TileDB-R 0.31.0

[johnkerl]

[sc-59686]

CRAN-check details:

$ alias dreb='docker run --rm -it --entrypoint=/bin/bash'

$ dreb eddelbuettel/r2u:jammy

$ apt update

$ apt install -y cmake git pandoc

$ cd /tmp

$ git clone https://github.com/TileDB-Inc/TileDB-R

$ cd TileDB-R/

$ git checkout kerl/0.31.0

$ Rscript -e 'remotes::install_deps(".", TRUE)'

root@62f14f109be1:/tmp/TileDB-R# R CMD build .
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘tiledb’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘tiledb_0.31.0.tar.gz’

root@62f14f109be1:/tmp/TileDB-R# R CMD check --as-cran --no-manual *.tar.gz
* using log directory ‘/tmp/TileDB-R/tiledb.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘tiledb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tiledb’ version ‘0.31.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [7s/11s] Note_to_CRAN_maintainers
Maintainer: ‘Isaiah Norton <isaiah@tiledb.com>’
* 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 .dll and .exe files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘tiledb’ can be installed ... [101s/101s] OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 116.6Mb
  sub-directories of 1Mb or more:
    libs    23.1Mb
    tiledb  90.9Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... WARNING
A complete check needs the 'checkbashisms' script.
See section ‘Configure and cleanup’ in the ‘Writing R Extensions’
manual.
* 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 whether startup messages can be suppressed ... 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 ... [14s/14s] 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
 WARNING
‘qpdf’ is needed for checks on size reduction of PDFs
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘pkgconfig-test.R’
  Running ‘tinytest.R’ [46s/50s]
 [47s/51s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/tmp/TileDB-R/tiledb.Rcheck/00check.log’
for details.

[mojaveazure]

Just saw this, but we should be running tests on win-builder to use CRAN's machinery for Windows builds in addition to our own Linux machines