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Test environments

  • local OS X install, R 3.5.2
  • ubuntu 14.04 (on travis-ci), R 3.5.2
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 1 note

  • This is a new release.

Responses to remarks I received from 1st submission

This is 2nd submission. As for the remarks I received from 1st submission:

1

Thanks, 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:...)
with no space after 'doi:', 'arXiv:' and angle brackets for auto-linking.

There are NO references describing the methods in this package.

2

Additionally, we see:
  Warning: Unexecutable code in man/set_collunit.Rd:
  notes = "my lake":
  Warning: Unexecutable code in man/set_dataset.Rd:
  notes = "my lake":
  Warning: Unexecutable code in man/toJSON-sites-method.Rd:
  Convert the: 
  Warning: Unexecutable code in man/toWide.Rd:
  Download all:

I have fixed the code so that it can be executed.

3

Please add \value to .Rd files regarding exported methods and explain the functions results in the  documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar)

Missing Rd-tags in up to 204 .Rd files, e.g.:
     add_chronology-collunit-chronology-data.frame-method.Rd: \value
     add_chronology.Rd: \value
     as.data.frame-authors-method.Rd: \value
     as.data.frame-chronologies-method.Rd: \value
     as.data.frame-chronology-method.Rd: \value
     as.data.frame-collunit-method.Rd: \value
     ...

Added @returns to function with descriptions. This adds the value tag to .Rd files

4

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user.
Does not seem necessary.
Please unwrap the examples if they are executable in < 5 sec, or create additionally small toy examples to allow automatic testing.
(You could also replace \dontrun{} with \donttest, if it takes longer than 5 sec to be executed, but it would be preferable to have automatic checks for functions. Otherwise, you can also write some tests.)

Please replace \dontrun{} by \donttest{} or unwap the examples if they 
can be executed in less than 5 sec per Rd-file.

Unwrapped some examples and replaced the \dontrun{} with a \donttest{} label. Most examples make calls to the Neotoma API and CANNOT use smaller toy datasets. Because of this, some examples take longer than 5 seconds and have to keep the \donttest{} label.

5

Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies.
Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().

We do not write elements in the user's homespace.

Responses to remarks I received from 2nd submission

This is 3rd submission. As for the remarks I received from 2nd submission:

1

Please provide a link to the used webservices (Neotoma Database) to the 
description field of your DESCRIPTION file in the form <http:...> or <https:...>
with angle brackets for auto-linking and no space after 'http:' and
'https:'.

Fixed.

2

Please add \value to .Rd files regarding exported methods and explain 
the functions results in the documentation. Please write about the 
structure of the output (class) and also what the output means. (If a
function does not return a value, please document that too, e.g.
\value{No return value, called for side effects} or similar)
Missing Rd-tags:
  chronologies-collunit-method.Rd: \value
  chronologies-collunits-method.Rd: \value
  chronologies-site-method.Rd: \value
  chronologies-sites-method.Rd: \value
  collunits-site-method.Rd: \value
  collunits-sites-method.Rd: \value
  datasets-collunit-method.Rd: \value
  datasets-collunits-method.Rd: \value
  datasets-site-method.Rd: \value
  datasets-sites-method.Rd: \value
  get_contacts.Rd: \value
  get_manual.Rd: \arguments
  get_publications.numeric.Rd: \value
  get_publications.publication.Rd: \value
  pipe.Rd: \arguments
  specimens-collunit-method.Rd: \value
  specimens-collunits-method.Rd: \value
  specimens-site-method.Rd: \value

All of the \value tags have been added. For the pipe.Rd function, we use the code from the purrr library We do not see any arguments being added into that function. In magrittr, there are two placeholders but they are used in the body of the pipe function - that is not our case.

As for the get_manual.Rd function, there are no parameters that the user needs to pass, it is a static function. I cannot find information on how to document this kind of "parameters".

3

\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by
the user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user. Does not seem necessary.
Please replace \dontrun with \donttest.

get_datasets.numeric.Rd: Please put functions which download data in
\donttest{}. ☑ Done
get_manual.Rd: if(interactive()) is sufficient. You don't need to wrap
it in \dontrun{} as well. ☑ Done
specimens-sites-method.Rd: I believe the same as for 
get_datasets.numeric.Rd. ☑ Done

Done as suggested

Responses to remarks I received from 3rd submission

1

Check: DESCRIPTION meta-information, Result: NOTE
Malformed Description field: should contain one or more complete sentences.

So, I originally sent:

Description: Access and manipulate data from the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>

because I was requested to add https://.. referencing the "Neotoma Paleoecology Database". With the Description above, I do not get any local errors when running the R CMD but for CRAN, I got the error that I was asked to correct.

After e-mailing the R-package-devel mailing list and providing them with my github link, I was advised to indent with 8 spaces on the second line and finish the line with a .

The Description field in the Description file now looks like:

Description: Access and manipulate data from the Neotoma Paleoecology Database. 
        <https://api.neotomadb.org/api-docs/>

There are no spaces after https:// and 8 indents have been added as requested.

I hope this is correct now, otherwise, please give me some more references/examples so that I can do it properly.

Remarks for Upgrade 1.0.3

Added JOSS Article PDF and fixed small errors in the API calls.