dbSpatial

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘class_structure.Rmd’ using rmarkdown

Quitting from class_structure.Rmd:32-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dbSendQuery()`:
! Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-989860c0-6cc3-41ea-822f-810e485a62d1.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
---
Backtrace:
     ▆
  1. └─dbSpatial::dbSpatial(...)
  2.   ├─base::suppressMessages(loadSpatial(conn = conn))
  3.   │ └─base::withCallingHandlers(...)
  4.   └─dbSpatial::loadSpatial(conn = conn)
  5.     ├─DBI::dbExecute(conn, query)
  6.     └─DBI::dbExecute(conn, query)
  7.       ├─DBI::dbSendStatement(conn, statement, ...)
  8.       └─DBI::dbSendStatement(conn, statement, ...)
  9.         ├─DBI::dbSendQuery(con
...[truncated]...
::loadSpatial(conn = conn)
  5.     ├─DBI::dbExecute(conn, query)
  6.     └─DBI::dbExecute(conn, query)
  7.       ├─DBI::dbSendStatement(conn, statement, ...)
  8.       └─DBI::dbSendStatement(conn, statement, ...)
  9.         ├─DBI::dbSendQuery(conn, statement, ...)
 10.         └─duckdb::dbSendQuery(conn, statement, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatial_operations.Rmd' failed with diagnostics:
Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-5a0e0350-48fa-42da-b214-a39158d0aaa9.duckdb_extension": Read-only file system
ℹ Context: rapi_prepare
ℹ Error type: INVALID
--- failed re-building ‘spatial_operations.Rmd’

SUMMARY: processing the following files failed:
  ‘class_structure.Rmd’ ‘getting_started.Rmd’ ‘spatial_operations.Rmd’

Error: Vignette re-building failed.
Execution halted

tests

Running ‘testthat.R’ [25s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbSpatial)
  > 
  > test_check("dbSpatial")
  Saving _problems/test-extract-15.R
  Saving _problems/test-spatial-functions-15.R
  Saving _problems/test-spatial-functions-35.R
  Saving _problems/test-spatial-functions-70.R
  Saving _problems/test-spatial-functions-95.R
  Saving _problems/test-spatial-functions-117.R
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-extract.R:8:3'): $ extracts column values ──────────────────────
  Error in `dbSendQuery(conn, statement, ...)`: Invalid Error: IO Error: Cannot open file "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/duckdb/extensions/v1.5.4/linux_amd64/spatial.duckdb_extension.tmp-5ecceff8-23c0-44b8-9370-c5df2a4d3005.duckdb_extension": Read-only file system
  i Context: rapi_prepare
  i Error type: INVALID

...[truncated]...
rethrow_rapi_prepare(conn@conn_ref, statement, env)
   13. │             ├─rlang::try_fetch(...)
   14. │             │ ├─base::tryCatch(...)
   15. │             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   16. │             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. │             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   18. │             │ └─base::withCallingHandlers(...)
   19. │             └─duckdb:::rapi_prepare(conn, query, env)
   20. ├─duckdb (local) `<fn>`(...)
   21. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
   22. │   └─rlang:::signal_abort(cnd, .file)
   23. │     └─base::signalCondition(cnd)
   24. └─rlang (local) `<fn>`(`<dckdb_rr>`)
   25.   └─handlers[[1L]](cnd)
   26.     └─duckdb:::rethrow_error_from_rapi(e, call)
   27.       └─rlang::abort(msg, call = call)
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘class_structure.Rmd’ using rmarkdown

Quitting from class_structure.Rmd:34-54 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `duckdb_result()`:
! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/tmp/Rtmp4DryzD/working_dir/RtmpTbvzam/dbSpatial-duckdb-extensions/v1.5.4/linux_amd64/spatial.duckdb_extension" threw an exception: "Missing DB manager"
ℹ Context: rapi_execute
ℹ Error type: INVALID
---
Backtrace:
     ▆
  1. └─dbSpatial::dbSpatial(...)
  2.   ├─base::suppressMessages(loadSpatial(conn = conn))
  3.   │ └─base::withCallingHandlers(...)
  4.   └─dbSpatial::loadSpatial(conn = conn)
  5.     ├─DBI::dbExecute(conn, "LOAD spatial")
  6.     └─DBI::dbExecute(conn, "LOAD spatial")
  7.       ├─DBI::dbSendStatement(conn, statement, ...)
  8.       └─DBI::dbSendStatement(conn, statement, ...)
  9.         ├─DB
...[truncated]...
eave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA)})
56: tools:::.buildOneVignette("spatial_operations.Rmd", "/data/gannet/ripley/R/packages/tests-clang/dbSpatial.Rcheck/vign_test/dbSpatial",     TRUE, FALSE, "spatial_operations", "UTF-8", "/tmp/Rtmp4DryzD/working_dir/RtmprEHBoE/file329be76ceb0fdb.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
  ‘class_structure.Rmd’ ‘getting_started.Rmd’ ‘spatial_operations.Rmd’

Error: Vignette re-building failed.
Execution halted