[R-pkg-devel] Checksums changed on CRAN without any visible modifications to files.
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 at 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 at 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 at 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 at 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 at 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 at 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 at statistik.tu-dortmund.de <mailto:ligges at 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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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]]