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JointAI (version 1.0.5)

Round 1

Test environments

  • local Windows 10, R 4.3.0
  • windows server 2022 x64 (via github actions), R 4.3.0
  • ubuntu 22.04.2 LTS (via github actions), R 4.2.3, R 4.3.0, devel
  • mac-OS Ventura 13.3.1 (via macOS builder), R 4.3.0
  • win-builder (oldrelease, devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

One reverse dependency: "remiod"; passed the check.

JointAI (version 1.0.4)

Round 1

Test environments

  • local Windows 10, R 4.2.1
  • windows server x64 (via github actions), R 4.1.2
  • ubuntu 20.04.4 LTS (via github actions), R 4.1.3, R 4.2.1, devel
  • mac-OS 10.16 (via github actions), R 4.2.1
  • win-builder (oldrelease, devel and release)

R CMD check results

0 errors | 0 warnings | 1 note

NOTE: (win-builder oldrelease)

Possibly mis-spelled words in DESCRIPTION: Erler (10:18) Lesaffre (10:40) Rizopoulos (10:25)

Package has help file(s) containing build-stage \Sexpr{} expressions but no 'build/partial.rdb' file.

Found the following (possibly) invalid URLs: URL: https://doi.org/10.1177/0962280217730851 From: man/JointAI.Rd Status: 503 Message: Service Unavailable

REPLY:

The issues only appear in the win-builder oldrelease.

The author names in the DESCRIPTION are spelled correctly.

I cannot find any occurrence of \Sexpr{} in the package (but \if{} and \out{} appear in the .Rd files generated by Roxygen2). When I run R CMD build, no 'build/partial.rdb' is included and I'm not sure how to change this.

The URL seems to be correct; they point to the correct websites and are specified in the @references section of the documentation as \doi{10.1177/0962280217730851}.

Reverse dependencies

One reverse dependency: "remiod"; passed the check.

JointAI (version 1.0.3)

Round 1

Test environments

  • local Windows 10, R 4.1.1
  • windows server x64 (via github actions), R 4.1.2
  • ubuntu 20.04.3 LTS (via github actions), R 4.0.5, R 4.1.2, devel
  • win-builder (oldrelease, devel and release)

R CMD check results

0 errors | 0 warnings | 1 note

NOTE:

Possibly misspelled words in DESCRIPTION: Erler (10:18) Lesaffre (10:40) Rizopoulos (10:25)

Found the following (possibly) invalid URLs: URL: https://doi.org/10.18637/jss.v100.i20 From: man/JointAI.Rd man/list_models.Rd Status: 404 Message: Not Found

Found the following (possibly) invalid DOIs: DOI: 10.18637/jss.v100.i20 From: DESCRIPTION inst/CITATION Status: Not Found Message: 404

REPLY: The DOI/URL in the CITATION, DESCRIPTION and \reference section of man/JointAI.Rd and man/list_models.Rd is for a new JSS publication that will be registered after publication on CRAN. (And the names of the authors in the DESCRIPTION are fact spelled correctly.)

Reverse dependencies

There are no reverse dependencies.

Reviewer comments

2021-11-27 Uwe Ligges

Thanks, we see:


   Found the following URLs which should use \doi (with the DOI name only):
     File 'JointAI.Rd':
       https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.18637%2Fjss.v100.i20&data=04%7C01%7Cn.erler%40erasmusmc.nl%7C931c6a6ed615439baa0508d9b17be3b8%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637735967925897409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GWvnOg8CZdyClEWsYiYbthNN6SZtZQzNmPTb0ROsIDQ%3D&reserved=0
     File 'list_models.Rd':
       https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.18637%2Fjss.v100.i20&data=04%7C01%7Cn.erler%40erasmusmc.nl%7C931c6a6ed615439baa0508d9b17be3b8%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637735967925907404%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Xq4TyvG66rGkvJF7n75wwPcEMLUu%2BSul2mB5qr7KXNg%3D&reserved=0

Please fix and resubmit.

Round 2

Submission comments

2021-11-28

I've fixed the DOIs the two references.

JointAI (version 1.0.2)

Round 1

Test environments

  • local Windows 10, R devel
  • windows server x64 (via github actions), R 3.6.3, R 4.0.3
  • ubuntu 16.04.7 LTS (via github actions), R 3.6.3, R 4.0.3, devel
  • macOS Catalina 10.15.6 (via github actions), R 4.0.3
  • win-builder (oldrelease, devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 1.0.1)

Round 1

Test environments

  • local Windows 10, R 4.0.3
  • windows server x64 (via github actions), R 3.6.3, R 4.0.3
  • ubuntu 16.04.7 LTS (via github actions), R 3.6.3, R 4.0.3, devel
  • macOS Catalina 10.15.6 (via github actions), R 4.0.3
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 1.0.0)

Round 1

Test environments

  • local Windows 10, R 4.0.2
  • windows server x64 (via github actions), R 3.6.3, R 4.0.2
  • ubuntu 16.04.7 LTS (via github actions), R 3.6.3, R 4.0.2, devel
  • macOS Catalina 10.15.6 (via github actions), R 4.0.2
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Note:

Found the following (possibly) invalid URLs: URL: http://mcmc-jags.sourceforge.net From: DESCRIPTION man/JointAI.Rd inst/doc/ModelSpecification.html README.md Status: 503 Message: Service Unavailable URL: http://mcmc-jags.sourceforge.net/ From: inst/doc/MCMCsettings.html inst/doc/SelectingParameters.html Status: 503 Message: Service Unavailable

It seems http://mcmc-jags.sourceforge.net/ is currently not available. This site is still linked to from the JAGS sourceforge repository (https://sourceforge.net/projects/mcmc-jags/), in which there were commits during the last few days. I expect that the site is only offline temporarily.

Reverse dependencies

There are no reverse dependencies.

Reviewer comments:

2020-08-28 Uwe Ligges

Thanks, we see:

   Found the following (possibly) invalid URLs:
     URL: https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmcmc-jags.sourceforge.net%2F&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=BnQmxD3TVZZhmJsK%2FEXn3VdM0yHnQiXKr%2BKoI2Lnb%2Bk%3D&reserved=0
       From: DESCRIPTION
             man/JointAI.Rd
             inst/doc/ModelSpecification.html
             README.md
       Status: 503
       Message: Service Unavailable
     URL: https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmcmc-jags.sourceforge.net%2F&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=BnQmxD3TVZZhmJsK%2FEXn3VdM0yHnQiXKr%2BKoI2Lnb%2Bk%3D&reserved=0
       From: inst/doc/MCMCsettings.html
             inst/doc/SelectingParameters.html
       Status: 503
       Message: Service Unavailable


Is this site expected to work again?



     URL: https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rdocumentation.org%2Fpackages%2FJointAI&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=PFxlgYV9CUMysfSwpq7WUNi0jDIdFjZ%2FMKkigq0Idj4%3D&reserved=0 (moved to
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rdocumentation.org%2Fpackages%2FJointAI&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=JUmFeBruGfIyJa6iwkQL%2BzRHlpJEROMCACl49KqyQnU%3D&reserved=0)
       From: README.md
       Status: 200
       Message: OK
     URL: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnerler.github.io%2FJointAI&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=vKboFCbEcw2iztBZCmyquUy90qRk%2Fa24G4L0501FwA4%3D&reserved=0 (moved to
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnerler.github.io%2FJointAI%2F&data=02%7C01%7Cn.erler%40erasmusmc.nl%7C0c7f767e3a2441d6e91708d84b44fbea%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637342106948860379&sdata=5qBicSOWF4HDqlmiY5pud%2BkyL0vgMTcCbHm1oi2yZ4w%3D&reserved=0)
       From: DESCRIPTION
       Status: 200
       Message: OK


Please change http --> https  or add trailing slashes where required.


   The Description field should not start with the package name,
     'This package' or similar.

   Size of tarball: 9353082 bytes

Not more than 5 MB for a CRAN package, please.

Please fix and resubmit.

Round 2

Submission comments

2020-08-29

All comments were addressed, specifically:

  • Website http://mcmc-jags.sourceforge.net/ is up again
  • URLs were changed to https (except for http://mcmc-jags.sourceforge.net/, which does not have a SSL certificate)
  • The Description was adjusted (now starts with "Joint analysis and imputation of incomplete data...")
  • The tarball size was reduced by excluding vignettes from the build and by using a different file format for large output files from testthat tests

Automatic check failure

Under Windows and Debian:

Found the following (possibly) invalid URLs:
  URL: https://nerler.github.io/JointAI (moved to https://nerler.github.io/JointAI/)
    From: DESCRIPTION
    Status: 200
    Message: OK

Round 3

Submission comments

2020-08-30

  • With regards to the automatic check: a trailing slash was added to the link in the DESCRIPTION

  • With regards to the current CRAN status (JointAI 0.6.1): ERROR: 1, WARN: 1, NOTE: 1, OK: 9

    • ERROR: 
      Version: 0.6.1
Check: examples, Result: ERROR
Running examples in 'JointAI-Ex.R' failed
...
> plot_imp_distr(impDF, id = "id", ncol = 3)
Error in plot_imp_distr(impDF, id = "id", ncol = 3) : 
  This function requires the package ggpubr to be installed.
      In JointAI 1.0.0 the function plot_imp_distr() does no longer return an error if ggpubr is not installed but an informative message.
    • WARNING: 
      Version: 0.6.1
Check: re-building of vignette outputs, Result: WARNING

Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
Consider formula(paste(x, collapse = " ")) instead.
      This warning is due to a change in R 4.0.0 and was addressed in JointAI 1.0.0
    • NOTE: 
      Version: 0.6.1
Check: Rd cross-references, Result: NOTE
Undeclared package ‘ordinal’ in Rd xrefs
See: <https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/JointAI-00check.html>
      JointAI 1.0.0 does no longer link to the package ordinal.

JointAI (version 0.6.0)

Round 1

Test environments

  • local Windows 7, R 3.6.1
  • ubuntu 14.04.5 LTS (on travis-ci), R 3.5.3, R 3.6.1, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.5.2)

Round 1

Test environments

  • local Windows 7, R 3.6.0
  • ubuntu 14.04.5 LTS (on travis-ci), R 3.5.3, R 3.6.0, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.5.1)

Round 1

Test environments

  • local Windows 7, R 3.6.0
  • ubuntu 14.04.5 LTS (on travis-ci), R 3.5.3, R 3.6.0, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.5.0)

Round 1

Test environments

  • local Windows 7, R 3.5.2
  • ubuntu 14.04.5 LTS (on travis-ci), R 3.4.4, R 3.5.2, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.4.0)

Round 1

Test environments

  • local Windows 7, R 3.5.1
  • ubuntu 14.04.5 LTS (on travis-ci), R 3.4.4, R 3.5.1, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 1 note

Note in win-builder R-oldrelease:

Author field differs from that derived from Authors@R
Author: 'Nicole S. Erler [aut, cre] (https://orcid.org/0000-0002-9370-6832)'
Authors@R: 'Nicole S. Erler [aut, cre] (0000-0002-9370-6832)'

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.3.0)

Round 1

Test environments

  • local Windows 7, R 3.5.1
  • ubuntu 14.04 (on travis-ci), R 3.4.4, R 3.5.0, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.2.0)

Round 1

Test environments

  • local Windows 7, R 3.5.1
  • ubuntu 14.04 (on travis-ci), R 3.4.4, R 3.5.0, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 notes

Reverse dependencies

There are no reverse dependencies.

JointAI (version 0.1.0)

Round 1

Test environments

  • local Windows 7, R 3.4.4
  • ubuntu 14.04 (on travis-ci), R 3.3.3, R 3.4.4, devel
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 0 note

  • checking CRAN incoming feasibility ... NOTE

    This is a new release. No additional notes.

Reverse dependencies

This is a new release, so there are no reverse dependencies.

Reviewer comments

2018-03-21 Swetlana Herbrandt

Thanks, you have code from the foreign package in your package, hence please add
all authors and copyright holders of foreign in the Authors@R field with the
appropriate roles.

From the CRAN policies you agreed to:

"The ownership of copyright and intellectual property rights of all components
of the package must be clear and unambiguous (including from the authors specification in the DESCRIPTION file). Where code is copied (or derived) from the work of others (including from R itself), care must be taken that any copyright/license statements are preserved and authorship is not misrepresented.

Preferably, an ‘Authors@R’ would be used with ‘ctb’ roles for the authors of such code. Alternatively, the ‘Author’ field should list these authors as contributors.

Where copyrights are held by an entity other than the package authors, this should preferably be indicated via ‘cph’ roles in the ‘Authors@R’ 
field, or using a ‘Copyright’ field (if necessary referring to an inst/COPYRIGHTS file)."


Please do not capitalize "Analysis" and "Imputation" in your description.

Please start your description with "Provides joint analysis and imputation of linear..." or something similar.

Please replace T and F by TRUE and FALSE in your Rd-files and your code.

Most of your examples are wrapped in \dontrun{} and hence not tested. 
Please unwrap the examples if that is feasible and if they can be executed in < 5 sec for each Rd file or create additionally small toy examples. Something like \examples{
        examples for users and checks:
        executable in < 5 sec
        \dontshow{
               examples for checks:
               executable in < 5 sec together with the examples above
               not shown to users
        }
        donttest{
               further examples for users (not used for checks)
        }
}
would be desirable.

Please fix and resubmit.

Round 2

Submission comments

2018-03-21

Addressed all previous comments, specifically:

  • It was an oversight that I was still using the code copied from another package. I removed the function write_SPSS that was using this code. Instead I am now using write.foreign from the foreign package. I have added this package to 'Suggests' in the DESCRIPTION file and am linking to it in the documentation of the relevant function in my package.

  • I have made the requested changes in the DESCRIPTION file.

  • All occurrences of T and F have been replaced by TRUE and FALSE.

  • Removed \dontrun{} from all but one example (all examples can be executed in <5 seconds). The example still in \dontrun{} exports a dataset and writes files into a temporary directory.

Reviewer comments

2018-03-22 Swetlana Herbrandt

Thanks, on CRAN now.