Multiple platform build/check report for BioC 3.14 - CHECK results for MetaboSignal on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: MetaboSignal

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaboSignal.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaboSignal_1.24.0.tar.gz

StartedAt: 2022-04-12 22:29:53 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:37:19 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 446.4 seconds

RetCode: 0

Status: OK

CheckDir: MetaboSignal.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaboSignal.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaboSignal_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaboSignal.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaboSignal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaboSignal' version '1.24.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MS_keggFinder 0.32   0.02    5.64
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaboSignal.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MetaboSignal_1.24.0.tar.gz && rm -rf MetaboSignal.buildbin-libdir && mkdir MetaboSignal.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaboSignal.buildbin-libdir MetaboSignal_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MetaboSignal_1.24.0.zip && rm MetaboSignal_1.24.0.tar.gz MetaboSignal_1.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 36 2634k   36  970k    0     0  1622k      0  0:00:01 --:--:--  0:00:01 1622k
 94 2634k   94 2498k    0     0  1551k      0  0:00:01  0:00:01 --:--:-- 1551k
100 2634k  100 2634k    0     0  1597k      0  0:00:01  0:00:01 --:--:-- 1597k

install for i386

* 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
  converting help for package 'MetaboSignal'
    finding HTML links ... done
    MS2_mergeNetworks                       html  
    MS2_ppiNetwork                          html  
    MS_changeNames                          html  
    MS_convertGene                          html  
    MS_distances                            html  
    MS_exportCytoscape                      html  
    MS_findMappedNodes                      html  
    MS_getPathIds                           html  
    MS_keggFinder                           html  
    MS_keggNetwork                          html  
    MS_nodeBW                               html  
    MS_reactionNetwork                      html  
    MS_removeDrugs                          html  
    MS_removeNode                           html  
    MS_replaceNode                          html  
    MS_shortestPaths                        html  
    MS_shortestPathsNetwork                 html  
    MS_tissueFilter                         html  
    MS_topologyFilter                       html  
    MetaboSignal_table                      html  
    directionality_reactions                html  
    hpaNormalTissue                         html  
    keggNet_example                         html  
    kegg_pathways                           html  
    mergedNet_example                       html  
    ppiNet_example                          html  
    regulatory_interactions                 html  
** 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

install for x64

* installing *source* package 'MetaboSignal' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaboSignal' as MetaboSignal_1.24.0.zip
* DONE (MetaboSignal)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MetaboSignal' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 Apr 12 22:36:54 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 
  13.62    1.39   15.59


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 Apr 12 22:37:11 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 
  15.25    0.70   16.50

name	user	system	elapsed
MS2_mergeNetworks	0.05	0.00	0.05
MS2_ppiNetwork	1.02	0.03	1.04
MS_changeNames	0	0	0
MS_convertGene	0.17	0.00	0.94
MS_distances	0.17	0.01	0.18
MS_exportCytoscape	0	0	0
MS_findMappedNodes	0.02	0.00	0.02
MS_getPathIds	0	0	0
MS_keggFinder	0.32	0.02	5.64
MS_keggNetwork	0	0	0
MS_nodeBW	0.05	0.00	0.05
MS_reactionNetwork	0	0	0
MS_removeDrugs	0	0	0
MS_removeNode	0.00	0.02	0.01
MS_replaceNode	0.00	0.01	0.02
MS_shortestPaths	0.02	0.02	0.03
MS_shortestPathsNetwork	0	0	0
MS_tissueFilter	0	0	0
MS_topologyFilter	1.04	0.06	1.11

name	user	system	elapsed
MS2_mergeNetworks	0.05	0.00	0.05
MS2_ppiNetwork	0.67	0.01	0.68
MS_changeNames	0	0	0
MS_convertGene	0.04	0.00	0.77
MS_distances	0.11	0.02	0.13
MS_exportCytoscape	0	0	0
MS_findMappedNodes	0	0	0
MS_getPathIds	0	0	0
MS_keggFinder	0.30	0.01	4.32
MS_keggNetwork	0	0	0
MS_nodeBW	0.04	0.00	0.05
MS_reactionNetwork	0	0	0
MS_removeDrugs	1.1	0.0	1.1
MS_removeNode	0.01	0.00	0.01
MS_replaceNode	0.02	0.00	0.02
MS_shortestPaths	0.01	0.00	0.01
MS_shortestPathsNetwork	0	0	0
MS_tissueFilter	0	0	0
MS_topologyFilter	0.14	0.00	0.14

CHECK results for MetaboSignal on tokay2

Summary

Command output

Installation output

Tests output

Example timings