gmane.linux.redhat.fedora.r.devel

[Fedora-r-devel-list] Review request

Pierre-Yves Chibon — 2012-05-13T17:47:02

Hi,

In order to update some Bioconductor R libraries to their latest version
I have a new dependency that has to be packaged.

The review request is there:
https://bugzilla.redhat.com/show_bug.cgi?id=821267

If someone has sometime to look into it :-)

Thanks in advance!
Pierre
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Re: [Fedora-r-devel-list] R-repo

Pierre-Yves Chibon — 2012-05-13T17:23:24

Time is definitively part of the answer the other part being the
challenge of rebuilding the repo once in a while when necessary.


R can be coupled with java as it can be with C/C++/fortran &so on, I
*assume* that this is what was done in this package (again, *assumed*).
If it is not the case, then for sure it should not be this way and it
should rely on system libraries.

R-repo is/was aiming at automatically generated RPM which mean that a
number of them are not 100% valid. At least it gives us a basis for
further improvement.

I have to say that from my side time is truly limiting and the situation
won't change (it will even get worse) with the fact that I am starting
the last year of my PhD but at least this time everything is publicly
available on github if there are people interested in the
maintenance/development of the project.


To be honest, I do not know, but I am not sure install.packages runs the
tests and thus it likely doesn't run into the circular dependency
problem which are most of the time of the type: A requires B which
suggests A (or similar).


There are no form of license check done atm in R-repo and it doesn't
rely on a central database.
The dependency tree is built by parsing the PACKAGES files from the
different repository. 
The R-repo-utility [1] contains the script doing the work (building the
tree, building the RPMs, checking for updates and so on).


Let me know if I can be of any help.

Regards,
Pierre

[1] https://github.com/pypingou/R-repo-utility
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Re: [Fedora-r-devel-list] R-repo

José Matos — 2012-05-12T12:45:18

After June 11th sure, until there I have 18h of classes per week for
undergrads, master and phd students and with a seven months old lovely
daughter there is not much of free time, oh and surely the scouts
work... :-)

My last surge for build R packages for Fedora is due to the academic work.
I have several students doing their master thesis using stochastic
differential equations in several domains and for that I suggested them
to use R packages since R is a language they learn in the course.

One of the packages that is appropriate is the Sim.DiffProc package. For
that package the chain dependency is relatively simple.

So if you do not mind I have several questions regarding this issue.

1) Why is r-repo.org not available for Fedora? Lack of time is a fair
answer. :-)

2) I noticed that you have R-xlsxjars packaged in r-repo, from a quick
glance it looks like it just packages a set of jar files. I am clueless
when it comes to java but are not those some kind of binary files that
could be replaced using dependencies for system libraries? I am aware
that jars can have different purposes but I am asking anyway.



Do you have any idea of how R install.packages deals with these cases?

While searching for further information I noticed that the corresponding
effort on the debian side is cran2deb
http://r-forge.r-project.org/scm/?group_id=247

and the active repository is available at http://debian-r.debian.net/

From the available discussion and from my previous work I know that
there are several issues to be tracked. One of them is the package
license and the other are the external (system libraries) dependencies.
Is this information stored in any central place (database)?


Thank for all your hard work and regards,

Re: [Fedora-r-devel-list] problems while building R-rJava

José Matos — 2012-05-11T20:00:13

Right, I got over this by installing R-java-devel.

Regards,

[Fedora-r-devel-list] problems while building R-rJava

José Matos — 2012-05-11T19:43:12

Hello,
    while chasing the several dependencies to build R-Sim-DiffProc I had
to build R-rJava, at moment that is failing while testing the examples.
Are there any suggestions to overcome this?

* checking examples ... ERROR
Running examples in 'rJava-Ex.R' failed
The error most likely occurred in:


[1] 0

+   f <- new(J("java.awt.Frame"), "Hello")
+   f$setVisible(TRUE)
+ }
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance",
.jfindClass(class),  :
  java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation
which requires it.
Calls: new -> new -> .J -> .jcall -> .jcheck -> .Call
Execution halted
error: Bad exit status from /tmp/rpmbuild/rpm-tmp.DdN0bT (%check)


Regards,

[Fedora-r-devel-list] Start bioconductor update

Pierre-Yves Chibon — 2012-04-26T15:07:06

Hi,

I have started to update a bunch of R packages to the latest version of
bioconductor.

Feel free to test and give karma:

F17:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc17,R-hgu95av2cdf-2.10.0-1.fc17,R-maanova-1.26.0-1.fc17,R-multtest-2.12.0-1.fc17,R-preprocessCore-1.18.0-1.fc17,R-ROC-1.32.0-1.fc17,R-qvalue-1.30.0-1.fc17,R-statmod-1.4.14-1.fc17,R-timeDate-2160.96-1.fc17,R-tkWidgets-1.34.0-1.fc17,R-DynDoc-1.34.0-1.fc17,R-widgetTools-1.34.0-1.fc17,R-XML-3.9.4-1.fc17,R-ALL-1.4.12-1.fc17,R-abind-1.4.0-2.fc17,R-BufferedMatrix-1.20.0-1.fc17
F16:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc16,R-hgu95av2cdf-2.10.0-1.fc16,R-maanova-1.26.0-1.fc16,R-multtest-2.12.0-1.fc16,R-preprocessCore-1.18.0-1.fc16,R-ROC-1.32.0-1.fc16,R-qvalue-1.30.0-1.fc16,R-statmod-1.4.14-1.fc16,R-timeDate-2160.96-1.fc16,R-tkWidgets-1.34.0-1.fc16,R-DynDoc-1.34.0-1.fc16,R-widgetTools-1.34.0-1.fc16,R-XML-3.9.4-1.fc16,R-ALL-1.4.12-1.fc16,R-abind-1.4.0-1.fc16,R-BufferedMatrix-1.20.0-1.fc16
F15:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc15,R-hgu95av2cdf-2.10.0-1.fc15,R-maanova-1.26.0-1.fc15,R-multtest-2.12.0-1.fc15,R-preprocessCore-1.18.0-1.fc15,R-ROC-1.32.0-1.fc15,R-qvalue-1.30.0-1.fc15,R-statmod-1.4.14-1.fc15,R-timeDate-2160.96-1.fc15,R-tkWidgets-1.34.0-1.fc15,R-DynDoc-1.34.0-1.fc15,R-widgetTools-1.34.0-1.fc15,R-XML-3.9.4-1.fc15,R-ALL-1.4.12-1.fc15,R-abind-1.4.0-1.fc15,R-BufferedMatrix-1.20.0-1.fc15

Thanks in advance!

Pierre
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Re: [Fedora-r-devel-list] R-repo

Pierre-Yves Chibon — 2012-02-29T21:21:19

Well the structure is there and a number of rpms available.
I have started on the update mechanism but I have only got around the
first round.
The spec are on github and I have no problem giving the rights to commit
if people are interested (<hint>, <hint> ;-)).


<irony>hm R ? circular dependencies? I think I've heard about that once
or twice </irony>

Pierre
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Re: [Fedora-r-devel-list] R-repo

José Matos — 2012-02-29T19:21:08

After almost two months going on what is the outcome of this project?

Back in September I wanted to package some R libraries and it took some
time to get all the packages due to the build requirement of each
package, I had to unravel the dependencies while deciding what was
necessary to bootstrap the process, and not even speaking about circular
references. Clearly a fun project... :-)

So this always makes a fun read. :-)

[Fedora-r-devel-list] [Fwd: Re: [Rd] Changed behaviour of 'R CMDINSTALL']

Pierre-Yves Chibon — 2012-01-11T15:53:15

Hi all,

Although using the latest version of R from updates-testing:
https://admin.fedoraproject.org/updates/FEDORA-2012-0119/
I could however recompile successfully R-zoo (arch specific) and
R-widgetTools (noarch) from their latest git version without errors. I
think this is worth noting.

Good day,
Pierre
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Re: [Fedora-r-devel-list] R-repo

Adam Huffman — 2012-01-04T10:27:52

Pierre,

Many thanks for this.  I've been working on some of the Bioinformatics
R packages off and on and it will be very helpful.  I'll send you any
useful changes I already have.

Cheers,
Adam
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[Fedora-r-devel-list] R-repo

Pierre-Yves Chibon — 2012-01-04T08:43:25

Dear all,

To the great despair of spot, I have started to build CRAN and
Bioconductor :-)
This time, I am trying to make things cleaner and more accessible.

I just uploaded all the spec files on github:
https://github.com/pypingou/R-repo-spec
and the scripts on:
https://github.com/pypingou/R-repo-utility

The whole project is hosted at http://r-repo.org

At the moment everything is still in a early stage (for example, the
r-repo-release rpm is not even done yet), but if you configure the repo
by hand, you should be able to get RPMs.

At least this time, if work becomes overwhelming again, what has been
done will remain accessible :-)

I would prefer to not announce this officially just yet, but some
feedback be nice (thus this email). So if you feel like testing and are
facing problem, let me know!

Hope this helps,
Best regards,
Pierre


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Re: [Fedora-r-devel-list] R-repo

Adam Huffman — 2012-01-04T10:27:52

Pierre,

Many thanks for this.  I've been working on some of the Bioinformatics
R packages off and on and it will be very helpful.  I'll send you any
useful changes I already have.

Cheers,
Adam
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[Fedora-r-devel-list] R-repo

Pierre-Yves Chibon — 2012-01-04T08:43:25

Dear all,

To the great despair of spot, I have started to build CRAN and
Bioconductor :-)
This time, I am trying to make things cleaner and more accessible.

I just uploaded all the spec files on github:
https://github.com/pypingou/R-repo-spec
and the scripts on:
https://github.com/pypingou/R-repo-utility

The whole project is hosted at http://r-repo.org

At the moment everything is still in a early stage (for example, the
r-repo-release rpm is not even done yet), but if you configure the repo
by hand, you should be able to get RPMs.

At least this time, if work becomes overwhelming again, what has been
done will remain accessible :-)

I would prefer to not announce this officially just yet, but some
feedback be nice (thus this email). So if you feel like testing and are
facing problem, let me know!

Hope this helps,
Best regards,
Pierre


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[Fedora-r-devel-list] Calls for tester

Pierre-Yves Chibon — 2011-11-12T20:38:30

Good day everyone,

As indicated on the planet, I just re-wrote almost completely R2spec,
tried to make the code cleaner.

This means that if you have code relying on it, it will most likely
break with this update, but I hope you'll find the new code
cleaner/easier to work with.

On the other-side I added things like unit-tests so I am confident the
code does what it's supposed to but I would appreciate if some of you
had/took the time to test it.

Feel free to shout any complains you may have,
Thanks,
Pierre

Update are:
F15: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc15
F16: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc16
EL5: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el5
EL6: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el6
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Re: [Fedora-r-devel-list] Plans for 2.14.0

Pierre-Yves Chibon — 2011-11-03T08:15:08

We were discussing about this yesterday with spot.
The question was related to this:
    o All packages must have a namespace, and one is created on
      installation if not supplied in the sources.  This means that any
      package without a namespace must be re-installed under this
      version of R (but previously-installed data-only packages without
      R code can still be used).

So we have 64 (-1 false positive) R packages in Fedora and all the one
which 
1) are not data-only packages
2) do not already contain a namespace
have to be rebuilt.

By first look, I think we have 6 data-only packages:
R-affydata, R-BSgenome.Celegans.UCSC.ce2, R-fibroEset, R-hgu133acdf,
R-hgu95av2cdf, R-hgu95av2probe 

So 57 packages would be affected by condition one.
By simple grep, 42 packages have a namespace from this 42 I can see that
R-BSgenome.Celegans.UCSC.ce2 is in.

So we would have to rebuild: 63 - 6 - 41 = 16 packages, sounds duable.

I might have done an error or miss something but that gives us a first
clue.

Hope this helps,
Pierre



What I did:
1) list of R packages:
$ pkgdb-cli list R-\*
... 
Total: 64 packages
2) Clone all of them:
$ for pkg in `pkgdb-cli list R-\* --nameonly`; do fedpkg clone $pkg;
done;
3) Get all the packages with namespace:
$ grep namespace -iR ./R-* |wc -l
42

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Re: [Fedora-r-devel-list] Plans for 2.14.0

Johannes Lips — 2011-11-03T07:39:43

Hi,

I just filed a bug about this:
https://bugzilla.redhat.com/show_bug.cgi?id=751003

Johannes
On 11/01/2011 12:30 PM, José Matos wrote:

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[Fedora-r-devel-list] Plans for 2.14.0

José Matos — 2011-11-01T11:30:50

Hi Tom,
    what are your plans for 2.14.0? I am asking in light of the
development plan of R.

    Specifically, in this case, I am interested on the F-16 case.

    Regards,

Re: [Fedora-r-devel-list] Errors in constructing SPEC from localsource.

Allen S. Rout — 2011-05-03T13:24:57


José Matos <jamatos-BxEiAy0842I< at >public.gmane.org> writes:


So here 

http://article.gmane.org/gmane.linux.redhat.fedora.r.devel/177

is the farthest I've gotten in formalizing that path.  I've waved that
around a few times; it doesn't seem to pick up a lot of traction.  If
the topic were simple, I'd tl;dr it, but I don't think it can really be
done.



I think that's what I'd call the "Narrow dependency graph"; that is,
"packages which are needed to install other packages", as opposed to
"Packages which are needed to CMD CHECK other packages".


So; if we take R2rpm as a building block, then I suggest the following
pseudocode, to build a repo:


build_a_repo()

Make a list from CRAN, consult some local metadata about busted
packages.

Pick an unbuilt package at random, and build it, until done. 

-----

build_a_package()

 generate the narrow and wide dependency graphs for your package. 
 
 generate the narrow graph of your wide dependencies.  
 (everything you need to install to run (everything you need to check (package p ))) 
 I'll call that G'.

 Remove from G' everything already installed. 

 Build everything in G' , disabling CHECK and ignoring Suggests,
 Enhances.  [ Can we also avoid the build-it-once, check %files, build
 it again step at this stage? ]

 Install everything in G'. 

 Build everything in G', enabling CHECK.   

 Packages that build and CHECK may be signed, and removed from the list
 of packages to be built.

-----


I split it up this way because it permits also the "Build this package
and its depgraph", which is where I came in. :)

This process also suggests some additional caching, at least the package
metadata from all the repos; It's going to be necessary to trace deps
across repos, of course.  If anyone has opinions about where that ought
to go, fire away.  I figure it'd go in /var/tmp/[something] , and not
expire for a week or more.  Since the build process is going to be
multi-day, anthing shorter than that will just be insane.



- Allen S. Rout

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Re: [Fedora-r-devel-list] Errors in constructing SPEC from local source.

Pierre-Yves Chibon — 2011-04-19T09:58:43

A bit late, but I just pushed the changes. Testers are welcome :)

Pierre

Re: [Fedora-r-devel-list] Errors in constructing SPEC from localsource.

José Matos — 2011-04-14T14:22:46

It would be nice to have a plan for this.

A boostrap stage where the dependencies are reduced just to build 
dependencies.

The identification of core packages required by other packages.

Debian has done it before, Dirk can provide feedback for specific issues we 
get.

Re: [Fedora-r-devel-list] Errors in constructing SPEC from local source.

Pierre-Yves Chibon — 2011-04-13T21:10:21

I'll try to push this on the git by the end of the week-end then :)


Well at the moment I see more R2rpm/R2spec has a tool to generate rpm or
spec individually as one would have to do to incorporate them into
Fedora. It is a spec generator tool which push the work up to building
the rpm (which it needs to fill the %file section anyway).
Specs needs manual inspection and curation sometime, one needs to run
rpmlint and so on.

My thoughts were that there was space for a tool to build the whole
dependency tree and run R2spec/R2rpm in the right order.
In my attempts to build CRAN I used your R script for that. I could this
way create 7 files and then I was just running these 7 files on after
the other.
My problem was more or less:
- Takes time to build (~1 week for the whole run)

- Lack of resources (although I improved on these but not enough)

- I did it the dirty way by doing : build all R packages in fileX in
mock - Install all rpm - build all R packages in fileX+1 in mock -
install all rpm.... - restart for another arch/release
I actually wonder, if one wants to give a shot at such project in a long
term, if looking into koji would not be a nice alternative: build all
the R packages from fileX for all arch/release - populate the repo as
they are build - build all the R packages from fileX+1 for all
arch/release... And this way at the end you have a repo which you know
works.
I always had the wish to support at least i686 and x86_64 on Fedora n
and n-1 RHEL 5 and 6, so 6 to 8 (if I added rawhide) build for each
packages. For this I though koji would make sense, but I never got
around to try to install it and configure vm builders.

- Not all the packages build, sometime because of the lack of outside
dependencies.
For this reason all the packages that fails have to be inspected by
hand.

- I have a script to update existing spec file but it does not check for
changes in the dependency tree and cran as well as bioconductor are so
good at changing the dependency tree at every releases...
So for every release of bioconductor, we have to update all the spec
files for most of their elements but the changelog basically (sounds
easy when I say it this way ^^).

Basically I would keep R2spec at a single package level and build on the
top a cran2rpm or so.


All this makes me think that I still have few thousands spec files
hanging somewhere and that I should actually make them accessible
somewhere (with a warning that a significant part of it is probably
outdated).


These were my thoughts when I was looking into it.

Hope this help,

Pierre