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[R-pkg-devel] Package (nprcgenekeepr) archived a few days after publication to CRAN

6 messages · Mark Sharp, Henrik Bengtsson, Ben Bolker +2 more

Original
Mark Sharp
# 
I submitted an update based on needing to make some changes due to dependencies. As appended below, I received a message July 25, 2025 that the updated package (1.0.8) was on its way to CRAN. I checked shortly after July 25th and the package was published. However, it appears 1.0.8 was removed on July 29th. I do not see a problem on https://cran-archive.r-project.org/web/checks/2025/2025-07-29_check_results_nprcgenekeepr.html

I have contacted CRAN-submissions at R-project.org <mailto:CRAN-submissions at R-project.org> to find out what I need to do to rectify this but have not gotten a response. Suggestions are welcome.

Mark
R. Mark Sharp, Ph.D.
7526 Meadow Green St.
San Antonio, TX 78251
mobile: 210-218-2868
rmsharp at me.com




Begin forwarded message:

From: ligges at statistik.tu-dortmund.de
Subject: [CRAN-pretest-publish] CRAN Submission nprcgenekeepr 1.0.8
Date: July 25, 2025 at 10:56:10?PM CDT
To: rmsharp at me.com
Cc: CRAN-submissions at R-project.org
Reply-To: CRAN-submissions at R-project.org

Dear maintainer,

thanks, package nprcgenekeepr_1.0.8.tar.gz is on its way to CRAN.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: *, Result: OK
Henrik Bengtsson
# 
Sorry to hear. From https://cran.r-project.org/src/contrib/PACKAGES.in (*):

"Package: nprcgenekeepr
X-CRAN-Comment: Archived on 2025-07-29 as issues were not corrected in time.
  .
  Tested elapsed times.
X-CRAN-History: Archived on 2022-11-03 as check problems were not corrected
despite reminders.
  Unarchived on 2025-04-24."

(*) That file is a hard-yo-remember "internal" URL. You can find it via
https://www.cranhaven.org/.


How this helps,

Henrik
On Thu, Jan 15, 2026, 09:52 R. Mark Sharp <rmsharp at me.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Ben Bolker
    

    

      
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I don't think that answers the OP's question (why was it archived
after apparently passing checks/being published)?

I do get one error (reproduced below) when I `R CMD check --as-cran`
on Linux with r-devel.

  I would say that the path of least resistance would be: (1) fix the
error (assuming you can reproduce it ...); (2) bump the version number
to 1.0.9 (or 1.0.8.1, whatever); (3) (re)submit to CRAN.

 [24s/43s] ERROR
Running the tests in ?tests/testthat.R? failed.
Last 13 lines of output:
    'test_saveDataframesAsFiles.R:11:3', 'test_saveDataframesAsFiles.R:37:3',
    'test_saveDataframesAsFiles.R:62:3'

  ?? Failed tests
????????????????????????????????????????????????????????????????
  ?? Failure ('test_print.summary.nprcgenekeeprErr.R:29:3'):
print.summary.nprcgenekeeprErr prints expected output ??
  Expected failure message to match regexp "produced output".
  Actual message:
  ? ? Expected `print(summary(qcStudbook(pedOne, reportErrors =
TRUE)))` to produce no output.
    ? Actual output:
    ? Error: The animal listed as a sire and also listed as a female
is: s1.\nError: The animal listed as a dam and also listed as a male
is: d1.\n\nPlease check and correct the pedigree file.\n \nAnimal
records where parent records are suspicous because of dates.\nOne or
more parents appear too young at time of birth.\n  dam sire id sex
 birth recordStatus exit  sireBirth   damBirth sireAge\n2  d2   s1 o2
 F 2009-03-17     original <NA> 2000-07-18 2015-09-16    8.66\n3  d2
s2 o3   F 2012-04-11     original <NA> 2006-06-19 2015-09-16
5.81\n4  d2   s2 o4   M 2006-04-13     original <NA> 2006-06-19
2015-09-16   -0.18\n  damAge\n2   -6.5\n3   -3.4\n4   -9.4

  [ FAIL 1 | WARN 0 | SKIP 24 | PASS 861 ]
  Error:
  ! Test failures.
  Execution halted

On Thu, Jan 15, 2026 at 1:13?PM Henrik Bengtsson

        
<henrik.bengtsson at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Mark Sharp
    

    

      
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Ben,

Thank you for the advice. I will submit a new minor revision after addressing the issue you pointed out.

Mark

R. Mark Sharp
7526 Meadow Green St.
San Antonio, TX 78251
mobile: 210-218-2868
rmsharp at me.com

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Michael Chirico
    

    

      
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Agree with Ben about just re-submitting.

The CRAN results shared show 1.0.8 had landed on CRAN, and was passing
tests:
https://cran-archive.r-project.org/web/checks/2025/2025-07-29_check_results_nprcgenekeepr.html

The GitHub CRAN mirror also shows 1.08 being the one landed on July 25:
https://github.com/cran/nprcgenekeepr/commits/master/

I also see from the CRAN e-mail that it was "on its way to CRAN" at 10 PM
CDT, so it doesn't look like a timezone mismatch issue, either.

Mike C

        
On Thu, Jan 15, 2026 at 10:29?AM Ben Bolker <bbolker at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Lluís Revilla
    

    

      
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Taking the opportunity of this issue to share some comments regarding this
situation.

This happens sometimes: one submit a new version that fixes issues, it is
accepted.
The (same or new) issues show up again soon after.
A CRAN member sees the previous (note?) deadline and the check issues
resulting on the package being archived.

More often than not the maintainer is left thinking that the issue is
fixed: The submission passed all checks of the submission process and the
last communication they got from CRAN was that it was on its way to CRAN.
However, some time later (as in this case), they find that the package was
archived soon after being accepted (without further notification [as per
CRAN processes and policies]).

Up to last year there were ~400 cases when a package was archived in less
than 7 days after being published, ~25% of them on the same day the new
version was published. For completeness this represents ~1% of the packages
ever archived.
If we extend the period to less than 14 days, they represent ~6% of
packages ever archived.

A new notification from CRAN (and maybe a deadline extension?) to these
active and responsive maintainers would reduce the friction to keep the
package available for users.

Cheers,

Llu?s

Missatge de Michael Chirico <michaelchirico4 at gmail.com> del dia dj., 15 de
gen. 2026 a les 20:32: