Multiple platform build/check report for BioC 3.22 - CHECK results for enrichViewNet on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4536
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4517
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 enrichViewNet on lconway

To the developers/maintainers of the enrichViewNet package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/enrichViewNet.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: enrichViewNet

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enrichViewNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enrichViewNet_1.7.0.tar.gz

StartedAt: 2025-08-03 20:56:06 -0400 (Sun, 03 Aug 2025)

EndedAt: 2025-08-03 20:59:55 -0400 (Sun, 03 Aug 2025)

EllapsedTime: 229.3 seconds

RetCode: 1

Status: ERROR

CheckDir: enrichViewNet.Rcheck

Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enrichViewNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enrichViewNet_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/enrichViewNet.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘enrichViewNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichViewNet’ version ‘1.7.0’
* 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 ‘enrichViewNet’ 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 code 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  x[1]: "[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edge
  x[1]: s\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"}
  x[1]: ,{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},{\"name\":\"cyHiddenAtt
  x[1]: ributes\",\"version\":\"1.0\"},{\"name\":\"cyNetworkRelations\",\"version\
  x[1]: ":\"1.0\"},{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"netw...
  y[1]: "[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edge
  y[1]: s\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"}
  y[1]: ,{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},{\"name\":\"cyHiddenAtt
  y[1]: ributes\",\"version\":\"1.0\"},{\"name\":\"cyNetworkRelations\",\"version\
  y[1]: ":\"1.0\"},{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"netw...
  
  [ FAIL 3 | WARN 1 | SKIP 0 | PASS 100 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/enrichViewNet.Rcheck/00check.log’
for details.

Installation output

enrichViewNet.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘enrichViewNet’ ...
** this is package ‘enrichViewNet’ version ‘1.7.0’
** using staged installation
** R
** data
** 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 (enrichViewNet)

Tests output

enrichViewNet.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(enrichViewNet)

> 
> ## Run all unit tests
> test_check("enrichViewNet")
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 100 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-methodsInternal.R:395:5'): extractInformationWhenNoIntersection() must return expected text ──
result$geneNodes not equal to expected$geneNodes.
Attributes: < Component "row.names": Numeric: lengths (11, 9) differ >
Component "id": Lengths (11, 9) differ (string compare on first 9)
Component "id": 1 string mismatch
Component "group": Lengths (11, 9) differ (string compare on first 9)
Component "alias": Lengths (11, 9) differ (string compare on first 9)
Component "alias": 1 string mismatch
── Failure ('test-methodsInternal.R:397:5'): extractInformationWhenNoIntersection() must return expected text ──
result$edges not equal to expected$edges.
Attributes: < Component "row.names": Numeric: lengths (14, 13) differ >
Component "source": Lengths (14, 13) differ (string compare on first 13)
Component "source": 2 string mismatches
Component "target": Lengths (14, 13) differ (string compare on first 13)
Component "target": 2 string mismatches
Component "interaction": Lengths (14, 13) differ (string compare on first 13)
── Failure ('test-methodsInternal.R:481:5'): createCXJSONForCytoscape() must return expected text ──
`result` not equal to `expected`.
1/1 mismatches
x[1]: "[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edge
x[1]: s\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"}
x[1]: ,{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},{\"name\":\"cyHiddenAtt
x[1]: ributes\",\"version\":\"1.0\"},{\"name\":\"cyNetworkRelations\",\"version\
x[1]: ":\"1.0\"},{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"netw...
y[1]: "[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edge
y[1]: s\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"}
y[1]: ,{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},{\"name\":\"cyHiddenAtt
y[1]: ributes\",\"version\":\"1.0\"},{\"name\":\"cyNetworkRelations\",\"version\
y[1]: ":\"1.0\"},{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"netw...

[ FAIL 3 | WARN 1 | SKIP 0 | PASS 100 ]
Error: Test failures
Execution halted

Example timings

enrichViewNet.Rcheck/enrichViewNet-Ex.timings

name	user	system	elapsed
createBasicEmap	1.083	0.052	1.142
createCXJSONForCytoscape	0.112	0.003	0.116
createEnrichMap	0.539	0.011	0.553
createEnrichMapMultiBasic	0.877	0.027	0.910
createEnrichMapMultiComplex	1.115	0.018	1.139
createMetaDataSectionCXJSON	0.001	0.000	0.001
createMultiEmap	1.476	0.032	1.516
createNetwork	0.053	0.013	0.068
createNetworkForCytoscape	0.032	0.006	0.038
demoGOST	0.034	0.007	4.311
extractInformationWhenIntersection	0.030	0.004	0.034
extractInformationWhenNoIntersection	0.207	0.029	4.166
extractNodesAndEdgesInformation	0.031	0.002	0.033
filterResults	0.002	0.001	0.003
formatInformationForCXJSON	0.032	0.002	0.033
isCytoscapeRunning	0.004	0.001	0.004
manageNameDuplicationInEmap	0.004	0.001	0.005
manageQueryDuplicationInEmap	0.000	0.000	0.001
parentalNapaVsDMSODEG	0.200	0.011	3.246
parentalNapaVsDMSOEnrichment	0.439	0.005	0.446
removeRootTerm	0.004	0.001	0.006
rosaNapaVsDMSODEG	0.138	0.007	3.744
rosaNapaVsDMSOEnrichment	0.425	0.024	0.452
validateCreateEnrichMapArguments	0.002	0.001	0.003
validateCreateEnrichMapMultiArguments	0.008	0.003	0.011
validateCreateEnrichMapMultiComplexArg	0.010	0.002	0.012
validateCreateEnrichMapSubSectionArguments	0.001	0.000	0.000
validateCreateNetworkArguments	0.002	0.001	0.002