3:42 p.m.
So, I've modified r2spec fairly heavily on my own. Pierre-Yves
suggested I bring conversation straight here, so I'm doing that.
I'll put a SRPM of my r2spec up at the next point when it works. It
worked earlier today, but of course I'm doing more surgery right now.
Here are the most visible changes I've made so far; Please hear them
as suggestions, not demands. :)
+ Takes R package metadata from repositories directly through
available.packages. Can load from many repos at once.
+ Cleanly handles multi-line fields in package metadata
+ Recursively chases Depends
+ including across repositories (i.e. CRAN depends on BioC)
+ Or Depends and Suggests, and Imports and Extends.
There's a lot more to this. Separate topic, separate post.
+ Uses a single template for specfile, instead of two long functions
with literal strings.
+ Permits template to be specified on the command line
+ String manipulation by regexp instead of iterated 'replace' and such.
+ Maintains a dependency graph to permit building an automated rpmbuild order.
[ toy additions ]
outputs GraphViz (dot format) illustrations of dependency graphs.
I know this is lots and lots of change. I hope you don't see it as
encroaching.
- Allen S. Rout
1:58 a.m.
Hi Allen
Thanks for all the work done :-)
On Thu, 2009-09-03 at 16:42 -0400, Allen S. Rout wrote:
+ Takes R package metadata from repositories directly through
available.packages. Can load from many repos at once.
Is it still able to fetch information from the package itself (if you
suddenly want to build the spec without internet connection) ?
+ Cleanly handles multi-line fields in package metadata
+ Uses a single template for specfile, instead of two long functions
with literal strings.
+ Permits template to be specified on the command line
+ String manipulation by regexp instead of iterated 'replace' and such.
That's for sure better than the crap I was using :)
+ Recursively chases Depends
+ including across repositories (i.e. CRAN depends on BioC)
+ Or Depends and Suggests, and Imports and Extends.
There's a lot more to this. Separate topic, separate post.
I'm not sure
here, why recursively chase the depends when you want to
build a single RPM ?
+ Maintains a dependency graph to permit building an automated
rpmbuild order.
That's a cool feature :)
[ toy additions ]
outputs GraphViz (dot format) illustrations of dependency graphs.
I have a script that does it for the entire bioconductor repo.
I know this is lots and lots of change. I hope you don't see it
as
encroaching.
It's not GPL for nothing ;-)
IMHO R2spec is really a tool that should keep doing what it is good at,
generating spec file.
However I could see the need for another tool that allows to
generate/build spec/rpm in a recursive manner. Basically allowing
sysadmin to build an entire repo easily.
Something for which you would do:
tool --build http://link/to/some/package.tar.gz
and which would generate all the spec file needed in order to be able to
build this package.
But then again, it's just my opinion and it can be worth to just have
everything in one tool instead of splitting :-)
Best regards,
Pierre
9:13 p.m.
Pierre-Yves <pingou-E11Oz7VxvVOXCRStZZN3OA(a)public.gmane.org> writes:
IMHO R2spec is really a tool that should keep doing what it is good
at, generating spec file. However I could see the need for another
tool that allows to generate/build spec/rpm in a recursive
manner. Basically allowing sysadmin to build an entire repo easily.
Something for which you would do: tool --build
http://link/to/some/package.tar.gz and which would generate all the
spec file needed in order to be able to build this package.
I haven't seen any responses to my package-deps thinking. I'm hoping
that's because everyone read it and said to themselves, "Wow, this
Allen fellow is an utter genius: How profoundly correct he is! ".
Yeah, right.
OK, here's the SRPM of my current state.
http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.0-asr.src.rpm
When I run that against ggplot2, I get a "broad" dependency graph of
152 packages. That's the list of packages that "should" be installed
to be able to R CMD CHECK all the packages, recursively.
That fact, the recursive Suggests graph, is why I think any tool that
builds a single spec needs to do the math; because there's no way we
can CHECK a package without doing it.
- Allen S. Rout
12:10 p.m.
On Wednesday 09 September 2009 Allen S. Rout wrote:
I haven't seen any responses to my package-deps thinking.
I'm hoping
that's because everyone read it and said to themselves, "Wow, this
Allen fellow is an utter genius: How profoundly correct he is! ".
Yeah, right.
The probable cause is more like "everyone would like to comment but REAL LIFE
(tm) got in the way", at least it was for me.
OK, here's the SRPM of my current state.
http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.0-asr.src.rpm
When I run that against ggplot2, I get a "broad" dependency graph of
152 packages. That's the list of packages that "should" be installed
to be able to R CMD CHECK all the packages, recursively.
Considering that cran has more than 1800 packages I would that this is small
subset. ;-)
That fact, the recursive Suggests graph, is why I think any tool
that
builds a single spec needs to do the math; because there's no way we
can CHECK a package without doing it.
What could be done, depending on the needs found, is to build a python library
where both R2spec and your tools use the code from.
- Allen S. Rout
--
José Abílio
2 p.m.
José Matos <jamatos-BxEiAy0842I(a)public.gmane.org> writes:
The probable cause is more like "everyone would like to comment
but REAL LIFE
(tm) got in the way", at least it was for me.
I understand entirely. :)
Considering that cran has more than 1800 packages I would that this
is small
subset. ;-)
yeah, but it's still honking huge compared to what I thought I'd be
able to do. It was when I saw that depgraph that I decided I would
just work on building sets instead of singles.
- Allen S. Rout
2:35 a.m.
On Thursday 03 September 2009 Allen S. Rout wrote:
So, I've modified r2spec fairly heavily on my own. Pierre-Yves
suggested I bring conversation straight here, so I'm doing that.
I'll put a SRPM of my r2spec up at the next point when it works. It
worked earlier today, but of course I'm doing more surgery right now.
Just for curiosity, do you create the %test section on the first passage? I
had to comment that section for bootstrap because I had cyclic dependencies
where test section of package A would depend on package B, and the test of
package B would depend on A.
- Allen S. Rout
--
José Abílio
2:16 p.m.
José Matos <jamatos-BxEiAy0842I(a)public.gmane.org> writes:
Just for curiosity, do you create the %test section on the first
passage? I had to comment that section for bootstrap because I had
cyclic dependencies where test section of package A would depend on
package B, and the test of package B would depend on A.
I'm hoping my previous message about dependencies has kind of answered
this question. I've tried to be clear, but the topic is twisty and
complex, and rife with politics.
My "branch" (If I may so dignify it) is now doing the following:
+ Generating the specfiles for a broad dependency tree of a package
+ Generating a rpm build script which will go through the specs, and
- build a RPM
- install the RPM
in an order which satisfies the narrow dependency tree.
I'm currently testing that one, it built the 162-package tree for
ggplot2 with a relatively small number of RPM build errors, which I
haven't yet solved.
I'm testing the r2spec package now, once I smack the bugs in my RPM of
it I'll stick it up for kibitzing.
Once _that_ is complete, I intend to automate the running of the R CMD
CHECKs.
- Allen S. Rout
2:04 p.m.
José Matos <jamatos-BxEiAy0842I(a)public.gmane.org> writes:
So you running a R CMD CHECK for all the newly installed packages?
Clever. :-)
Right. Since by definition we know we can't "CHECK packages before
using the RPM", the best I could come up with was "CHECK packages
before considering them suitable for distribution".
I would welcome some other theory; it totally squicks me to have the
check facility available yet not use it before I get an RPM out of the
process.
When I suggested doing a conservative CHECK during build, and then the
full CHECK afterwards, the R folks shrugged and asked "why bother with
the first one?". And I can't disagree.
- Allen S. Rout
8:45 p.m.
On Thu, 3 Sep 2009, Allen S. Rout wrote:
So, I've modified r2spec fairly heavily on my own. Pierre-Yves
suggested I bring conversation straight here, so I'm doing that.
I'll put a SRPM of my r2spec up at the next point when it works. It
worked earlier today, but of course I'm doing more surgery right now.
I checked the list subject, and do not see that the URL for a
new version has been mentioned. Pierre-Yves' version worked
well for me with some mechanical edits to handle versioning
valued, and to break some R CMD CHECK dependency loops to
permit bootstrapping new package groups in.
This was on a packaging effort for a couple hundred CRAN
financial and econometric R add on packages, earlier this year
-- Russ herrold
12:44 p.m.
R P Herrold <herrold-lD49m8UYmPxWk0Htik3J/w(a)public.gmane.org> writes:
On Thu, 3 Sep 2009, Allen S. Rout wrote:
> So, I've modified r2spec fairly heavily on my own. Pierre-Yves
> suggested I bring conversation straight here, so I'm doing that.
>
> I'll put a SRPM of my r2spec up at the next point when it works. It
> worked earlier today, but of course I'm doing more surgery right now.
I checked the list subject, and do not see that the URL for a new
version has been mentioned.
Wierd. I've thought I've mentioned several of them now. Have any of
you seen any of those messages?
http://article.gmane.org/gmane.linux.redhat.fedora.r.devel/200
is the most recent, referring to my 2.6.2.
Pierre-Yves' version worked well for me with some mechanical
edits
to handle versioning valued, and to break some R CMD CHECK
dependency loops to permit bootstrapping new package groups in.
This was on a packaging effort for a couple hundred CRAN financial
and econometric R add on packages, earlier this year
I'm definitely focusing on building a whole dependency tree as a
coordinated effort. I've attempted to formalize the (IMO poor) fit
between the R ideas about package deps, and the RPM ideas.
http://article.gmane.org/gmane.linux.redhat.fedora.r.devel/177
- Allen S. Rout
9:50 a.m.
On Mon, 28 Sep 2009, Allen S. Rout wrote:
http://article.gmane.org/gmane.linux.redhat.fedora.r.devel/200
is the most recent, referring to my 2.6.2.
http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.2-asr.src.rpm
noted there is a dead link when I seek to pull it
-- Russ herrold
12:14 p.m.
R P Herrold <herrold-lD49m8UYmPxWk0Htik3J/w(a)public.gmane.org> writes:
http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.2-asr.src.rpm
noted there is a dead link when I seek to pull it
Well, crap. Should be there now.
It looks like the last time I copied over the 'binary' rpm, and not
the src. They're both still there.
- Allen S. Rout
12:27 p.m.
On Wed, 30 Sep 2009, Allen S. Rout wrote:
R P Herrold <herrold-lD49m8UYmPxWk0Htik3J/w(a)public.gmane.org>
writes:
> http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.2-asr.src.rpm
> noted there is a dead link when I seek to pull it
Well, crap. Should be there now.
thank you ... looking at it now
-- Russ herrold
5335
days inactive
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days old
r-devel@lists.fedoraproject.org
13 comments
4 participants
participants (4)
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Allen S. Rout -
José Abílio Matos -
Pierre-Yves Chibon -
R P Herrold