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This page was generated on 2023-03-24 11:06:56 -0400 (Fri, 24 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4546
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4307
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4299
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 1155/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaboSignal 1.29.0  (landing page)
Andrea Rodriguez-Martinez
Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023)
git_url: https://git.bioconductor.org/packages/MetaboSignal
git_branch: devel
git_last_commit: 721a86d
git_last_commit_date: 2022-11-01 11:14:22 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.29.0
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_1.29.0.tar.gz
StartedAt: 2023-03-24 03:19:31 -0400 (Fri, 24 Mar 2023)
EndedAt: 2023-03-24 03:34:17 -0400 (Fri, 24 Mar 2023)
EllapsedTime: 885.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaboSignal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MetaboSignal.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboSignal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaboSignal’ version ‘1.29.0’
* 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
get_molecule_type: no visible binding for global variable
  'regulatory_interactions'
Undefined global functions or variables:
  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-3.17-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/4.3/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
snapshotDate(): 2023-03-21
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2023-03-21
** testing if installed package can be loaded from final location
snapshotDate(): 2023-03-21
** testing if installed package keeps a record of temporary installation path
* DONE (MetaboSignal)

Tests output

MetaboSignal.Rcheck/tests/runTests.Rout


R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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")
snapshotDate(): 2023-03-21

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 -- Fri Mar 24 03:34:03 2023 
*********************************************** 
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 
 32.776   1.730  46.212 

Example timings

MetaboSignal.Rcheck/MetaboSignal-Ex.timings

nameusersystemelapsed
MS2_mergeNetworks0.0990.0040.139
MS2_ppiNetwork2.6610.0303.700
MS_changeNames000
MS_convertGene0.0810.0071.010
MS_distances0.2080.0110.219
MS_exportCytoscape0.0000.0000.001
MS_findMappedNodes0.0030.0020.005
MS_getPathIds000
MS_keggFinder0.2950.0063.504
MS_keggNetwork000
MS_nodeBW0.0420.0070.066
MS_reactionNetwork000
MS_removeDrugs0.0060.0010.007
MS_removeNode0.0190.0010.021
MS_replaceNode0.0200.0020.030
MS_shortestPaths0.0310.0040.042
MS_shortestPathsNetwork000
MS_tissueFilter000
MS_topologyFilter0.3600.0350.509