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

Fri Jun 29 10:52:51 CEST 2018

Thx Henrik.

That's indeed one of the issues: right now these minor and defendable
changes are not reflected in the version or filename. Hence there's really
no way to know the tarball (and hence the checksums) changed other than a
build suddenly failing. Our sysadmin proposed to add eg _1 or _patched to
the updated tarball, but I also realize this would require a lot of changes
in other places. I wish I knew a way this could be avoided without causing
trouble elsewhere, but I'm not inventive enough alas.

The other three packages mentioned in that issue, don't even show a visible
change. So in those cases, all (text) files in the tarball are identical
and yet the checksum somehow changed as well. There it's even more
baffling, but I'm more confident that this should be solvable on CRAN
without interfering with other things.

Cheers
Joris

On Thu, Jun 28, 2018 at 6:50 PM, Henrik Bengtsson <
henrik.bengtsson using gmail.com> wrote:

> 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]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

-- 
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

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