CRAN error (MKL)

[grantmcdermott]

https://www.stats.ox.ac.uk/pub/bdr/Rblas/MKL/jgd.out

Error log

* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/jgd.Rcheck’
* using R Under development (unstable) (2026-09-25 r90590)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
    GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-09-28 13:42:29 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘jgd/DESCRIPTION’ ... OK
* this is package ‘jgd’ version ‘0.2.0’
* 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 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 ‘jgd’ can be installed ... [4s/10s] OK
* used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* checking package 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 use of S3 registration ... 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 line widths ... 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [20s/170s]
 [21s/171s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(jgd)
  > 
  > test_check("jgd")
  jgd: connect(unix:///nonexistent-jgd-test.sock) failed: 2
  jgd: connect(unix:///nonexistent-jgd-env-test.sock) failed: 2
  jgd: connect(unix:///nonexistent-jgd-opt-test.sock) failed: 2
  jgd: connect(unix:///nonexistent-jgd-draw-test.sock) failed: 2
  jgd: connect(unix://localhost/nonexistent-jgd-localhost-test.sock) failed: 2
  jgd: connect(unix://localhost/nonexistent-jgd-localhost-draw.sock) failed: 2
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(tcp://127.0.0.1:1) failed: 111
  jgd: connect(/tmp/Rtmpyh2YV5/working_dir/RtmppPvdBs/jgd-test-ef37e425bc146.sock) failed: 111
  Saving _problems/test-group-ops-683.R
  jgd: connect(unix:///nonexistent-jgd-info-test.sock) failed: 2
  [ FAIL 1 | WARN 4 | SKIP 29 | PASS 169 ]
  
  ══ Skipped tests (29) ══════════════════════════════════════════════════════════
  • Named pipes only available on Windows (1): 'test-device-basic.R:83:3'
  • On CRAN (28): 'test-device-basic.R:3:1', 'test-device-basic.R:10:1',
    'test-device-basic.R:17:1', 'test-device-basic.R:25:1',
    'test-device-basic.R:36:1', 'test-device-basic.R:43:1',
    'test-device-basic.R:53:1', 'test-device-basic.R:59:1',
    'test-device-basic.R:65:1', 'test-device-basic.R:72:1',
    'test-device-basic.R:94:1', 'test-frame-ext.R:225:3',
    'test-frame-ext.R:429:3', 'test-frame-ext.R:491:3',
    'test-frame-output.R:216:1', 'test-frame-output.R:226:1',
    'test-frame-output.R:241:1', 'test-frame-output.R:251:1',
    'test-frame-output.R:271:1', 'test-group-ops.R:346:3',
    'test-group-ops.R:526:3', 'test-malformed-json.R:121:3',
    'test-malformed-json.R:151:3', 'test-malformed-json.R:171:3',
    'test-plotindex-buffering.R:132:3', 'test-resize-plotindex-content.R:133:3',
    'test-resize-plotindex-lines.R:128:3', 'test-resize-plotnumber.R:132:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-group-ops.R:675:3'): unclosed group is auto-closed at device close with warning ──
  Error in `if (bg$get_exit_status() != 0) {     stop("Mock server exited with error: ", bg$read_error()) }`: argument is of length zero
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(...) at test-group-ops.R:675:3
   2. │ └─testthat:::expect_condition_matching_(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─jgd:::with_mock_jgd(...)
   8.   └─server$collect() at ./helper-mock-server.R:337:3
  
  [ FAIL 1 | WARN 4 | SKIP 29 | PASS 169 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/jgd.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:58.01, 34.85 + 8.86

@eitsupi I'm slammed at work for the next week. (And also have to resolve a separate vscode-R version issue.) Are you able to take a look in the interim? Thanks!

[eitsupi]

I took a look. This does not appear to be MKL-specific.

The immediate failure comes from the mock-server test infrastructure.
On Unix, start_mock_server_local() currently treats the socket file appearing as the readiness signal, but the underlying socket is created with bind() followed by listen().
This leaves a small window where the path exists but the server is not yet listening, which is consistent with the preceding connect(...sock) failed: 111 in the log.

After that failed connection, the mock server remains waiting for a client, while collect() waits only 10 seconds and assumes get_exit_status() is non-NULL.
processx explicitly returns NULL there if the process is still running, which explains the final argument is of length zero.

I think the appropriate fix is to use an explicit readiness file on Unix as well, written only after conn_create_unix_socket() has returned, and to make collect() handle a NULL/NA exit status defensively. I haven't decided yet whether I'll have time to prepare the fix myself.

---

Separately, going forward, please do not bump the jgd version or submit a CRAN release without discussing it with me first.
#74 was opened and merged, and the 0.2.0 release was prepared, before I had any opportunity to review or even know that a release was being made.
Release decisions create follow-up maintenance work for both of us, so I need future releases to be coordinated in advance.

[eitsupi]

#76