[R-pkg-devel] Checksums changed on CRAN without any visible modifications to files.

Thu Jun 28 18:50:42 CEST 2018

Below are more details on/examples of changes due to ORCID URLs being
added to the DESCRIPTION file (from
https://github.com/easybuilders/easybuild-easyconfigs/pull/6446#issuecomment-396574744):

$ diff -ru RWeka.orig RWeka
diff -ru RWeka.orig/DESCRIPTION RWeka/DESCRIPTION

--- RWeka.orig/DESCRIPTION 2018-01-07 16:27:10.000000000 +0100
+++ RWeka/DESCRIPTION 2018-05-23 11:45:56.000000000 +0200
@@ -26,12 +26,12 @@
 License: GPL-2
 NeedsCompilation: no
 Packaged: 2018-01-07 15:04:47 UTC; hornik
-Author: Kurt Hornik [aut, cre] (0000-0003-4198-9911),
+Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
   Christian Buchta [ctb],
   Torsten Hothorn [ctb],
   Alexandros Karatzoglou [ctb],
   David Meyer [ctb],
-  Achim Zeileis [ctb] (0000-0003-0918-3766)
+  Achim Zeileis [ctb] (<https://orcid.org/0000-0003-0918-3766>)
 Maintainer: Kurt Hornik <Kurt.Hornik using R-project.org>
 Repository: CRAN
 Date/Publication: 2018-01-07 16:17:29
diff -ru RWeka.orig/MD5 RWeka/MD5
--- RWeka.orig/MD5 2018-01-07 16:27:10.000000000 +0100
+++ RWeka/MD5 2018-05-23 11:45:56.000000000 +0200
@@ -1,5 +1,5 @@
 5ee28414fe580928907527d9e4217845 *CHANGELOG
-4aae74779d3a1de0fdc64beec22078ee *DESCRIPTION
+fe0f10b7f193e91112c978228acaa5ae *DESCRIPTION
 41b1dde3a37014e3c2c5fa208fc47167 *NAMESPACE
 f9a81f720aebf5398a94efa32a2047a5 *R/AAA.R
 e8b6adbe6a0b2cf61f433762e1fd16dd *R/arff.R

It looks like such updates to existing tarballs cause troubles
downstream (e.g. EasyBuild).  Although these updates are minor (in a
functional sense), it does mean that we cannot guarantee that everyone
gets identical installs.

/Henrik
On Wed, Jun 27, 2018 at 7:03 AM Joris Meys <Joris.Meys using ugent.be> wrote:
>
> Correction: In the case of mgcv it was the publication date that changed
> for some reason. Our sysadmins keep reaching out to me in the hope to
> resolve this. Is there a way they can reach out so this can be clarified?
>
> For reference, the latest issue on mgcv :
> https://github.com/easybuilders/easybuild-easyconfigs/issues/6501
>
> Cheers
> Joris
>
> On Wed, Jun 27, 2018 at 3:30 PM, Joris Meys <Joris.Meys using ugent.be> wrote:
>
> > Dear Uwe,
> >
> > sorry to bother you again with it, but I was wondering if you had some
> > more idea about what happened. I just received another one, this time about
> > mgcv_1.8-23.tar.gz. It goes beyond my understanding as to why the MD5 sums
> > would change without any change to the package. Is there anything I can
> > check at this side to make it easier for you?
> >
> > Cheers
> > Joris
> >
> > On Thu, Jun 14, 2018 at 6:55 PM, Joris Meys <Joris.Meys using ugent.be> wrote:
> >
> >> Dear Uwe,
> >>
> >> Thank you for willing to take a look. In the report it was about the
> >> following tarballs :
> >>
> >> pkgmaker_0.22.tar.gz
> >> rngtools_1.2.4.tar.gz
> >> RcppProgress_0.4.tar.gz
> >>
> >> Our sysadmin tried diff -ru, but couldn't find any difference in the text
> >> files.
> >>
> >> Cheers
> >> Joris
> >>
> >> On Thu, Jun 14, 2018 at 5:46 PM, Uwe Ligges <
> >> ligges using statistik.tu-dortmund.de> wrote:
> >>
> >>>
> >>>
> >>> On 13.06.2018 15:40, Joris Meys wrote:
> >>>
> >>>>
> >>>>
> >>>> On Wed, Jun 13, 2018 at 3:16 PM, Uwe Ligges <
> >>>> ligges using statistik.tu-dortmund.de <mailto:ligges using statistik.tu-dortmund.de>>
> >>>> wrote:
> >>>>
> >>>>
> >>>>     When CRAN repacks and changes the DESCRIPTION file, the checksums
> >>>>     change, of course.
> >>>>
> >>>>     Best,
> >>>>     Uwe Ligges
> >>>>
> >>>>
> >>>> Dear Uwe,
> >>>>
> >>>> I understood that from the previous issue. In this case however, none
> >>>> of the files -including the DESCRIPTION file- were changed. Am I right in
> >>>> suspecting that a package is repacked when moved to the archive?
> >>>>
> >>>
> >>> No, we do not repack generally then. Perhaps the package got orphaned?
> >>>
> >>>
> >>> Which package / tarball were you talking about? I can take a look why
> >>> that one was changed and inspect why the checksum changed.
> >>>
> >>> Best,
> >>> Uwe Ligges
> >>>
> >>>
> >>>
> >>>  I
> >>>
> >>>> suspect that the tool used to repack the package is using gzip, and it
> >>>> is possible to repack without adding a timestamp as explained here :
> >>>>
> >>>> https://serverfault.com/questions/110208/different-md5sums-f
> >>>> or-same-tar-contents
> >>>>
> >>>> I can explain the different checksums when some things are changed to
> >>>> our HPC sysadmins, but they have -understandibly- difficulties with
> >>>> checksums changing for released source tarballs. Is it possible to adapt
> >>>> the archiving so that at least for identical tarballs the md5 sums remain
> >>>> the same? Or if you have other suggestions to deal with this without having
> >>>> to change hardcoded checksums in the easybuild repos, that would be very
> >>>> welcome too.
> >>>>
> >>>> Cheers
> >>>> Joris
> >>>>
> >>>> --
> >>>> Joris Meys
> >>>> Statistical consultant
> >>>>
> >>>> Department of Data Analysis and Mathematical Modelling
> >>>> Ghent University
> >>>> Coupure Links 653, B-9000 Gent (Belgium)
> >>>> <https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+G
> >>>> ent,%C2%A0Belgium&entry=gmail&source=g>
> >>>>
> >>>> tel: +32 (0)9 264 61 79
> >>>> -----------
> >>>> Biowiskundedagen 2017-2018
> >>>> http://www.biowiskundedagen.ugent.be/
> >>>>
> >>>> -------------------------------
> >>>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> >>>>
> >>>
> >>
> >>
> >> --
> >> Joris Meys
> >> Statistical consultant
> >>
> >> Department of Data Analysis and Mathematical Modelling
> >> Ghent University
> >> Coupure Links 653, B-9000 Gent (Belgium)
> >>
> >> <https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>
> >>
> >> tel: +32 (0)9 264 61 79
> >> -----------
> >> Biowiskundedagen 2017-2018
> >> http://www.biowiskundedagen.ugent.be/
> >>
> >> -------------------------------
> >> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> >>
> >
> >
> >
> > --
> > Joris Meys
> > Statistical consultant
> >
> > Department of Data Analysis and Mathematical Modelling
> > Ghent University
> > Coupure Links 653, B-9000 Gent (Belgium)
> >
> > <https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>
> >
> > tel: +32 (0)9 264 61 79
> > -----------
> > Biowiskundedagen 2017-2018
> > http://www.biowiskundedagen.ugent.be/
> >
> > -------------------------------
> > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> >
>
>
>
> --
> Joris Meys
> Statistical consultant
>
> Department of Data Analysis and Mathematical Modelling
> Ghent University
> Coupure Links 653, B-9000 Gent (Belgium)
> <https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>
>
> tel: +32 (0)9 264 61 79
> -----------
> Biowiskundedagen 2017-2018
> http://www.biowiskundedagen.ugent.be/
>
> -------------------------------
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
>         [[alternative HTML version deleted]]
>
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