ropensci/stats19

stats19 is archived

Robinlovelace opened this issue · 8 comments

Robinlovelace commented

https://cran.r-project.org/package=stats19 currently shows:

Package ‘stats19’ was removed from the CRAN repository.

Formerly available versions can be obtained from the archive.

Archived on 2021-10-20 as check problems were not corrected in time.

A summary of the most recent check results can be obtained from the check results archive.

Please use the canonical form https://CRAN.R-project.org/package=stats19 to link to this page.

Robinlovelace commented

Message from CRAN:

If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

ackage stats19_1.5.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211012_003745/Windows/00check.log
Status: 1 WARNING, 1 NOTE
Debian: https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211012_003745/Debian/00check.log
Status: 1 NOTE

Last released version's CRAN status: ERROR: 10, OK: 4
See: https://CRAN.R-project.org/web/checks/check_results_stats19.html

Last released version's additional issues:
M1mac https://www.stats.ox.ac.uk/pub/bdr/M1mac/stats19.out

CRAN Web: https://cran.r-project.org/package=stats19

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
https://stat.ethz.ch/mailman/listinfo/r-package-devel
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211012_003745/
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Robin Lovelace rob00x@gmail.com'

Found the following (possibly) invalid URLs:
URL: https://codecov.io/gh/ropensci/stats19 (moved to https://app.codecov.io/gh/ropensci/stats19)
From: README.md
Status: 200
Message: OK
URL: https://doi.org/10.1136/bmj.b4469
From: inst/doc/blog.html
inst/doc/stats19.html
Status: 403
Message: Forbidden

Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'blog.Rmd' using rmarkdown
--- finished re-building 'blog.Rmd'

--- re-building 'stats19-training-setup.Rmd' using rmarkdown
--- finished re-building 'stats19-training-setup.Rmd'

--- re-building 'stats19-training.Rmd' using rmarkdown

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

  date, intersect, setdiff, union

--- finished re-building 'stats19-training.Rmd'

--- re-building 'stats19-vehicles.Rmd' using rmarkdown
Data provided under OGL v3.0. Cite the source and link to:
www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2018.csv'
length 14803084 bytes (14.1 MB)

downloaded 14.1 MB

Quitting from lines 29-31 (stats19-vehicles.Rmd)
Error: processing vignette 'stats19-vehicles.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'stats19-vehicles.Rmd'

--- re-building 'stats19.Rmd' using rmarkdown
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Accidents_2017.zip'
length 3997883 bytes (3.8 MB)

downloaded 3.8 MB

Quitting from lines 142-146 (stats19.Rmd)
Error: processing vignette 'stats19.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'stats19.Rmd'

SUMMARY: processing the following files failed:
'stats19-vehicles.Rmd' 'stats19.Rmd'

Error: Vignette re-building failed.
Execution halted

Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Robin Lovelace rob00x@gmail.com'

Found the following (possibly) invalid URLs:
URL: https://codecov.io/gh/ropensci/stats19 (moved to https://app.codecov.io/gh/ropensci/stats19)
From: README.md
Status: 301
Message: Moved Permanently
URL: https://doi.org/10.1136/bmj.b4469
From: inst/doc/blog.html
inst/doc/stats19.html
Status: 403
Message: Forbidden

Robinlovelace commented

My unanswered response from 8 days ago:

Thanks, I've submitted a new version with the updated codecov URL.

I am fairly certain the other issues were false positives.

  1. Regarding the issue with this URL https://doi.org/10.1136/bmj.b4469 I have double checked and it seems like a working URL. How should I change it if that is the URL recommended by the academic journal?

  2. Regarding the warning, it seems that readr was not installed on the test server, that is outside my sphere of influence.

Robin

Robinlovelace commented

My response today:

Just as a follow up, I have not yet had a response to the questions below and it seems that the package has been archived.
I plan to resubmit another version. In the meantime if someone could find time to respond to my comments/questions explaining why I think there was a 'false positive' rejection I would be very grateful.
All the best,
Robin
Thanks, I've submitted a new version with the updated codecov URL.
I am fairly certain the other issues were false positives.

  1. Regarding the issue with this URL https://doi.org/10.1136/bmj.b4469 I have double checked and it seems like a working URL. How should I change it if that is the URL recommended by the academic journal?
  2. Regarding the warning, it seems that readr was not installed on the test server, that is outside my sphere of influence.
layik commented

heh! Will follow this up at first chance.

Robinlovelace commented

Resubmitted 🤞 cc @agila5 also, let's wait and see.

  • 👍1
Robinlovelace commented

New error, should have used urlchecker before resubmission.

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2021-10-20 as check problems were not
    corrected in time.

Found the following (possibly) invalid URLs:
  URL: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/743853/reported-road-casualties-gb-notes-definitions.pdf
    From: inst/doc/blog.html
    Status: 404
    Message: Not Found

https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211020_120707/Windows/00check.log

Robinlovelace commented

More issues : (

Dear maintainer,

package stats19_1.5.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211020_120707/Windows/00check.log
Status: 1 ERROR, 1 WARNING, 1 NOTE
Debian: https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211020_120707/Debian/00check.log
Status: 1 ERROR, 1 WARNING, 1 NOTE

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
https://stat.ethz.ch/mailman/listinfo/r-package-devel
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
https://win-builder.r-project.org/incoming_pretest/stats19_1.5.0_20211020_120707/
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Robin Lovelace rob00x@gmail.com'

New submission

Package was archived on CRAN

CRAN repository db overrides:
X-CRAN-Comment: Archived on 2021-10-20 as check problems were not
corrected in time.

Found the following (possibly) invalid URLs:
URL: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/743853/reported-road-casualties-gb-notes-definitions.pdf
From: inst/doc/blog.html
Status: 404
Message: Not Found

Flavor: r-devel-windows-ix86+x86_64
Check: tests, Result: ERROR
Running 'skip-download.R' [0s]
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(stats19)
Data provided under OGL v3.0. Cite the source and link to:
www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
>
> test_check("stats19")
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip'
== Skipped tests ===============================================================
* On CRAN (13)

== Failed tests ================================================================
-- Error (test-utils.R:37:3): locate_files & locate_one_file works -------------
Error in `utils::download.file(zip_url, destfile = destfile, quiet = silent)`: cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip'
Backtrace:
    x
 1. \-stats19::dl_stats19(file_name = fn) test-utils.R:37:2
 2.   \-utils::download.file(zip_url, destfile = destfile, quiet = silent)

[ FAIL 1 | WARN 2 | SKIP 13 | PASS 33 ]
Error: Test failures
Execution halted

Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'blog.Rmd' using rmarkdown
--- finished re-building 'blog.Rmd'

--- re-building 'stats19-training-setup.Rmd' using rmarkdown
--- finished re-building 'stats19-training-setup.Rmd'

--- re-building 'stats19-training.Rmd' using rmarkdown

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

  date, intersect, setdiff, union

--- finished re-building 'stats19-training.Rmd'

--- re-building 'stats19-vehicles.Rmd' using rmarkdown
Data provided under OGL v3.0. Cite the source and link to:
www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2018.csv'
Quitting from lines 29-31 (stats19-vehicles.Rmd)
Error: processing vignette 'stats19-vehicles.Rmd' failed with diagnostics:
cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2018.csv'
--- failed re-building 'stats19-vehicles.Rmd'

--- re-building 'stats19.Rmd' using rmarkdown
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Accidents_2017.zip'
Quitting from lines 85-86 (stats19.Rmd)
Error: processing vignette 'stats19.Rmd' failed with diagnostics:
cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Accidents_2017.zip'
--- failed re-building 'stats19.Rmd'

SUMMARY: processing the following files failed:
'stats19-vehicles.Rmd' 'stats19.Rmd'

Error: Vignette re-building failed.
Execution halted

Flavor: r-devel-linux-x86_64-debian-gcc
Check: tests, Result: ERROR
Running 'skip-download.R' [0s/0s]
Running 'testthat.R' [2s/2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(stats19)
Data provided under OGL v3.0. Cite the source and link to:
www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
>
> test_check("stats19")
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip'
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (13)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-utils.R:37:3): locate_files & locate_one_file works ─────────────
Error in `utils::download.file(zip_url, destfile = destfile, quiet = silent)`: cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip'
Backtrace:
    █
 1. └─stats19::dl_stats19(file_name = fn) test-utils.R:37:2
 2.   └─utils::download.file(zip_url, destfile = destfile, quiet = silent)

[ FAIL 1 | WARN 2 | SKIP 13 | PASS 33 ]
Error: Test failures
Execution halted

Flavor: r-devel-linux-x86_64-debian-gcc
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
...
--- re-building 'blog.Rmd' using rmarkdown
--- finished re-building 'blog.Rmd'

--- re-building 'stats19-training-setup.Rmd' using rmarkdown
--- finished re-building 'stats19-training-setup.Rmd'

--- re-building 'stats19-training.Rmd' using rmarkdown

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

  date, intersect, setdiff, union

--- finished re-building 'stats19-training.Rmd'

--- re-building 'stats19-vehicles.Rmd' using rmarkdown
Data provided under OGL v3.0. Cite the source and link to:
www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2018.csv'
Quitting from lines 29-31 (stats19-vehicles.Rmd)
Error: processing vignette 'stats19-vehicles.Rmd' failed with diagnostics:
cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2018.csv'
--- failed re-building 'stats19-vehicles.Rmd'

--- re-building 'stats19.Rmd' using rmarkdown
trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Accidents_2017.zip'
Quitting from lines 85-86 (stats19.Rmd)
Error: processing vignette 'stats19.Rmd' failed with diagnostics:
cannot open URL 'https://data.dft.gov.uk/road-accidents-safety-data/dftRoadSafetyData_Accidents_2017.zip'
--- failed re-building 'stats19.Rmd'

SUMMARY: processing the following files failed:
'stats19-vehicles.Rmd' 'stats19.Rmd'

Error: Vignette re-building failed.
Execution halted

Robinlovelace commented

It's now back on CRAN 🎉 but see #215