cran-comments.md

In stan-dev/projpred: Projection Predictive Feature Selection

Test environments

• Local:
  • R version 4.3.2 (2023-10-31) on Ubuntu 22.04.3 LTS system (platform: x86_64-pc-linux-gnu (64-bit))
  • R version 4.2.3 (2023-03-15 ucrt) on Windows 10 system (platform: x86_64-w64-mingw32 (64-bit))
• win-builder:
  • R-devel (R Under development (unstable) (2023-12-13 r85679 ucrt))
  • R-release (R version 4.3.2 (2023-10-31 ucrt))
  • R-oldrelease (R version 4.2.3 (2023-03-15 ucrt))
• macOS builder:
  • R version 4.3.0 Patched (2023-05-18 r84451) on macOS Ventura 13.3.1 system (platform: aarch64-apple-darwin20 (64-bit)) (r-release-macosx-arm64|4.3.0|macosx|macOS 13.3.1 (22E261)|Mac mini|Apple M1||en_US.UTF-8|macOS 11.3|clang-1403.0.22.14.1|GNU Fortran (GCC) 12.2.0)

R CMD check results

Except for the R-oldrelease check on win-builder (see below), all checks gave neither ERRORs nor WARNINGs.

Local checks

Linux

The local check with R version 4.3.2 under Linux gave the following NOTE:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Frank Weber <fweber144[ at ]protonmail.com>'

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

Currently, the 'cmdstanr' package (https://mc-stan.org/cmdstanr/) is not available on CRAN yet. The 'cmdstanr' backend can be used in 'projpred''s unit tests, but it is not necessary for 'projpred' to work. As this NOTE says, we have added the repository URL for the 'cmdstanr' package to the 'DESCRIPTION' file (field 'Additional_repositories').

Windows

The local check with R version 4.2.3 under Windows gave the following NOTEs:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Frank Weber <fweber144[ at ]protonmail.com>'

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/0471200611
    From: inst/doc/latent.html
    Status: 403
    Message: Forbidden

* checking package dependencies ... NOTE
Package suggested but not available for checking: 'unix'

* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'unix'

* checking examples ... [18s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
as.matrix.projection 5.45    0.3    5.75

As can be seen in the first NOTE, the URL reported as inaccessible is created from a DOI. In fact, this URL is accessible, so we think this can be safely ignored. For an explanation of the 'cmdstanr'-related content of the first NOTE, see above.

The 'unix' package mentioned in the second and the third NOTE is not available for Windows, but it is only mentioned in 'projpred''s documentation, so has no impact on functionality.

The runtime of the 'as.matrix.projection' example (see the fourth NOTE) may sometimes be slightly > 10s (see also below).

win-builder checks

R-devel

The R-devel check on win-builder gave the following NOTEs:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Frank Weber <fweber144[ at ]protonmail.com>'

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

* checking package dependencies ... NOTE
Package suggested but not available for checking: 'unix'

For an explanation of these NOTEs, see the explanations for the local checks above.

R-release

The R-release check on win-builder gave the following NOTEs:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Frank Weber <fweber144[ at ]protonmail.com>'

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'unix', 'cmdstanr'

* checking examples ... [38s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                      user system elapsed
as.matrix.projection 11.02   0.53   11.52

For an explanation of these NOTEs, see the explanations for the local checks above.

R-oldrelease

The R-oldrelease check on win-builder gave the following NOTEs:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Frank Weber <fweber144[ at ]protonmail.com>'

Suggests or Enhances not in mainstream repositories:
  cmdstanr
Availability using Additional_repositories specification:
  cmdstanr   yes   https://mc-stan.org/r-packages/

Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/0471200611
    From: inst/doc/latent.html
    Status: 403
    Message: Forbidden

* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'unix', 'cmdstanr'

* checking examples ... [42s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                      user system elapsed
as.matrix.projection 12.21   0.53   12.76

For an explanation of these NOTEs, see the explanations for the local checks above.

The R-oldrelease check on win-builder also gave the following ERROR:

Running the tests in 'tests/testthat.R' failed.
[...]
Caused by error in `initializePtr()`:
  ! function 'cholmod_factor_ldetA' not provided by package 'Matrix'
[...]
lme4 (local) initializePtr()

However, this error was not reproducible on a local Windows system with R 4.2.3 (see the local checks above). Furthermore, this error does not seem to be related to 'projpred', but rather at least one of its dependencies. Hence, there is probably nothing that can be done in 'projpred' to avoid this error.

macOS builder

The macOS builder check gave the following NOTE:

* checking package dependencies ... NOTE
Package suggested but not available for checking: 'cmdstanr'

For an explanation of this NOTE, see the explanations for the local checks above.

Downstream dependencies

There is one downstream dependency for this package: 'brms'. This downstream dependency has been checked locally (with the 'projpred' version submitted here).

stan-dev/projpred documentation built on April 15, 2024, 11:10 p.m.