killNode(): Check failures on R-universe Linux

[HenrikBengtsson]

https://henrikbengtsson.r-universe.dev/parallelly

Unit test:

parallelly/inst/testme/test-killNode.R

Lines 70 to 86 in 5e77854

	message("- Waiting for cluster nodes to terminate")
	## It might take a moment before the background
	## workers are shutdown after having been signaled
	timeout <- Sys.time() + 30.0
	repeat {
	alive <- isNodeAlive(cl)
	print(alive)
	stopifnot(
	length(alive) == length(cl),
	is.logical(alive)
	)
	if (!any(alive, na.rm = TRUE)) break
	if (Sys.time() > timeout) {
	stop("One or more cluster nodes are still running after 30 seconds")
	}
	Sys.sleep(0.5)
	}

fails on R-universe Linux builders (only):

2025-05-10T03:33:43.9582552Z   Running ‘test-killNode.R’ [1s/31s]
2025-05-10T03:33:43.9648487Z  [9s/35s] ERROR
2025-05-10T03:33:43.9656251Z Running the tests in ‘tests/test-killNode.R’ failed.
2025-05-10T03:33:43.9657591Z Last 13 lines of output:
2025-05-10T03:33:43.9658926Z     TRUE   TRUE 
2025-05-10T03:33:43.9659254Z   Node 1 Node 2 
2025-05-10T03:33:43.9660012Z     TRUE   TRUE 
2025-05-10T03:33:43.9660353Z   Node 1 Node 2 
2025-05-10T03:33:43.9660622Z     TRUE   TRUE 
2025-05-10T03:33:43.9660885Z   Node 1 Node 2 
2025-05-10T03:33:43.9661146Z     TRUE   TRUE 
2025-05-10T03:33:43.9661415Z   Node 1 Node 2 
2025-05-10T03:33:43.9661676Z     TRUE   TRUE 
2025-05-10T03:33:43.9661947Z   Node 1 Node 2 
2025-05-10T03:33:43.9662215Z     TRUE   TRUE 
2025-05-10T03:33:43.9662517Z   Error in eval(ei, envir) : 
2025-05-10T03:33:43.9662995Z     One or more cluster nodes are still running after 30 seconds
2025-05-10T03:33:43.9663701Z   Calls: <Anonymous> ... eval -> eval -> source -> withVisible -> eval -> eval
2025-05-10T03:33:43.9664296Z   Execution halted
2025-05-10T03:33:44.2620175Z * checking for unstated dependencies in vignettes ... OK
2025-05-10T03:33:44.2783828Z * checking package vignettes ... OK
2025-05-10T03:33:44.2786236Z * checking running R code from vignettes ... SKIPPED
2025-05-10T03:33:44.2790205Z * checking re-building of vignette outputs ... SKIPPED
2025-05-10T03:33:44.2793032Z * DONE
2025-05-10T03:33:44.2796384Z 
2025-05-10T03:33:44.2797794Z Status: 1 ERROR
2025-05-10T03:33:44.2801122Z See
2025-05-10T03:33:44.2801860Z   ‘/__w/cran/cran/parallelly.Rcheck/00check.log’
2025-05-10T03:33:44.2802300Z for details.
2025-05-10T03:33:44.2803860Z 
2025-05-10T03:33:44.4912519Z ##[error]Check: tests, Result: ERROR
    Running ‘test-all.equal.connection.R’
    Running ‘test-as.cluster.R’
    Running ‘test-availableCores.R’
    Running ‘test-availableWorkers.R’
    Running ‘test-cgroups.R’
    Running ‘test-cpuLoad.R’
    Running ‘test-freeCores.R’
    Running ‘test-freePort.R’
    Running ‘test-isConnectionValid.R’
    Running ‘test-isForkedChild.R’
    Running ‘test-killNode.R’ [1s/31s]
  Running the tests in ‘tests/test-killNode.R’ failed.
  Last 13 lines of output:
      TRUE   TRUE 
    Node 1 Node 2 
      TRUE   TRUE 
    Node 1 Node 2 
      TRUE   TRUE 
    Node 1 Node 2 
      TRUE   TRUE 
    Node 1 Node 2 
      TRUE   TRUE 
    Node 1 Node 2 
      TRUE   TRUE 
    Error in eval(ei, envir) : 
      One or more cluster nodes are still running after 30 seconds
    Calls: <Anonymous> ... eval -> eval -> source -> withVisible -> eval -> eval
    Execution halted

See also

Full logs from 2025-05-09: logs_38365589033.zip

[HenrikBengtsson]

Cannot reproduce this using https://github.com/r-universe-org/base-image:

docker run -it -v "$HOME/futureverse:/tmp/futureverse"  runiverse/base bash
...

root@1e69c8822db8:/tmp/futureverse# R CMD check parallelly_1.44.0-9023.tar.gz --library=mylib --no-manual --no-vignettes
* using log directory ‘/tmp/futureverse/parallelly.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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
* using options ‘--no-manual --no-vignettes’
* checking for file ‘parallelly/DESCRIPTION’ ... OK
* this is package ‘parallelly’ version ‘1.44.0-9023’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘parallelly’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 whether startup messages can be suppressed ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
/usr/bin/nm: /tmp/futureverse/mylib/parallelly/libs/parallelly.so: no symbols
/usr/bin/nm: /tmp/futureverse/mylib/parallelly/libs/parallelly.so: no symbols


See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.equal.connection.R’
  Running ‘test-as.cluster.R’
  Running ‘test-availableCores.R’
  Running ‘test-availableWorkers.R’
  Running ‘test-cgroups.R’
  Running ‘test-cpuLoad.R’
  Running ‘test-freeCores.R’
  Running ‘test-freePort.R’
  Running ‘test-isConnectionValid.R’
  Running ‘test-isForkedChild.R’
  Running ‘test-killNode.R’
  Running ‘test-makeClusterMPI.R’
  Running ‘test-makeClusterPSOCK.R’
  Running ‘test-makeClusterSequential.R’
  Running ‘test-options-and-envvars.R’
  Running ‘test-r_bug18119.R’
  Running ‘test-startup.R’
  Running ‘test-utils,cluster.R’
  Running ‘test-utils.R’
 OK
* 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
* DONE

Status: 1 NOTE
See
  ‘/tmp/futureverse/parallelly.Rcheck/00check.log’
for details.