Skip to content

Latest commit

 

History

History
395 lines (302 loc) · 13.3 KB

cran-comments.md

File metadata and controls

395 lines (302 loc) · 13.3 KB

Resubmission (version 0.2.1)

Reduce the example run time for suspicious_env_outliers to pass the check. This time, force the example to use only one core, so the ratio of elapsed time to user time should be smaller.

Update (version 0.2.1)

This is a minor update for the package, addressing the recent upgrade of the fastshap package and lightening the examples to run in under 5 seconds.

Test environments

  1. Local macOS Ventura 13.4, R version 4.3.0

  2. Github actions

  • Windows Server 2022 x64 (build 20348), R version 4.3.0 (2023-04-21 ucrt)
  • Ubuntu 22.04.2 LTS, R version 4.3.0 (2023-04-21)
  • Ubuntu 22.04.2 LTS, R Under development (unstable) (2023-06-07 r84523)
  • Ubuntu 22.04.2 LTS, R version 4.2.3 (2023-03-15)
  • macOS Monterey 12.6.5, R version 4.3.0 (2023-04-21)
  1. devtools check
  • Windows, R Under development (unstable) (2023-06-09 r84528 ucrt), devtools::check_win_devel()
  • Windows, R version 4.3.0 (2023-04-21 ucrt), devtools::check_win_release()
  • Windows, R version 4.2.3 (2023-03-15 ucrt), devtools::check_win_oldrelease()
  • macOS 13.3.1 (22E261), R version 4.3.0 Patched (2023-05-18 r84451), devtools::check_mac_release()
  • Fedora Linux R-devel clang gfortran, Ubuntu Linux 20.04.1 LTS R-release GCC, Windows Server 2022 R-devel 64 bit, devtools::check_rhub()

R CMD check

There were no ERRORs or WARNINGs.

There were two NOTEs that are only found on Windows (r-hub):

* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ''NULL''
* checking for detritus in the temp directory ... NOTE
Found the following files/directories:
  'lastMiKTeXException'

As noted in R-hub issue #560, the first NOTE could be due to something in R-hub and can be ignored. And as noted in R-hub issue #503, the second NOTE could be due to a bug/crash in MiKTeX and can likely be ignored.

There was one NOTE only found on r-hub Linux:

* checking HTML version of manual ... NOTE
Skipping checking HTML validation: no command 'tidy' found
```
This NOTE is unrelated to my package and can likely be ignored.

## Resubmission (version 0.2.0)

Reduce example run time for `detect_envi_change` and `variable_contrib` to pass the check. Because I cannot reproduce this issue on any other machines, I have to resubmit the package to figure it out.

## Update (version 0.2.0)

This is a major update for the pacakge. Overall, Shapley values-based functions were generalized for external models, and new functions were added to diagnose the impacts of a changing environment. Details can be found in `NEWS.md`.

### Test environments

1. Local macOS Ventura 13.1, R version 4.0.4 and macOS Monterey 12.6, R version 4.2.1

2. Github actions

- Windows Server x64 (build 20348), R version 4.2.2 (2022-10-31 ucrt)
- Ubuntu 22.04.1 LTS, R version 4.2.2 (2022-10-31)
- Ubuntu 22.04.1 LTS, R Under development (unstable) (2023-01-12 r83603)
- Ubuntu 22.04.1 LTS, R version 4.1.3 (2022-03-10)
- macOS Big Sur/Monterey 10.16, R version 4.2.2 (2022-10-31)

3. `devtools` check

- Windows, R Under development (unstable) (2023-01-13 r83612 ucrt), `devtools::check_win_devel()`
- Windows, R version 4.2.2 (2022-10-31 ucrt), `devtools::check_win_release()`
- Windows, R version 4.1.3 (2022-03-10), `devtools::check_win_oldrelease()`
- MacOS 11.5.2, R version 4.2.1 Patched (2022-06-23 r82516), `devtools::check_mac_release()`
- Linux, `devtools::check_rhub()`

### R CMD check

There is no error or warning. It got one note about "checking CRAN incoming feasibility". Some machines (e.g. Windows) detected some possible invalid URLs/DOIs and miss-spellings (as listed below). I manually checked them and they are fine.

```
Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/joc.5086
    From: man/future_worldclim2.Rd
          man/worldclim2.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1109/ICDM.2008.17
    From: man/isotree_po.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1109/TKDE.2019.2947676
    From: man/isotree_po.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/jbi.13402
    From: man/evaluate_po.Rd
    Status: 503
    Message: Service Unavailable

Found the following (possibly) invalid DOIs:
  DOI: 10.1002/joc.5086
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
  DOI: 10.1109/ICDM.2008.17
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
  DOI: 10.1109/TKDE.2019.2947676
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
    
Possibly mis-spelled words in DESCRIPTION:
  Brunner (15:9)
  Caporaso (30:38)
  Fick (28:66)
  Guha (17:5)
  Hariri (14:51)
  Hijmans (29:14)
  Kononenko (23:60)
  Liu (13:45, 15:63)
  Lundberg (21:45)
  Mishra (17:15)
  Noce (30:28)
  SCiForest (12:54)
  Santini (30:55)
  Schrijvers (17:39)
  Shapley (19:39, 20:58)
  Zhou (14:5, 16:20)
  bioclimatic (28:5)
  iForest (11:50)
  itsdm (24:45)
  trumbelj (23:43)
```

## Update (version 0.1.3)

Changes to this version are minor and can be found in `NEWS.md`. Fixed a bug in function `print.VariableAnalysis`, modified a few printout formats in function `plot.POEvaluation`, and improved the usage of function `plot.ShapDependence`.

### Test environments

1. Local macOS Monterey 12.5.1, R version 4.0.4

2. Github actions

- Windows Server x64 (build 20348), R version 4.2.1 (2022-06-23 ucrt)
- Ubuntu 20.04.5 LTS, R version 4.2.1 (2022-06-23)
- Ubuntu 20.04.5 LTS, R Under development (unstable) (2022-09-05 r82812)
- Ubuntu 20.04.4 LTS, R version 4.1.3 (2022-03-10)
- macOS Big Sur/Monterey 10.16, R version 4.2.1 (2022-06-23)

3. `devtools` check

- Windows, R Under development (unstable) (2022-09-09 r82828 ucrt), `devtools::check_win_devel()`
- Windows, R version 4.2.1 (2022-06-23 ucrt), `devtools::check_win_release()`
- Windows, R version 4.1.3 (2022-03-10), `devtools::check_win_oldrelease()`
- MacOS, R version 4.2.1 Patched (2022-06-23 r82516), `devtools::check_mac_release()`
- Linux, `devtools::check_rhub()`

### R CMD check

There is no error or warning. It got some notes of invalid URLs only on some Windows machines. I manually check these links and all of them seem still available.

```
Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/joc.5086
    From: man/future_worldclim2.Rd
          man/worldclim2.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/jbi.13402
    From: man/evaluate_po.Rd
    Status: 503
    Message: Service Unavailable
```

It also got some possible miss-spellings on Windows oldrelease. I double checked all of them and they are not mis-spelled.

```
Possibly mis-spelled words in DESCRIPTION:
  Brunner (15:9)
  Caporaso (30:38)
  Fick (28:66)
  Guha (17:5)
  Hariri (14:51)
  Hijmans (29:14)
  Kononenko (23:60)
  Liu (13:45, 15:63)
  Lundberg (21:45)
  Mishra (17:15)
  Noce (30:28)
  SCiForest (12:54)
  Santini (30:55)
  Schrijvers (17:39)
  Shapley (19:39, 20:58)
  Zhou (14:5, 16:20)
  bioclimatic (28:5)
  iForest (11:50)
  itsdm (24:45)
  trumbelj (23:43)
```

## Resubmission (version 0.1.2)

Remove the unnecessary email link in README.

## Update (version 0.1.2)

Changes to this version are minor and can be found in `NEWS.md`. For version 0.1.1, there was an CRAN check warning: *Required orphaned package: `gtools`* in one of the dependencies. Not sure how long the maintainer would fix the issue, so decide to remove the dependency and include an internal function to do the work.

### Test environments

1. Local macOS Monterey 12.4, R version 4.0.4

2. Github actions

- Windows Server x64 (build 20348), R version 4.2.0 (2022-04-22 ucrt)
- Ubuntu 20.04.4 LTS, R version 4.2.0 (2022-04-22)
- Ubuntu 20.04.4 LTS, R Under development (unstable) (2022-06-18 r82503)
- Ubuntu 20.04.4 LTS, R version 4.1.3 (2022-03-10)
- macOS Big Sur/Monterey 10.16, R version 4.2.0 (2022-04-22)

3. `devtools` check

- Windows, R Under development (unstable) (2022-06-18 r82503 ucrt), `devtools::check_win_devel()`
- Windows, R version 4.2.0 (2022-04-22 ucrt), `devtools::check_win_release()`
- Windows, R version 4.1.3 (2022-03-10), `devtools::check_win_oldrelease()`
- Linux, `devtools::check_rhub()`

### R CMD check

There is no error or warning. It got some notes of invalid URLs only on some machines:

```
Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/joc.5086
    From: man/future_worldclim2.Rd
          man/worldclim2.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/jbi.13402
    From: man/evaluate_po.Rd
    Status: 503
    Message: Service Unavailable

Found the following (possibly) invalid file URI:
  URI: [email protected]
    From: README.md

Found the following (possibly) invalid DOIs:
  DOI: 10.1002/joc.5086
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
```

I manually check these links and all of them seem still available. One of them is my email address. So I believe these are okay.

## Resubmission (version 0.1.1)

Due to an dependency loading failure on Windows, the package did not pass the incoming checks. Try it again.

## Update (version 0.1.1)

Changes to this version are minor and can be found in `NEWS.md`. Because there is an update in dependency `ecospat` that will break some functions. Additionally, the author of the dependency `isotree` suggests some updates. A new submission would be necessary to keep `isotree` updating smoothly.

### Test environments

1. Local macOS Monterey 12.1, R version 4.0.2

2. Github actions

- Microsoft Windows Server 2019 10.0.17763, R version 4.1.2 (2021-11-01)
- Ubuntu 20.04.3 LTS, R version 4.1.2 (2021-11-01)
- Ubuntu 20.04.3 LTS, R Under development (unstable) (2022-01-01 r81419)
- Ubuntu 20.04.3 LTS, R version 4.0.5 (2021-03-31)

3. `devtools` check

- Windows, R Under development, `devtools::check_win_devel()`
- Windows, R version 4.1.2, `devtools::check_win_release()`
- Windows, R version 4.0.5, `devtools::check_win_oldrelease()`
- Linux, `devtools::check_rhub()`

## Resubmission

This is a resubmission. Thanks very much for the comments from Gregor Seyer. The issues pointed out are fixed. The responses are as follows:

>Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'worldclim'

As a dataset, WorldClim and CMCC-BioClimInd are written in single quotes.

>If there are references describing the methods in your package, please 
add these in the description field of your DESCRIPTION file in the form
authors (year) <doi:...>
  authors (year) <arXiv:...>
  authors (year, ISBN:...)
or if those are not available: <https:...>
  with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for 
auto-linking.
(If you want to add a title as well please put it in quotes: "Title")

All necessary references are added in DESCRIPTION. The narrative is modified a bit correspondingly.

>Please make sure that you do not change the user's options, par or 
working directory. If you really have to do so within functions, please 
ensure with an *immediate* call of on.exit() that the settings are reset 
when the function is exited. e.g.:
...
old <- options()         # code line i
on.exit(options(old))     # code line i+1
...
options(timeout = 1e5)
...
e.g.: cmcc_bioclim.R, future_cmcc_bioclim.R, future_worldclim2.R, 
worldclim2.R
If you're not familiar with the function, please check ?on.exit. This 
function makes it possible to restore options before exiting a function 
even if the function breaks. Therefore it needs to be called immediately 
after the option change within a function.

Oops, this is a rookie mistake. Deleted these settings from functions. It is good to know the safe way to change user's options within package functions.

## Test environments

1. Local macOS Monterey 12.1, R version 4.0.2

2. Github actions

- Microsoft Windows Server 2019 10.0.17763, R version 4.1.2 (2021-11-01)
- Ubuntu 20.04.3 LTS, R version 4.1.2 (2021-11-01)
- Ubuntu 20.04.3 LTS, R Under development (unstable) (2022-01-01 r81419)
- Ubuntu 20.04.3 LTS, R version 4.0.5 (2021-03-31)

3. rhub/devtools check

- Windows Server 2022, R-devel, 64 bit
- Fedora Linux, R-devel, clang, gfortran
- Ubuntu Linux 20.04.1 LTS, R-release, GCC
- x86_64-w64-mingw32 (64-bit), R version 4.0.5 (2021-03-31)
- x86_64-w64-mingw32 (64-bit), R Under development (unstable) (2022-01-03 r81439 ucrt)
- x86_64-w64-mingw32 (64-bit), R version 4.1.2 (2021-11-01)

## R CMD check results

There is no error or warning. It got one note related to CRAN release:

```
New submission

Possibly misspelled words in DESCRIPTION:
  Brunner (12:9)
  Caporaso (28:38)
  Fick (26:66)
  Guha (14:5)
  Hariri (11:51)
  Hijmans (27:14)
  Kononenko (21:56)
  Liu (10:45, 12:63)
  Lundberg (18:60)
  Mishra (14:15)
  Noce (28:28)
  SCiForest (9:54)
  Santini (28:56)
  Schrijvers (14:39)
  Shapley (16:52, 18:5)
  Zhou (11:5, 13:20)
  bioclimatic (26:5)
  iForest (8:50)
  itsdm (22:45)
  trumbelj (21:39)
```

- This is a new release.
- These possibly misspelled words are not misspelled. 

## Others notes

On rhub check: Windows Server 2022, R-devel, 64 bit, it got an extra note:

```
Found the following files/directories:
'lastMiKTeXException'
```
It seems related to knit. I can't reproduce this note anywhere else.

I pre-compiled the package vignettes to save checking time. They already be tested on multiple platforms.