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This page was generated on 2022-06-24 11:08:09 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 lconway


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 1112/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaboSignal 1.27.1  (landing page)
Andrea Rodriguez-Martinez
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/MetaboSignal
git_branch: master
git_last_commit: 0d79c71
git_last_commit_date: 2022-06-07 06:48:54 -0400 (Tue, 07 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetaboSignal
Version: 1.27.1
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_1.27.1.tar.gz
StartedAt: 2022-06-23 21:05:08 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:10:42 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 334.1 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_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MetaboSignal.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* 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 ‘1.27.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MS_keggFinder  0.285  0.015   8.153
MS_convertGene 0.038  0.006   5.787
* 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-3.16-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 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
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 -- Thu Jun 23 21:10:33 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 
 15.593   0.842  17.335 

Example timings

MetaboSignal.Rcheck/MetaboSignal-Ex.timings

nameusersystemelapsed
MS2_mergeNetworks0.0430.0060.049
MS2_ppiNetwork0.9520.0240.978
MS_changeNames000
MS_convertGene0.0380.0065.787
MS_distances0.8800.0090.891
MS_exportCytoscape0.0000.0010.000
MS_findMappedNodes0.0020.0010.003
MS_getPathIds000
MS_keggFinder0.2850.0158.153
MS_keggNetwork000
MS_nodeBW0.0270.0070.034
MS_reactionNetwork000
MS_removeDrugs0.0040.0010.005
MS_removeNode0.0070.0010.008
MS_replaceNode0.0080.0010.009
MS_shortestPaths0.0160.0030.019
MS_shortestPathsNetwork0.0000.0010.000
MS_tissueFilter000
MS_topologyFilter0.1080.0160.124