Re: Pacakge norm (was Re: [Rd] orphaning CRAN packages)
(Ted Harding) wrote:
On 09-Apr-05 Prof Brian Ripley wrote:
The known problems are in the file
http://www.r-project.org/nocvs/R.check/r-devel/norm-00check.txt
No showstoppers, so given the saga of Ted's connectivity, I would
suggest waiting for the release on April 18.
There are no declared dependencies, nor did I find any searching the
code.
Thanks for the pointer. Yes, they look innocuous enough.
On the precautionary principle, however, it would be worth
dealing with the ".Fortran" warnings, since this would
safeguard against the possibility of name clash if some
other package used the same names.
Question 1:
I take it that all that's needed here is to search for
all such calls, e.g.
.Fortran("tobsn", ...)
and make sure that it one becomes
.Fortran("tobsn", ... ,PACKAGE=norm)
and so on?
Yes, but PACKAGE="norm" (quotes!)
This could be done without installing any new R (though
being able to check against the latest would be added
assurance), as also could be possible amendements related
to the "Rd" warnings (which, however, only affect "help"
and other documentation issues).
None the less,
Question 2.
It would still be interesting to test out the compilability
of the latest R on the machine I would be installing the
new one on anyway (SuSE Linux 7.2 from 2001), since this
would have oldish math libs ...
I think I have sussed out how to keep different versions
of R on the same machine, namely:
a) Edit /usr/bin/R and change
R_HOME_DIR=/usr/lib/R
to
R_HOME_DIR=/usr/lib/R-x.y.z
as appropriate.
b) Rename the directory /usr/lib/R to /usr/lib/R-x.y.z
c) Rename /usr/bin/R to /usr/bin/R-x.y.z
d) (pro tem) Make a symbolic link
ln -s /usr/bin/R-x.y.z /usr/bin/R
No, it is much simpler (and cleaner) to specify the installation
directory using
./configure --prefix=/the/path/to/R-2.0.1
After make, make install, you can start R-2.0.1 by
/the/path/to/R-2.0.1/bin/R
Uwe
Then one can install a new R without thinking about it,
provided one remembers to delete the symbolic link before
starting (or will the new installation do this all by
itself?).
Have I missed anything?
Thanks, and best wishes,
Ted.
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RE: Pacakge norm (was Re: [Rd] orphaning CRAN packages)
On 09-Apr-05 Prof Brian Ripley wrote:
> The known problems are in the file
>
> http://www.r-project.org/nocvs/R.check/r-devel/norm-00check.txt
>
> No showstoppers, so given the saga of Ted's connectivity, I would
> suggest waiting for the release on April 18.
>
> There are no declared dependencies, nor did I find any searching the
> code.
Thanks for the pointer. Yes, they look innocuous enough.
On the precautionary principle, however, it would be worth
dealing with the ".Fortran" warnings, since this would
safeguard against the possibility of name clash if some
other package used the same names.
Question 1:
I take it that all that's needed here is to search for
all such calls, e.g.
.Fortran("tobsn", ...)
and make sure that it one becomes
.Fortran("tobsn", ... ,PACKAGE=norm)
and so on?
This could be done without installing any new R (though
being able to check against the latest would be added
assurance), as also could be possible amendements related
to the "Rd" warnings (which, however, only affect "help"
and other documentation issues).
None the less,
Question 2.
It would still be interesting to test out the compilability
of the latest R on the machine I would be installing the
new one on anyway (SuSE Linux 7.2 from 2001), since this
would have oldish math libs ...
I think I have sussed out how to keep different versions
of R on the same machine, namely:
a) Edit /usr/bin/R and change
R_HOME_DIR=/usr/lib/R
to
R_HOME_DIR=/usr/lib/R-x.y.z
as appropriate.
b) Rename the directory /usr/lib/R to /usr/lib/R-x.y.z
c) Rename /usr/bin/R to /usr/bin/R-x.y.z
d) (pro tem) Make a symbolic link
ln -s /usr/bin/R-x.y.z /usr/bin/R
Then one can install a new R without thinking about it,
provided one remembers to delete the symbolic link before
starting (or will the new installation do this all by
itself?).
Have I missed anything?
Thanks, and best wishes,
Ted.
__
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Pacakge norm (was Re: [Rd] orphaning CRAN packages)
The known problems are in the file http://www.r-project.org/nocvs/R.check/r-devel/norm-00check.txt No showstoppers, so given the saga of Ted's connectivity, I would suggest waiting for the release on April 18. There are no declared dependencies, nor did I find any searching the code. On Sat, 9 Apr 2005, Uwe Ligges wrote: (Ted Harding) wrote: On 09-Apr-05 Uwe Ligges wrote: [EMAIL PROTECTED] wrote: Dear R Developers, the following CRAN packages do not cleanly pass R CMD check for quite some time now and did not have any updates since the time given. Several attempts by the CRAN admins to contact the package maintainers had no success. norm, 1.0-9, 2002-05-07, WARN It would be serious if 'norm' were to lapse, since it is part of the 'norm+cat+mix+pan' family, and people using any of these are likely to have occasion to use the others. I'd offer to try to clean up 'norm' myself if only I were up-to-date on R itself (I'm waiting for 2.1.0 to come out, which I understand is scheduled to happen soon, yes?). Ted, that's great! R-2.1.0 is scheduled to be released on April 18 (see http://developer.r-project.org/). It would be even better if you could try out the recent beta release of R-2.1.0 right now in order to spot some possible bugs before release. So it is the perfect occasion to clean up "norm" on R-2.1.0 beta this weekend. ;-) Best, Uwe Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Apr-05 Time: 13:02:22 -- XFMail -- __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] orphaning CRAN packages
(Ted Harding) wrote: On 09-Apr-05 Uwe Ligges wrote: (Ted Harding) wrote: It would be serious if 'norm' were to lapse, since it is part of the 'norm+cat+mix+pan' family, and people using any of these are likely to have occasion to use the others. I'd offer to try to clean up 'norm' myself if only I were up-to-date on R itself (I'm waiting for 2.1.0 to come out, which I understand is scheduled to happen soon, yes?). Ted, that's great! R-2.1.0 is scheduled to be released on April 18 (see http://developer.r-project.org/). It would be even better if you could try out the recent beta release of R-2.1.0 right now in order to spot some possible bugs before release. So it is the perfect occasion to clean up "norm" on R-2.1.0 beta this weekend. ;-) Well, I'll see what I can do ... though this weekend may not offer a lot of free time! No need to apologise, I just tried to take advantage of the current enthusiasm on your side. ;-) Bearing in mind Martin's and Dirk's comments, going for 2.1.0-beta right now seems unlikely to lead to any grief compared with waiting for the final release. So at any rate I could start looking at it over the next week sometime. However, there's a question or two. 1. Simply for the sake of having a look at 'norm', I think this may depend only on things which are part of R-base, so I should not need to download any "recommended" packages. Or are there things in "recommended" which are likely to be presumed? (I've always taken such things for granted since they have been installed by default when I've installed from RPMs; I've not done a full R compilation before, at least not for several years). 2. Is there a way to get, off CRAN say, a listing of which packages are "recommended"? I suffer from slow connection (5min/MB if I'm lucky, and lucky to stay fully connected for more than an hour or two -- even R-base is going to take at least an hour), so I don't want to just connect and do tools/rsync-recommended as suggested on CRAN since this may silently drop into a black hole at some point. I'd sooner do it all piecemeal, knowing what's supposed to be on the way and able to start again at that point if there are problems. But this means knowing which are the recommended ones. (This, by the way, is why I'd been waiting for 2.1.0, since it then becomes worth while making an expedition to a fast connection or negotiating with someone to do me a CD; but with the above assurances I suppose I can go ahead now anyway!) Two questions, one answer: The beta versions available from CRAN/src/base-prerelease already contain recommended packages. ./configure make make install should be sufficient, in principle. make check would be nice in order to spot errors on your platform. Uwe Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Apr-05 Time: 16:16:35 -- XFMail -- __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] orphaning CRAN packages
On 09-Apr-05 Uwe Ligges wrote: > (Ted Harding) wrote: >> It would be serious if 'norm' were to lapse, since it is >> part of the 'norm+cat+mix+pan' family, and people using any >> of these are likely to have occasion to use the others. >> >> I'd offer to try to clean up 'norm' myself if only I were >> up-to-date on R itself (I'm waiting for 2.1.0 to come out, >> which I understand is scheduled to happen soon, yes?). > > Ted, that's great! > > R-2.1.0 is scheduled to be released on April 18 (see > http://developer.r-project.org/). > > It would be even better if you could try out the recent beta > release of R-2.1.0 right now in order to spot some possible > bugs before release. > > So it is the perfect occasion to clean up "norm" on R-2.1.0 beta > this weekend. ;-) Well, I'll see what I can do ... though this weekend may not offer a lot of free time! Bearing in mind Martin's and Dirk's comments, going for 2.1.0-beta right now seems unlikely to lead to any grief compared with waiting for the final release. So at any rate I could start looking at it over the next week sometime. However, there's a question or two. 1. Simply for the sake of having a look at 'norm', I think this may depend only on things which are part of R-base, so I should not need to download any "recommended" packages. Or are there things in "recommended" which are likely to be presumed? (I've always taken such things for granted since they have been installed by default when I've installed from RPMs; I've not done a full R compilation before, at least not for several years). 2. Is there a way to get, off CRAN say, a listing of which packages are "recommended"? I suffer from slow connection (5min/MB if I'm lucky, and lucky to stay fully connected for more than an hour or two -- even R-base is going to take at least an hour), so I don't want to just connect and do tools/rsync-recommended as suggested on CRAN since this may silently drop into a black hole at some point. I'd sooner do it all piecemeal, knowing what's supposed to be on the way and able to start again at that point if there are problems. But this means knowing which are the recommended ones. (This, by the way, is why I'd been waiting for 2.1.0, since it then becomes worth while making an expedition to a fast connection or negotiating with someone to do me a CD; but with the above assurances I suppose I can go ahead now anyway!) Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Apr-05 Time: 16:16:35 -- XFMail -- __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] orphaning CRAN packages
On 9 April 2005 at 16:23, Martin Maechler wrote:
| Since R 2.1.0 is now in beta testing, we consider it very
| stable, and having less bugs than any other version of R, so
| please ("everyone!") follow Uwe's advice and install R 2.1.0"beta"
FYI, for those using Debian, packages can be had from the so-called
'experimental' archive (i.e. needs a sources.list entry for experiremental),
or directly from the pool directory
http://ftp.debian.org/debian/pool/main/r/r-base/
This provides the April 3 snapshot still tagged 'alpha'; I'll probably add a
beta release tonight or tomorrow and insert that into Debian's unstable
archive.
Dirk
--
Better to have an approximate answer to the right question than a precise
answer to the wrong question. -- John Tukey as quoted by John Chambers
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Re: [Rd] orphaning CRAN packages
> "Ted" == Ted Harding <[EMAIL PROTECTED]>
> on Sat, 09 Apr 2005 13:02:22 +0100 (BST) writes:
Ted> On 09-Apr-05 Uwe Ligges wrote:
>> [EMAIL PROTECTED] wrote:
>>
>>> Dear R Developers,
>>>
>>> the following CRAN packages do not cleanly pass R CMD
>>> check for quite some time now and did not have any
>>> updates since the time given. Several attempts by the
>>> CRAN admins to contact the package maintainers had no
>>> success.
>>>
>>> norm, 1.0-9, 2002-05-07, WARN
Ted> It would be serious if 'norm' were to lapse, since it
Ted> is part of the 'norm+cat+mix+pan' family, and people
Ted> using any of these are likely to have occasion to use
Ted> the others.
Indeed! I had a very similar thought but couldn't afford your
offer (below), so thanks a lot !
Ted> I'd offer to try to clean up 'norm' myself if only I
Ted> were up-to-date on R itself (I'm waiting for 2.1.0 to
Ted> come out, which I understand is scheduled to happen
Ted> soon, yes?).
yes, as Uwe has already confirmed.
Since R 2.1.0 is now in beta testing, we consider it very
stable, and having less bugs than any other version of R, so
please ("everyone!") follow Uwe's advice and install R 2.1.0"beta"
Martin
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Re: [Rd] orphaning CRAN packages
(Ted Harding) wrote: On 09-Apr-05 Uwe Ligges wrote: [EMAIL PROTECTED] wrote: Dear R Developers, the following CRAN packages do not cleanly pass R CMD check for quite some time now and did not have any updates since the time given. Several attempts by the CRAN admins to contact the package maintainers had no success. norm, 1.0-9, 2002-05-07, WARN It would be serious if 'norm' were to lapse, since it is part of the 'norm+cat+mix+pan' family, and people using any of these are likely to have occasion to use the others. I'd offer to try to clean up 'norm' myself if only I were up-to-date on R itself (I'm waiting for 2.1.0 to come out, which I understand is scheduled to happen soon, yes?). Ted, that's great! R-2.1.0 is scheduled to be released on April 18 (see http://developer.r-project.org/). It would be even better if you could try out the recent beta release of R-2.1.0 right now in order to spot some possible bugs before release. So it is the perfect occasion to clean up "norm" on R-2.1.0 beta this weekend. ;-) Best, Uwe Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Apr-05 Time: 13:02:22 -- XFMail -- __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] orphaning CRAN packages
On 09-Apr-05 Uwe Ligges wrote: > [EMAIL PROTECTED] wrote: > >> Dear R Developers, >> >> the following CRAN packages do not cleanly pass R CMD check >> for quite some time now and did not have any updates since >> the time given. Several attempts by the CRAN admins to contact >> the package maintainers had no success. >> >> norm, 1.0-9, 2002-05-07, WARN It would be serious if 'norm' were to lapse, since it is part of the 'norm+cat+mix+pan' family, and people using any of these are likely to have occasion to use the others. I'd offer to try to clean up 'norm' myself if only I were up-to-date on R itself (I'm waiting for 2.1.0 to come out, which I understand is scheduled to happen soon, yes?). Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Apr-05 Time: 13:02:22 -- XFMail -- __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] orphaning CRAN packages
[EMAIL PROTECTED] wrote: Dear R Developers, the following CRAN packages do not cleanly pass R CMD check for quite some time now and did not have any updates since the time given. Several attempts by the CRAN admins to contact the package maintainers had no success. norm, 1.0-9, 2002-05-07, WARN sound, 0.6, 2002-08-31, WARN Hmm, does anybody use sound extensively or does anybody use its data structures? If not: tuneR contains quite a lot of the functionality of sound and I would agree to port missing functionality (seem to be just a few functions) to tuneR (which is based on S4 rather than the S3 methods "sound" is base on). So it won't hurt if sound is moved way from CRAN one day. Uwe Bhat, 0.9-07, 2003-11-04, WARN HI, 0.1, 2003-11-04, WARN mmlcr, 1.3.2, 2003-11-15, WARN mvnmle, 0.1-4, 2003-08-21, WARN If you are the author or maintainer of one of these packages, or a user and are interested that the package stays in the main CRAN package area (including binaries for various platforms), please consider taking over as maintainer of the respective package. Otheriwse we will orphanize the packages after the release of R 2.1.0 in 10 days. In addition, the Orphaned directory of CRAN currently contains anm,2004-09-30,1.9.1 fdim,2004-09-30,1.9.1 kza,2005-01-15,2.0.1 meanscore,2004-09-30,1.9.1 npmc,2004-09-30,1.9.1 phyloarray,2004-09-30,1.9.1 seao.gui,2004-09-30,1.9.1 seao,2004-09-30,1.9.1 twostage,2004-09-30,1.9.1 We try hard to keep all packages on CRAN working "out of the box", hence we need to remove packages that are no longer actively maintained. Best, Fritz __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] orphaning CRAN packages
Dear R Developers, the following CRAN packages do not cleanly pass R CMD check for quite some time now and did not have any updates since the time given. Several attempts by the CRAN admins to contact the package maintainers had no success. norm, 1.0-9, 2002-05-07, WARN sound, 0.6, 2002-08-31, WARN Bhat, 0.9-07, 2003-11-04, WARN HI, 0.1, 2003-11-04, WARN mmlcr, 1.3.2, 2003-11-15, WARN mvnmle, 0.1-4, 2003-08-21, WARN If you are the author or maintainer of one of these packages, or a user and are interested that the package stays in the main CRAN package area (including binaries for various platforms), please consider taking over as maintainer of the respective package. Otheriwse we will orphanize the packages after the release of R 2.1.0 in 10 days. In addition, the Orphaned directory of CRAN currently contains anm,2004-09-30,1.9.1 fdim,2004-09-30,1.9.1 kza,2005-01-15,2.0.1 meanscore,2004-09-30,1.9.1 npmc,2004-09-30,1.9.1 phyloarray,2004-09-30,1.9.1 seao.gui,2004-09-30,1.9.1 seao,2004-09-30,1.9.1 twostage,2004-09-30,1.9.1 We try hard to keep all packages on CRAN working "out of the box", hence we need to remove packages that are no longer actively maintained. Best, Fritz -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
