* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pathling.Rcheck’
* using R Under development (unstable) (2025-08-30 r88742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘pathling/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathling’ version ‘8.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/6s] NOTE
Maintainer: ‘"Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>’

New maintainer:
  "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>
Old maintainer(s):
  "Australian e-Health Research Centre, CSIRO"
    <ontoserver-support@csiro.au>

Found the following (possibly) invalid URLs:
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#datasets
    From: man/pathling_read_datasets.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#delta-lake
    From: man/pathling_read_delta.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#delta-lake-1
    From: man/ds_write_delta.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#fhir-bulk-data-api
    From: man/pathling_read_bulk.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#fhir-bundles
    From: man/pathling_read_bundles.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#managed-tables
    From: man/pathling_read_tables.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#managed-tables-1
    From: man/ds_write_tables.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#ndjson
    From: man/pathling_read_ndjson.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#ndjson-1
    From: man/ds_write_ndjson.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#parquet
    From: man/pathling_read_parquet.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/fhirpath-query#parquet-1
    From: man/ds_write_parquet.Rd
    Status: 404
    Message: Not Found
  URL: https://pathling.csiro.au/docs/libraries/sql-on-fhir
    From: man/ds_view.Rd
    Status: 404
    Message: Not Found
* 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 ‘pathling’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘purrr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
pathling_read_bulk: no visible global function definition for
  ‘spark_connection’
pathling_read_bulk: no visible global function definition for
  ‘invoke_static’
pathling_read_bulk: no visible binding for global variable ‘duration’
pathling_read_bulk: no visible global function definition for
  ‘j_invoke_new’
to_java_list: no visible global function definition for ‘j_invoke_new’
Undefined global functions or variables:
  duration invoke_static j_invoke_new spark_connection
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs