, weights = NULL,  :
  'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4
> 
> proc.time()
   user  system elapsed 
 27.802   1.221  29.965 

Example timings

MetaboSignal.Rcheck/MetaboSignal-Ex.timings

nameusersystemelapsed
MS2_mergeNetworks0.1610.0090.172
MS2_ppiNetwork1.7370.0261.858
MS_changeNames000
MS_convertGene0.0830.0080.970
MS_distances0.1880.0100.197
MS_exportCytoscape000
MS_findMappedNodes0.0040.0020.005
MS_getPathIds000
MS_keggFinder0.4890.0094.707
MS_keggNetwork0.0000.0000.001
MS_nodeBW0.0460.0070.052
MS_reactionNetwork0.0000.0000.001
MS_removeDrugs0.0050.0020.006
MS_removeNode0.0130.0020.015
MS_replaceNode0.0160.0010.017
MS_shortestPaths0.0260.0030.030
MS_shortestPathsNetwork0.0010.0000.000
MS_tissueFilter000
MS_topologyFilter0.3620.0290.391