[R][CI] r-recheck-most test failing

[hiroyuki-sato]

Describe the bug, including details regarding any error messages, version, and platform.

I'm not familiar with R, but the CI(r-recheck-most) is failing, and it doesn’t look like anyone has reported it yet. Just in case, I wanted to report it, so I created this issue.

@github-actions crossbow submit -g r fail r-recheck-most test

#50610 (comment)
#50651 (comment)

duckdb error?

Package: duckdb
Check: whether package can be installed
Old result: OK
New result: ERROR
Error: Found potential problems
Execution halted
Error: Process completed with exit code 1.

Run cat("\n------- Check results summary ------\n")
  cat("\n------- Check results summary ------\n")
  tools::summarize_check_packages_in_dir_results("newpkg-checklogs")
  
  # Check for regressions
  cat("\n------- Check for regressions ------\n")
  changes <- tools::check_packages_in_dir_changes("newpkg-checklogs", "oldpkg-checklogs")
  if(nrow(changes)){
    cat("Changes:\n")
    print(changes)
    stop("Found potential problems")
  } else {
    cat("No changes between old and new version\n")
  }
  shell: Rscript {0}
  env:
    R_LIBS_USER: /home/runner/work/crossbow/crossbow/pkglib
    _R_CHECK_FORCE_SUGGESTS_: FALSE
    _R_CHECK_CRAN_INCOMING_: FALSE
    _R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_: TRUE
    _R_CHECK_ELAPSED_TIMEOUT_: 3600
    GITHUB_ACTIONS: 
    CI: 

------- Check results summary ------
Check status summary:
                  ERROR NOTE  OK
  Source packages     0    1   0
  Reverse depends     4   21 142

Check results summary:
arrow ... NOTE
* checking compiled code ... NOTE
rdepends_ABCDscores ... OK
rdepends_AFR ... OK
rdepends_APCalign ... OK
rdepends_ARDECO ... OK
rdepends_ClickHouseHTTP ... OK
rdepends_DBI ... OK
rdepends_DominoDataR ... OK
rdepends_EEAaq ... OK
rdepends_EZbakR ... OK
rdepends_Eunomia ... OK
rdepends_FakeDataR ... OK
rdepends_GGIR ... OK
rdepends_LifemapR ... OK
rdepends_MolgenisArmadillo ... OK
rdepends_NBDCtools ... OK
rdepends_OlinkAnalyze ... OK
rdepends_RAthena ... OK
rdepends_RKaggle ... OK
rdepends_RSQLite.toolkit ... OK
rdepends_RaMS ... OK
rdepends_SQL ... OK
rdepends_Seurat ... NOTE
* checking compiled code ... NOTE
rdepends_SkeletalVis ... OK
rdepends_a5R ... NOTE
* checking compiled code ... NOTE
rdepends_aNCA ... OK
rdepends_adbi ... OK
rdepends_analogsea ... OK
rdepends_antaresRead ... OK
rdepends_araponga ... OK
rdepends_arkdb ... OK
rdepends_assemblykor ... OK
rdepends_birdnetR ... OK
rdepends_blockr.io ... OK
rdepends_brickster ... OK
rdepends_cansim ... OK
rdepends_capesR ... OK
rdepends_carbondata ... OK
rdepends_censo2022arg ... NOTE
* checking compiled code ... NOTE
rdepends_censobr ... OK
rdepends_citestR ... OK
rdepends_clinTrialData ... OK
rdepends_cnefetools ... OK
rdepends_connector ... OK
rdepends_connector.databricks ... OK
rdepends_coxstream ... NOTE
* checking compiled code ... NOTE
rdepends_craftgrn ... NOTE
* checking compiled code ... NOTE
rdepends_crawlee ... OK
rdepends_datadiff ... OK
rdepends_dataverifyr ... OK
rdepends_datazoom.social ... OK
rdepends_db2pq ... OK
rdepends_dbMatrix ... NOTE
* checking compiled code ... NOTE
rdepends_diagFDR ... OK
rdepends_diffdfs ... OK
rdepends_dpkg ... OK
rdepends_dtsmartr ... OK
rdepends_duckdb ... ERROR
* checking whether package ‘duckdb’ can be installed ... ERROR
rdepends_duckplyr ... OK
rdepends_duckspatial ... OK
rdepends_eam ... NOTE
* checking compiled code ... NOTE
rdepends_ebirdst ... OK
rdepends_econdatasets ... OK
rdepends_eyeris ... OK
rdepends_fabricQueryR ... OK
rdepends_fastreg ... OK
rdepends_feather ... OK
rdepends_ffm ... OK
rdepends_filecacher ... OK
rdepends_finnts ... OK
rdepends_foundry ... OK
rdepends_framework ... ERROR
* checking tests ... ERROR
rdepends_freestiler ... NOTE
* checking compiled code ... NOTE
rdepends_gatoRs ... OK
rdepends_gbifdb ... OK
rdepends_geoarrow ... NOTE
* checking compiled code ... NOTE
rdepends_geobr ... OK
rdepends_geocodebr ... OK
rdepends_geoflow ... NOTE
* checking dependencies in R code ... NOTE
rdepends_geslaR ... OK
rdepends_golfastr ... OK
rdepends_greenR ... NOTE
* checking compiled code ... NOTE
rdepends_hawkinR ... OK
rdepends_healthbR ... NOTE
* checking compiled code ... NOTE
rdepends_hubUtils ... OK
rdepends_huggingfaceR ... OK
rdepends_isoorbi ... OK
rdepends_isoreader2 ... OK
rdepends_kuzuR ... OK
rdepends_laminr ... OK
rdepends_lbugr ... OK
rdepends_leakr ... OK
rdepends_lessR ... OK
rdepends_locatr ... OK
rdepends_marginaleffects ... OK
rdepends_mark ... OK
rdepends_mrgsim.parallel ... OK
rdepends_multimolang ... OK
rdepends_myIO ... OK
rdepends_nanoarrow ... NOTE
* checking compiled code ... NOTE
rdepends_nanoparquet ... OK
rdepends_nascaR.data ... OK
rdepends_nc ... OK
rdepends_neonUtilities ... OK
rdepends_neonstore ... NOTE
* checking DESCRIPTION meta-information ... NOTE
rdepends_nflreadr ... OK
rdepends_nhanesdata ... OK
rdepends_nhdplusTools ... OK
rdepends_nhlscraper ... NOTE
* checking compiled code ... NOTE
rdepends_noctua ... OK
rdepends_omock ... OK
rdepends_opencpu ... OK
rdepends_orbital ... OK
rdepends_osdc ... OK
rdepends_overturemapsr ... OK
rdepends_parqr ... OK
rdepends_parquetize ... OK
rdepends_perspectiveR ... OK
rdepends_pins ... ERROR
* checking tests ... ERROR
rdepends_pipr ... OK
rdepends_pleioh2g ... OK
rdepends_plumber ... OK
rdepends_plumber2 ... OK
rdepends_pointblank ... OK
rdepends_positron.tutorials ... OK
rdepends_precviasBR ... OK
rdepends_pxmake ... OK
rdepends_pysparklyr ... OK
rdepends_r4ds.tutorials ... OK
rdepends_rDeckgl ... OK
rdepends_rMIDAS2 ... OK
rdepends_rMosaic ... OK
rdepends_radiant.data ... OK
rdepends_rb3 ... OK
rdepends_rcdf ... OK
rdepends_receptiviti ... OK
rdepends_redquack ... OK
rdepends_repfun ... OK
rdepends_rerddapUtils ... OK
rdepends_retraction ... OK
rdepends_riemtan ... NOTE
* checking compiled code ... NOTE
rdepends_rio ... OK
rdepends_rsynthbio ... OK
rdepends_rtemis ... OK
rdepends_rxode2 ... OK
rdepends_sakura ... NOTE
* checking compiled code ... NOTE
rdepends_sfarrow ... OK
rdepends_sooty ... OK
rdepends_sparklyr ... OK
rdepends_spatialGE ... NOTE
* checking compiled code ... NOTE
rdepends_starvz ... NOTE
* checking compiled code ... NOTE
rdepends_strand ... OK
rdepends_tidyCDISC ... OK
rdepends_tidylaslog ... OK
rdepends_tidyquery ... OK
rdepends_tiledb ... NOTE
* checking compiled code ... NOTE
rdepends_tinytrail ... OK
rdepends_toonlite ... NOTE
* checking compiled code ... NOTE
rdepends_topics ... OK
rdepends_torchvision ... OK
rdepends_umweltapir ... OK
rdepends_verdata ... OK
rdepends_vetiver ... ERROR
* checking tests ... ERROR
rdepends_vigicaen ... OK
rdepends_volrisk ... OK
rdepends_workspace ... OK
rdepends_worldmet ... OK
rdepends_z22 ... OK

------- Check for regressions ------
Changes:
Package: EZbakR
Check: R code for possible problems
Old result: NOTE
New result: OK

Package: duckdb
Check: compiled code
Old result: NOTE

Package: duckdb
Check: whether package can be installed
Old result: OK
New result: ERROR
Error: Found potential problems
Execution halted
Error: Process completed with exit code 1.

Component(s)

Continuous Integration

[KHARSHAVARDHAN-eng]

Investigation of the CI artifacts from the failing r-recheck-most Crossbow run (#30600965885) shows that this failure was caused by a transient compilation error in the baseline oldpkg environment rather than a regression in Apache Arrow.

Log Findings

1. duckdb (oldpkg):
   duckdb source compilation failed during the baseline oldpkg (arrow 25.0.0) check due to a compiler process termination:

   make: *** wait: No child processes. Stop.
   make: *** Waiting for unfinished jobs....
   make: *** wait: No child processes. Stop.
   ERROR: compilation failed for package 'duckdb'
   * removing '/__w/crossbow/crossbow/oldpkg/duckdb.Rcheck/duckdb'
   

2. duckdb (newpkg):
   duckdb compiled and installed cleanly against development arrow (25.0.0.9000):

   * checking whether package 'duckdb' can be installed ... OK
   * checking tests ... OK
   Status: 1 NOTE
   

3. framework / pins / vetiver:
   All three packages have identical test failure counts in both oldpkg and newpkg:

   • framework: FAIL 3 | WARN 31 | SKIP 97 | PASS 634 (Identical in oldpkg & newpkg)
   • pins: FAIL 1 | SKIP 41 | PASS 130 (Identical in oldpkg & newpkg)
   • vetiver: FAIL 2 | WARN 2 | SKIP 71 | PASS 226 (Identical in oldpkg & newpkg)

Across all 167 reverse dependencies checked, 0 packages experienced regressions in newpkg.

Root Cause & CI Mechanism

The CI failure in the Show results step occurs because r-devel/recheck invokes R's tools::check_packages_in_dir_changes("newpkg-checklogs", "oldpkg-checklogs"). This function flags any package status difference between oldpkg and newpkg as a change, even when a package transitions from ERROR in oldpkg to OK in newpkg, leading to stop("Found potential problems").

Recommendation

No code or CI changes are needed in Apache Arrow. A re-run of r-recheck-most or closing this issue as transient is recommended.