[Rcpp-devel] Help with R CMD CHECK for rtree package

[Dirk Eddelbuettel]

On 5 May 2021 at 15:54, Kent Johnson wrote:
| I am a maintainer of this package - https://github.com/akoyabio/rtree - originally inspired by this example - https://gallery.rcpp.org/articles/Rtree-examples/. This package wraps the rtree implementation from BH 1.7.2.0-3 to provide fast methods for finding points nearby to other points in large data sets.
| 
|  I want to submit the package to CRAN but I have a CMD CHECK warning on Windows that I can't resolve.
| 
| Running CMD CHECK from GitHub Actions, on Microsoft Windows Server 2019 10.0.17763, I get this error message:
| -- R CMD check results ---------------------------------------- rtree 0.2.0 ----
| Duration: 1m 42.7s
| 
| > checking whether package 'rtree' can be installed ... WARNING
|   See below...
| 
| 0 errors v | 1 warning x | 0 notes v
| Error: Error: R CMD check found WARNINGs
| Execution halted
| Error: Process completed with exit code 1.

It actually failed for me on RHub and on Win-Builder once I removed the
hard-equality constraint on a BH version no longer on CRAN:

  LinkingTo: Rcpp, BH (== 1.72.0-3)

That makes in unbuildable in most situations, I fear.
 
| The full output is here: https://github.com/akoyabio/rtree/runs/2502841486?check_suite_focus=true
| The message says "See below..." but there is nothing below?
| 
| Running on my local Windows 10 PC I get this warning and a note:
| -- R CMD check results ---------------------------------------- rtree 0.2.0 ----
| Duration: 1m 2.2s
| 
| > checking whether package 'rtree' can be installed ... WARNING
|   See below...
| 
| > checking compiled code ... NOTE
|   Note: information on .o files for x64 is not available
|   File 'C:/Research/rtree.Rcheck/rtree/libs/x64/rtree.dll':
|     Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
|     Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
|     Found 'printf', possibly from 'printf' (C)

We would have to find out where this comes from.  But for starters, can you
make it work at your end with the currently released BH version, 1.75.0-0 ?

Dirk

|   Compiled code should not call entry points which might terminate R nor
|   write to stdout/stderr instead of to the console, nor use Fortran I/O
|   nor system RNGs. The detected symbols are linked into the code but
|   might come from libraries and not actually be called.
| 
|   See 'Writing portable packages' in the 'Writing R Extensions' manual.
| 
| 0 errors v | 1 warning x | 1 note x
| Error: R CMD check found WARNINGs
| Execution halted
| 
| Exited with status 1.
| 
| Again I have the "See below..." message and a confusing NOTE - I do not have any calls to abort, exit or printf in my code.
| 
| Any help in fixing the warning and note is much appreciated. If this is not an appropriate place to ask, please let me know what would be better. I'm perplexed.
| 
| Thank you,
| Kent Johnson
| Principal Software Developer
| Akoya Biosciences
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-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org