| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-12 12:06 -0400 (Sat, 12 Jul 2025).
| 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" | 4783 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4520 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4564 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4506 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4507 |
| 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 657/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| enrichViewNet 1.7.0 (landing page) Astrid Deschênes
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: enrichViewNet |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:enrichViewNet.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings enrichViewNet_1.7.0.tar.gz |
| StartedAt: 2025-07-11 21:59:29 -0400 (Fri, 11 Jul 2025) |
| EndedAt: 2025-07-11 22:03:00 -0400 (Fri, 11 Jul 2025) |
| EllapsedTime: 211.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: enrichViewNet.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:enrichViewNet.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings enrichViewNet_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/enrichViewNet.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.22-bioc/meat/enrichViewNet.Rcheck/00check.log’
for details.
enrichViewNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL enrichViewNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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)
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-pc-linux-gnu
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
enrichViewNet.Rcheck/enrichViewNet-Ex.timings
| name | user | system | elapsed | |
| createBasicEmap | 0.955 | 0.028 | 0.983 | |
| createCXJSONForCytoscape | 0.087 | 0.001 | 0.088 | |
| createEnrichMap | 0.451 | 0.005 | 0.456 | |
| createEnrichMapMultiBasic | 0.697 | 0.006 | 0.704 | |
| createEnrichMapMultiComplex | 1.439 | 0.008 | 1.448 | |
| createMetaDataSectionCXJSON | 0.001 | 0.000 | 0.001 | |
| createMultiEmap | 0.818 | 0.056 | 0.875 | |
| createNetwork | 0.045 | 0.005 | 0.050 | |
| createNetworkForCytoscape | 0.026 | 0.000 | 0.026 | |
| demoGOST | 0.054 | 0.011 | 1.492 | |
| extractInformationWhenIntersection | 0.032 | 0.000 | 0.032 | |
| extractInformationWhenNoIntersection | 0.200 | 0.013 | 1.435 | |
| extractNodesAndEdgesInformation | 0.025 | 0.008 | 0.032 | |
| filterResults | 0.002 | 0.001 | 0.003 | |
| formatInformationForCXJSON | 0.027 | 0.004 | 0.031 | |
| isCytoscapeRunning | 0.003 | 0.001 | 0.004 | |
| manageNameDuplicationInEmap | 0.004 | 0.000 | 0.003 | |
| manageQueryDuplicationInEmap | 0 | 0 | 0 | |
| parentalNapaVsDMSODEG | 0.237 | 0.034 | 3.129 | |
| parentalNapaVsDMSOEnrichment | 0.438 | 0.056 | 0.494 | |
| removeRootTerm | 0.005 | 0.000 | 0.005 | |
| rosaNapaVsDMSODEG | 0.128 | 0.025 | 3.505 | |
| rosaNapaVsDMSOEnrichment | 0.351 | 0.099 | 0.449 | |
| validateCreateEnrichMapArguments | 0.002 | 0.001 | 0.003 | |
| validateCreateEnrichMapMultiArguments | 0.011 | 0.000 | 0.010 | |
| validateCreateEnrichMapMultiComplexArg | 0.011 | 0.000 | 0.010 | |
| validateCreateEnrichMapSubSectionArguments | 0 | 0 | 0 | |
| validateCreateNetworkArguments | 0.002 | 0.000 | 0.002 | |