Re: About different opinions of version numbering schemes containg '.' and '-' (Was: [devteam-bioc] BioConductor phyloseq defines relation to not yet existing ade4 version])
On 2 June 2018 at 13:11, Andreas Tille wrote:
| Hi,
|
| I was digging in my archive about another issue where a dash '-' in a
| version number creates an issue in our packaging. I could imagine that
IIRC a really loooooong time ago it did -- I think when Charles wrote
cran2deb as a Summer of Code project I may have recommended the regexp switch
from - to . yet I think we have not needed it for a long time.
| we include some list in dh-update-R where we do the needed replacements
| (currently for ade4 and quantmod) even if I'd prefer if upstream would
| stop using "random signs" instead of the proper version released version
| number.
That is unnecessarily strong language that not only "not helps" but
distracts.
R (at CRAN) check these things too (which I why I am very surprised about
that Graham found with tseries and about which I will follow up with
upstream).
Consider the following R code (!!)
R> p1 <- as.package_version("4.1-9")
R> p2 <- as.package_version("4.1.13")
R> p1 < p2
[1] TRUE
R> p1 > p2
[1] FALSE
R>
so R itself is perfectly capably to treat version Depends (in something
modeled strongly on what we do). And it seems to do just what we do:
edd@rob:~$ dpkg --compare-versions 4.1-9 lt 4.1.13 && echo TRUE
TRUE
edd@rob:~$ dpkg --compare-versions 4.1-9 gt 4.1.13 && echo TRUE
edd@rob:~$
I think we both allow 1.2-3 and 1.2.3 and Debian can build 1.2-3-1 and
1.2.3-1 equaly well off them.
Dirk
| Kind regards
|
| Andreas.
|
| ----- Forwarded message from Andreas Tille <andreas@an3as.eu> -----
|
| Date: Thu, 17 Nov 2016 16:14:43 +0100
| From: Andreas Tille <andreas@an3as.eu>
| To: Martin Morgan <martin.morgan@roswellpark.org>, Gordon Ball <gordon@chronitis.net>
| Cc: Bioconductor Package Maintainer <maintainer@bioconductor.org>
| Subject: Re: [devteam-bioc] BioConductor phyloseq defines relation to not yet existing ade4 version
|
| Hi Martin,
|
| On Thu, Nov 17, 2016 at 07:04:51AM -0500, Martin Morgan wrote:
| > On 11/17/2016 06:54 AM, Maintainer wrote:
| > >Hi again,
| > >
| > >sorry for nagging again but does anybody have a clue how to use phyloseq
| > >if it requires a not yet released ade4 (>= 1.7.2)? I think it is just a
| > >typo and should be ade4 (>= 1.7-2) but a confirmation of this assumpion
| > >would be very helpful.
| >
| > (a) the Writing R Extensions manual
| > https://cran.r-project.org/doc/manuals/r-release/R-exts.html says
| >
| > The mandatory ‘Version’ field gives the version of the package. This is a
| > sequence of at least two (and usually three) non-negative integers separated
| > by single ‘.’ or ‘-’ characters. The canonical form is as shown in the
| > example [0.5-1], and a version such as ‘0.01’ or ‘0.01.0’ will be handled as
| > if it were ‘0.1-0’.
|
| I fully agree that 1.7.2 and 1.7-2 are perfectly valid version numbers.
|
| > (b) R installs the package, indicating that from it's perspective the
| > dependency is satisfied.
| >
| > From these I think the answer is that it is not technically a typo, and that
| > you would not be making an assumption that the intention was 1.7-2.
|
| May be R is able to resolve the version declared as 1.7.2 inside the
| DESCRIPTION as 1.7-2 installed on the system. However, I consider it
| quite strange that a non-existing version number (while 1.7.2 is valid
| it does not exist anyway) can resolve the dependency relation. The
| quote above does not define any relation between a string containing a
| '-' and a '.'. This fact might make R tolerant against the non-matching
| version string - but Debian is not.
|
| However, in the Debian packaging system is 1.7-2 < 1.7.2. Since we now
| have a new helper system that parses DESCRIPTION files and puts the
| result into the Debian package control information this now creates an
| unresolvable conflict. Your arguing does not leave me any better
| conclusion than to really patch the DESCRIPTION file to get a valid
| version match with ade4 in case you do not consider the non-matching
| string as a bug.
|
| Kind regards
|
| Andreas.
|
| > >On Fri, Nov 11, 2016 at 10:59:44AM +0100, Andreas Tille wrote:
| > >>Hi,
| > >>
| > >>the address specified under "Maintainer" at the phyloseq download page
| > >>unfortunatel bounces. Do you have any hint what to do next?
| > >>
| > >>Kind regards
| > >>
| > >> Andreas.
| > >>
| > >>----- Forwarded message from Andreas Tille <andreas@an3as.eu> -----
| > >>
| > >>Date: Fri, 11 Nov 2016 10:54:31 +0100
| > >>From: Andreas Tille <andreas@an3as.eu>
| > >>To: "Paul J. McMurdie" <mcmurdie@stanford.edu>, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
| > >>Subject: BioConductor phyloseq defines relation to not yet existing ade4 version
| > >>
| > >>Hi Paul,
| > >>
| > >>I intend to upgrade phyloseq for Debian to version 1.8.0. However, the
| > >>import relation ade4 (>= 1.7.2) defined in the DESCRIPTION can not be
| > >>fullfilled since the latest version of ade4 is 1.7-4 (which is lower
| > >>than 1.7.2 by version comparison rules). I suspect you intended to
| > >>specify rather
| > >>
| > >> ade4 (>= 1.7-2)
| > >>
| > >>Could you please confirm this suspicion?
| > >>
| > >>Kind regards
| > >>
| > >> Andreas.
| > >>
| > >>--
| > >>http://fam-tille.de
| > >>
| > >>----- End forwarded message -----
| > >>
| > >>--
| > >>http://fam-tille.de
| > >
| >
| >
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| >
|
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|
| ----- End forwarded message -----
|
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--
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org
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