Multiple platform build/check report for BioC 3.24 - BUILD results for ndexr on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4936
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"	4621
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*

BUILD results for ndexr on kjohnson3

To the developers/maintainers of the ndexr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ndexr.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: ndexr

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ndexr

StartedAt: 2026-05-21 17:11:57 -0400 (Thu, 21 May 2026)

EndedAt: 2026-05-21 17:12:01 -0400 (Thu, 21 May 2026)

EllapsedTime: 4.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ndexr
###
##############################################################################
##############################################################################


* checking for file ‘ndexr/DESCRIPTION’ ... OK
* preparing ‘ndexr’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ndexr-vignette.Rmd’ using rmarkdown

Quitting from ndexr-vignette.Rmd:119-122 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ndex_helper_httpResponseHandler()`:
! POST: [ http://www.ndexbio.org/v2/search/network?start=0&size=100 ]
data:
 {"searchString":"EGFR"} 
...
Some internal server error occurred (500):

[errorCode]
NDEx_Exception

[message]
Uncaught exception jakarta.ws.rs.NotAllowedException: RESTEASY003650: No resource method found for GET, return 405 with Allow header

[stackTrace]
java.base/java.lang.Thread.getStackTrace(Thread.java:2451)
org.ndexbio.model.errorcodes.NDExError.stackTrace(NDExError.java:108)
org.ndexbio.model.errorcodes.NDExError.<init>(NDExError.java:60)
org.ndexbio.model.exceptions.NdexException.<init>(NdexException.java:61)
org.ndexbio.rest.exceptions.mappers.DefaultExceptionMapper.toResponse(DefaultExceptionMapper.java:56)
org.jboss.resteasy.core.ExceptionHandler.executeExceptionMapper(ExceptionHandler.java:139)
org.jboss.resteasy.core.ExceptionHandler.handleException(ExceptionHandler.java:306)
org.jboss.resteasy.core.SynchronousDispatcher.writeException(SynchronousDispatcher.java:205)
org.jboss.resteasy.core.SynchronousDispatcher.lambda$invoke$4(SynchronousDispatcher.java:236)
org.jboss.resteasy.core.SynchronousDispatcher.lambda$preprocess$0(SynchronousDispatcher.java:154)
org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:321)
org.jboss.resteasy.core.SynchronousDispatcher.preprocess(SynchronousDispatcher.java:157)
org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:229)
org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:222)
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:55)
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:51)
jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:196)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:165)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:482)
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:673)
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:344)
org.apache.coyote.ajp.AjpProcessor.service(AjpProcessor.java:431)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:896)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1736)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63)
java.base/java.lang.Thread.run(Thread.java:1583)


[timeStamp]
2026-05-21 14:12:00,522
---
Backtrace:
    ▆
 1. └─ndexr::ndex_find_networks(ndexcon, "EGFR")
 2.   └─ndexr:::ndex_rest_POST(ndexcon, route = route, data = query)
 3.     └─ndexr:::ndex_helper_httpResponseHandler(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
POST: [ http://www.ndexbio.org/v2/search/network?start=0&size=100 ]
data:
 {"searchString":"EGFR"} 
...
Some internal server error occurred (500):

[errorCode]
NDEx_Exception

[message]
Uncaught exception jakarta.ws.rs.NotAllowedException: RESTEASY003650: No resource method found for GET, return 405 with Allow header

[stackTrace]
java.base/java.lang.Thread.getStackTrace(Thread.java:2451)
org.ndexbio.model.errorcodes.NDExError.stackTrace(NDExError.java:108)
org.ndexbio.model.errorcodes.NDExError.<init>(NDExError.java:60)
org.ndexbio.model.exceptions.NdexException.<init>(NdexException.java:61)
org.ndexbio.rest.exceptions.mappers.DefaultExceptionMapper.toResponse(DefaultExceptionMapper.java:56)
org.jboss.resteasy.core.ExceptionHandler.executeExceptionMapper(ExceptionHandler.java:139)
org.jboss.resteasy.core.ExceptionHandler.handleException(ExceptionHandler.java:306)
org.jboss.resteasy.core.SynchronousDispatcher.writeException(SynchronousDispatcher.java:205)
org.jboss.resteasy.core.SynchronousDispatcher.lambda$invoke$4(SynchronousDispatcher.java:236)
org.jboss.resteasy.core.SynchronousDispatcher.lambda$preprocess$0(SynchronousDispatcher.java:154)
org.jboss.resteasy.core.interception.jaxrs.PreMatchContainerRequestContext.filter(PreMatchContainerRequestContext.java:321)
org.jboss.resteasy.core.SynchronousDispatcher.preprocess(SynchronousDispatcher.java:157)
org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:229)
org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:222)
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:55)
org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:51)
jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:196)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:165)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:482)
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:673)
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:344)
org.apache.coyote.ajp.AjpProcessor.service(AjpProcessor.java:431)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:896)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1736)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63)
java.base/java.lang.Thread.run(Thread.java:1583)


[timeStamp]
2026-05-21 14:12:00,522

--- failed re-building ‘ndexr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘ndexr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted