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update cran comments
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jeffreyhanson committed Feb 14, 2024
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Dear CRAN volunteers,

Thank you very much for reviewing this submission. This submission aims to fix the issues causing the package to fail CRAN checks. Specifically, it fixes the compiler warnings (e.g., on Debian-clang flavor) and unit test errors (i.e., on Fedora flavors). I have also taken this opportunity to update the package to be compatible with the upcoming Matrix package (version >= 1.4-2), whilst maintaining backwards compatibility with previous versions.
Thank you for reviewing this submission. This submission contains updates for the _surveyvoi_ package to fix (i) aliasing for the package manual entry, (ii) uneeded C++11 specification, and (iii) installation for Windows on arm64 systems.

Cheers,

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# R CMD check results

0 errors | 0 warnings | 2 notes
0 errors | 0 warnings | 3 notes

# Notes

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**The package uses the gurobi R package that is distributed with Gurobi software suite (and not available on CRAN). The DESCRIPTION, README, and package documentation provide instructions for installing the gurobi R package.**

* Found the following (possibly) invalid URLs:
URL: https://doi.org/10.1111/1365-2664.14309
From: README.md
Status: 503
Message: Service Unavailable
* found the following (possibly) invalid URLs:
URL: https://support.gurobi.com/hc/en-us/articles/4534161999889-How-do-I-install-Gurobi-Optimizer
From: man/approx_optimal_survey_scheme.Rd
man/env_div_survey_scheme.Rd
man/feasible_survey_schemes.Rd
man/geo_cov_survey_scheme.Rd
man/optimal_survey_scheme.Rd
man/surveyvoi.Rd
man/weighted_survey_scheme.Rd
inst/doc/surveyvoi.html
Status: 403
Message: Forbidden

**I have checked this URL and can confirm that it is valid.**

# System requirements

The package has system requirements. Some of these requirements are mandatory -- and are required for successful installation -- and others are optional. To ensure that all mandatory requirements are available on CRAN systems, I have checked the software installed on CRAN's various systems. Briefly, this information was obtained from the [Windows toolchain](https://github.com/r-windows/rtools-packages); [macOS toolchain](https://github.com/R-macos/recipes) toolchains; [rcheckserver Debian meta-package](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages); and via correspondence with CRAN volunteers.

Below, I have provided a markdown table detailing whether each system requirement is optional or mandatory under various operating systems. I have also included details and URLs verifying the availability of mandatory system requirements on each of CRAN's systems. Where URLs are provided for certain software on certain operating systems (e.g., for gmpxx on Windows), the URL points directly to the source code for the relevant toolchain (e.g., the RTools for Windows) for including the software.

| Software | Debian | Fedora | Windows | macOS |
|:--------|:---------:|:--------:|:------:|:------:|
| JAGS (>= 4.3.0) | Optional | Optional |Optional | Optional |
| fftw3 (>= 3.3) | Mandatory (1) | Mandatory (1) | Mandatory (1) | Mandatory (1) |
| gmp (>= 6.2.1) | Mandatory (2) | Mandatory (3) | [Mandatory](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) |
| gmpxx (>= 6.2.1) | [Mandatory (2)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | Mandatory (3) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) |
| mpfr (>= 4.1.0) | [Mandatory (4)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | Mandatory (4) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-mpfr/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/mpfr) |
| autoconf (>= 2.69) | Optional | Optional | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/autoconf) |
| automake (>= 1.16.5) | Optional | Optional | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/automake) |

(1) This requirement is available on all of CRAN's servers because the PoissonBinomial R package relies on the fftw3 library as a system requirement and this package passes checks on all systems (see https://cran.r-project.org/package=PoissonBinomial).

(2) This requirement is available on CRAN's Debian server(s) because it is available via the Debian libgmp3-dev package, and this package is a dependency of the rcheckserver Debian meta-package.

(3) This requirement is available on CRAN's Fedora server(s) because Prof. Brian Ripely checked that that the gmp-devel RPM is available on each machine (i.e., https://fedora.pkgs.org/35/fedora-x86_64/gmp-devel-6.2.0-7.fc35.i686.rpm.html) (Prof Brian Ripley, personal communication, August 25, 2022).

(4) This requirement is available on all of CRAN's servers because the Rmpfr R package relies on the mpfr library as a system requirement and this package passes checks on all systems (see https://cran.r-project.org/package=Rmpfr).

# Downstream dependencies

There are no existing packages that depend on this package.

# Comments from CRAN volunteers on previous submissions

* Correct your SystemRequirements.

**Thanks for catching this. I have added the C++ bindings for the GMP library (i.e., gmpxx) to the SystemRequirements field, and updated the minimum versions number for gmp and gmpxx.**

* Correct your configure script (see 'Writing R Extensions' for recommendations for using autoconf to write a *reliable* script, including logging what it does).

**Thank you for the suggestion. I have updated the configure script to use autoconf and provide logging.**

* Inform the maintainers of binary packages, as this is a new
requirement on external software. It seems the macOS ones are not built
with C++ bindings (and you could and should have checked for yourself
from the published 'recipes' at https://github.com/R-macos/recipes).

**Thank you very much for this advice. I am sorry that I did not check these requirements prior to my previous submission. After submitting a pull request to the maintainer of the macOS binary package (https://github.com/R-macos/recipes/pull/19), the macOS libraries now include C++ bindings for GMP. I have also confirmed with the maintainer of the Windows binary packages that the C++ bindings for GMP are available via Rtools (https://github.com/rwinlib/utils/issues/1#issuecomment-912371834). Additionally, to ensure that outdated versions of GMP do not cause issues on Windows systems, the package now uses the RWinLib infrastructure to obtain recent versions of gmp and gmpxx (https://github.com/rwinlib/gmp), see `tools/winlibs.R`). Since the package passes checks on the WinBuilder and macOS builder platforms, I am hopeful that these issues have been resolved.**

* Please always add all authors, contributors and copyright holders in the Authors@R field with the appropriate roles. e.g.: Free Software Foundation, Inc. Please explain in the submission comments what you did about this issue.

**This comment was raised on a previous submission wherein the Free Software Foundation was listed as a copyright holder. Previously, the foundation was listed a copyright holder because the package contained a header file from the gmp library to help ensure that dependencies were available. Since the dependencies should now all be available on CRAN's systems, the header file has been removed and, as such, the foundation has been removed as a copyright holder.**

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