cran-comments.md

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

title: "cran-comments" author: "Manuel Chevalier" date: "01/07/2022" output: github_document

Submission of crestr 1.2.1 (04/01/2023)

I release this version to address the request of Prof. Ripley:

For the record, the current failure is

--- re-building ‘using-gbif4crest.Rmd’ using rmarkdown Quitting from lines 66-77 (using-gbif4crest.Rmd) Error: processing vignette 'using-gbif4crest.Rmd' failed with diagnostics: could not translate host name "gbif4crest.cvqgy2mnjwtg.eu-west-3.rds.amazonaws.com" to address: Name or service not known

--- failed re-building ‘using-gbif4crest.Rmd’

and I have seen it several times this month.

-- Brian D. Ripley, [e-mail] Emeritus Professor of Applied Statistics, University of Oxford

I have added a more proper way of dealing with the connection problem when it arises. This new package version also contains some minor fixes (cf NEWS.md).

Tests run

• First, I ran local test:

devtools::check()
devtools::check(manual = TRUE, remote = TRUE, incoming = TRUE)

These two tests returned No ERRORs, No WARNINGs, No NOTEs.

• Then I did the following:

devtools::build(manual = TRUE)
R CMD CHECK /Users/mchevali1/GitHub/Rpackages/crestr_1.2.0.tar.gz
R CMD CHECK --as-cran /Users/mchevali1/GitHub/Rpackages/crestr_1.2.0.tar.gz

Status: OK. No ERROR, No WARNING, No NOTE.

• Then, I ran the following tests for Windows:

devtools::check_win_release('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)
devtools::check_win_devel('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)
devtools::check_win_oldrelease('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)

This returns some NOTEs about webpages listed in the documentation. The links were tested and are fully functional (there were already present in previous versions). The one also one NOTE about a possibly misspelled word, but I checked it and it is correctly spellt.

• Finally, I ran the following tests

devtools::check_rhub('/Users/mchevali1/GitHub/Rpackages/crestr')
rhub::check_for_cran('/Users/mchevali1/GitHub/Rpackages/crestr_1.2.1.tar.gz')
rhub::check_on_linux('/Users/mchevali1/GitHub/Rpackages/crestr_1.2.1.tar.gz')
rhub::check_with_rdevel('/Users/mchevali1/GitHub/Rpackages/crestr_1.2.1.tar.gz')
rhub::check_with_rrelease('/Users/mchevali1/GitHub/Rpackages/crestr_1.2.1.tar.gz')

All tests ran without any ERROR or WARNING. I got the following NOTE for the Fedora environments: checking HTML version of manual ... NOTE Skipping checking HTML validation: no command 'tidy' found. I cannot change that Tidy is not on the path, or update Tidy on the external Fedora Linux server.

Submission of crestr 1.2.0 (01/09/2022)

Tests run

• First, I ran local test:

devtools::check()
devtools::check(manual = TRUE, remote = TRUE, incoming = TRUE)

These two tests returned No ERRORs, No WARNINGs, No NOTEs.

• Then I did the following:

devtools::build(manual = TRUE)
R CMD CHECK /Users/mchevali1/GitHub/Rpackages/crestr_1.2.0.tar.gz
R CMD CHECK --as-cran /Users/mchevali1/GitHub/Rpackages/crestr_1.2.0.tar.gz

Status: OK. No ERROR, No WARNING, No NOTE.

• Then, I ran the following tests for Windows:

devtools::check_win_release('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)
devtools::check_win_devel('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)
devtools::check_win_oldrelease('/Users/mchevali1/GitHub/Rpackages/crestr', quiet=TRUE)

This returns some NOTEs about webpages listed in the documentation. The links were tested and are fully functional (there were already present in previous versions). The one also one NOTE about a possibly misspelled word, but I checked it and it is correctly spellt.

• Finally, I ran the following tests

devtools::check_rhub('/Users/mchevali1/GitHub/Rpackages/crestr')
rhub::check_for_cran('/Users/mchevali1/GitHub/Rpackages/crestr_1.2.0.tar.gz')

I got the following NOTEs, which I cannot act on. Some of them were already prsent in the previous versions of the package I sbumitted.

* checking for detritus in the temp directory ... NOTE Found the following files/directories:   'lastMiKTeXException'
* checking HTML version of manual ... NOTE Skipping checking HTML validation: no command 'tidy' found

What's new in v1.2.0?

An array of new functions has been added and some minor bugs have also been corrected.

• Removing some unnecessary debugging prints
• Adapting the crestr reference
• Adding a check on the column names of PSE
• Fastening the LOO function
• Adding a sorting parameter to the LOO() function
• Adding the pdf_ranges() function.
  • Also included as an invisible output of the plot_violinPDFs()
• Adding the plot.scatterPDFs() graphical output.
• Adding taxonComposition() to get the size distribution of the composing species.
• Minor bugs fixed
  • If no distributions are extracted, the calibration could be used.
  • combinedPDFs() could bug if only one variable
  • Filters by elevation added to getClimateSpace()
  • print(ntaxa) was 1 off
  • Minor naming issues with export()
  • plot_climateSpace() and plot_taxaCharacteristics() were issuing a warning when no climate values are available and add_modern is TRUE (coordinates are available but no climate)

<--------------------------------------------->

Previous submissions. Versions already on CRAN

<--------------------------------------------->

Submission of crestr 1.1.0 (01/07/2022)

Resubmission

• First NOTE about incorrect links (see below):
  • The two links with changes have been corrected. The other three are correct and I do not know why they trigger a NOTE. They are valid URLs.

Found the following (possibly) invalid URLs:
  URL: https://cgiarcsi.community/2019/01/24/global-aridity-index-and-potential-evapotranspiration-climate-database-v2/ (moved to https://csidotinfo.wordpress.com/2019/01/24/global-aridity-index-and-potential-evapotranspiration-climate-database-v2/)
    From: man/accClimateVariables.Rd
    Status: 200
    Message: OK
  URL: https://doi.org/10.1002/joc.5086
    From: inst/doc/calibration-data.html
    Status: 503
    Message: Service Unavailable
  URL: https://figshare.com/articles/GBIF_for_CREST_database/6743207 (moved to https://figshare.com/articles/dataset/GBIF_for_CREST_database/6743207)
    From: man/connect_local_sqlite3.Rd
          man/crest.get_modern_data.Rd
    Status: 200
    Message: OK
  URL: https://www.doi.org/10.1002/jqs.2850
    From: inst/doc/theory.html
    Status: 503
    Message: Service Unavailable
  URL: https://www.researchgate.net/publication/235641869_Daily_High-Resolution-Blended_Analyses_for_Sea_Surface_Temperature
    From: inst/doc/calibration-data.html
    Status: 403
    Message: Forbidden

• Second NOTE about the present of an undesired file ('crestr_1.1.0.pdf')
  • The file was removed.

First submission

I have run several tests for windows, linux and osx, similarly to what I did for the previous version. No ERRORS or WARNINGS. Some tests generated a NOTE about the accessibility of some webpages. These links are correct and identifical to the previous versions of the package.

• crestr is now compatible with the SQLite3 gbif4crest database. It is therefore usable offline.
  • Access: https://figshare.com/articles/dataset/GBIF_for_CREST_database/6743207

crestr 1.0.3

This version has not been submitted to CRAN yet

• Fixing minor bugs, including:
  • If the climate field didn't match the column names of selectedTaxa, some functions were crashing (at least plot_climateSpace) because no distribution data were extracted.
  • Checks to ensure the column names of climate_space and distributions are correct for crest.set_modern_data()
  • Check to ensure the selectedTaxa has default values for all selected variables.

Submission of crestr v1.0.2 (25/04/2022)

This version contains very small adjustements of the package, as described below. Most changes are aestetic in nature and relate to the design of the plots.

List of changes

• Minor bugs fixed on the plots

  • Title of the LOO plot adapted from 'variable name [unit]' to 'Leave-one-out anomalies for\nvariable name [unit]'
  • Title of stratigraphic diagrams can spread across many lines now
  • The thickness of the lines on the samplePDFs plot has been revised to show a greater range.
  • Labels added to the y-axes on the histograms of the climate space plot.
  • Labels added to the y-axis of the histograms and pdf plots of the taxaCharacteristics figure.
  • Adding caption on LOO diagram (+ and - anomalies)
  • Fixing title problem on plot_diagram()
  • Adding a colouring option for hiatus(es) on plot.crestObj()
  • Fixed problem of opening empty plotting windows when exporting the figures to files
  • Changing default value for bar_width in plot_loo() and plot_diagram()

• Replacing the parameter fullPosterior by fullUncertainties in export().

• Typos in the documentation have been fixed.

• The text of the vignettes was updated to reflect changes in the manuscript. Nothing really significant.

• Fixing bug related to ai.sqrt in crest.get_modern_data(). Only the climate space data were transformed.

• Excluding all the distribution grid cells without any climate data.

• Replaced class(dat) == 'RasterLayer' by inherits(dat, 'RasterLayer')

• Improved documentation

Tests

I ran the same tests as I did to release v1.0.0, and did not get any ERRORS or WARNINGS. Some tests gave NOTES, but these are not things I can or should fix.

• Possibly misspelled words in DESCRIPTION: Palaeoecological (3:9)
  • This is the proper spelling of the word in British English, and it is in the title of the reference. It cannot be changed.
• Found the following (possibly) invalid URLs: URL: https://doi.org/10.1002/joc.5086 and URL: https://www.doi.org/10.1002/jqs.2850. Status: 503. Message: Service Unavailable
  • These links function perfectly. The note only appeared for one test.
• checking for detritus in the temp directory ... NOTE Found the following files/directories: lastMiKTeXException'
  • Not sure how to act on that.

Re-submission #2

Thank you for the tips on how to ameliorate the package. I have now included all your suggestions, including:

• I have added a reference to the associated scientific publication in the DESCRIPTION file.
• I have used suppressWarnings() instead of options(warn=-1)
• I have now moved all the example and vignette outputs to tempdir()
• I have replaced my code by the suggested code to protect the user's par() options.
• I have added a return value for all the functions, even when they do not return anything (eg. plot functions). Five .Rd files have no \value{} because they are datasets.

I re-run all the test indicated below with the adapted code and I similarly get no ERRORS, no WARNINGS and no NOTES, except the 'CRAN first submission' NOTE.

Re-submission #1

• I have now replaced all the http by https.
• The webpage (https://journals.ametsoc.org/view/journals/clim/20/22/2007jcli1824.1.xml) still seems to create some issues with windows builts, but I have no idea how to fix this. So I have replaced it by an alternative one.
• This other address (https://www.ncei.noaa.gov/products/world-ocean-atlas) seems to sometimes create problems (Message: libcurl error code 35:). Sometimes it passes the tests, sometimes it doesn't. Since I really don't know much in this area, I have no idea how to fix this. If you have any suggestion on how to fix this, please let me know how. Otherwise, it will have to stay as it is since there is no alternative link I can use.

First submission

crestr 1.0.0 is a package designed to estimate climate parameters from fossil bio-prxoies. Its application will primarily (and uniquely?) for academic purposes.

Test environments

• local OS X install, 11.5.2, R 4.0.2
• win-builder, using devtools::check_win_devel(), devtools::check_win_release() and devtools::check_win_oldrelease()
• r-hub (windows, Ubuntu and Fedora)

Local build

There were no ERRORs, WARNINGs or NOTES.

• Package built by ```{r eval = FALSE} devtools::build(manual = TRUE)

* Package checked by
```{bash eval=FALSE}
R CMD CHECK /Users/mchevali1/GitHub/Rpackages/crestr_1.0.0.tar.gz
Status: OK

• Package checked by ```{bash eval=FALSE} R CMD CHECK --as-cran /Users/mchevali1/GitHub/Rpackages/crestr_1.0.0.tar.gz Status: OK Notes: New Submission

## WIN_DEVEL

There were no ERRORs or WARNINGs. In all three cases, there was 1 NOTE because this is a first submission.

* `devtools::check_win_devel()` resulted in:

Status: 1 NOTE

checking CRAN incoming feasibility ... NOTE Maintainer: 'Manuel Chevalier [e-mail]' New submission

* `devtools::check_win_release()` resulted in:

Status: 1 NOTE

checking CRAN incoming feasibility ... NOTE Maintainer: 'Manuel Chevalier [e-mail]' New submission

* `devtools::check_win_oldrelease()` resulted in:

Status: 1 NOTE

checking CRAN incoming feasibility ... NOTE Maintainer: 'Manuel Chevalier [e-mail]' New submission

I also receive this message, about possibly invalid URL links in my documentation? These links have been tested and are all valid.

Found the following (possibly) invalid URLs: URL: From: inst/doc/technicalities.html Message: Empty URL URL: http://www.gbif.org (moved to https://www.gbif.org/) From: inst/doc/calibration-data.html Status: 200 Message: OK URL: https://doi.org/10.1175/2007JCLI1824.1 From: inst/doc/calibration-data.html Status: 403 Message: Forbidden URL: https://figshare.com/articles/GBIF_for_CREST_database/6743207 (moved to https://figshare.com/articles/dataset/GBIF_for_CREST_database/6743207) From: inst/doc/calibration-data.html Status: 200 Message: OK

## R-HUB

Here, I have checked the package using five tests from the `rhub` package. The check_on_linux(), check_on_windows(), check_on_fedora() and check_with_rrelease() tests returned no ERRORs, WARNINGs or NOTEs. The check_for_cran() tests returned no ERRORs or WARNINGs but consistently returned 1 NOTE about this being a `New Submission.


### `check_for_cran()`


```{r eval=FALSE}
rhub::check_for_cran()

The result is:

Build ID:   crestr_1.0.0.tar.gz-30e2d9b176a94f78a99daadacb217642
Platform:   Windows Server 2008 R2 SP1, R-devel, 32/64 bit
Submitted:  4 minutes 40.5 seconds ago
Build time: 4 minutes 38.3 seconds

NOTES:

* checking CRAN incoming feasibility ... NOTE
    Maintainer: 'Manuel Chevalier <[e-mail]>'
    New submission

Build ID:   crestr_1.0.0.tar.gz-b57f7bfffecd44678fa9ca9e9946b952
Platform:   Fedora Linux, R-devel, clang, gfortran
Submitted:  32 minutes 22.6 seconds ago
Build time: 32 minutes 18.9 seconds

NOTES:

* checking CRAN incoming feasibility ... NOTE
    Maintainer: ‘Manuel Chevalier <[e-mail]>’
    New submission

Build ID:   crestr_1.0.0.tar.gz-5c3d432d86854ec293f7652eda1f6d06
Platform:   Ubuntu Linux 20.04.1 LTS, R-release, GCC
Submitted:  33 minutes 21.1 seconds ago
Build time: 33 minutes 18.4 seconds

NOTES:

* checking CRAN incoming feasibility ... NOTE
    Maintainer: ‘Manuel Chevalier <[e-mail]>’
    New submission

check_on_linux()

There were no ERRORs, WARNINGs or NOTEs.

crestr 1.0.0: OK

Build ID:   crestr_1.0.0.tar.gz-dc673de0252b4cba8194bb373b7c6b52
Platform:   Debian Linux, R-release, GCC
Submitted:  17 minutes 56.7 seconds ago
Build time: 17 minutes 51.3 seconds

check_on_windows()

There were no ERRORs, WARNINGs or NOTEs.

crestr 1.0.0: OK

Build ID:   crestr_1.0.0.tar.gz-9919cfcd7a02431ca7e812efa3cfc5ae
Platform:   Windows Server 2008 R2 SP1, R-release, 32/64 bit
Submitted:  4 minutes 22.3 seconds ago
Build time: 4 minutes 14.1 seconds

check_on_fedora()

There were no ERRORs, WARNINGs or NOTEs.

crestr 1.0.0: OK

Build ID:   crestr_1.0.0.tar.gz-6036f1ec9af147d89d5b6567672c8deb
Platform:   Fedora Linux, R-devel, GCC
Submitted:  32 minutes 7.9 seconds ago
Build time: 32 minutes 0.9 seconds

check_with_rrelease()

There were no ERRORs, WARNINGs or NOTEs.

crestr 1.0.0: OK

Build ID:   crestr_1.0.0.tar.gz-08b855ec473f423683638ad89025890e
Platform:   Debian Linux, R-release, GCC
Submitted:  32 minutes 30.1 seconds ago
Build time: 32 minutes 22.2 seconds

Downstream dependencies

There are no downstream dependencies for this package.

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.