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Today's Topics:
1. R 1.8.0 alpha (Peter Dalgaard BSA)
2. zero inflated models (Maren Wellenreuther)
3. potentially nasty interaction between R 1.8.0 and tetex
(A.J. Rossini)
4. Re: potentially nasty interaction between R 1.8.0 and tetex
(Peter Dalgaard BSA)
5. Re: potentially nasty interaction between R 1.8.0 and tetex
(A.J. Rossini)
6. rank(*) with NAs -- new option "keep" desired (Martin Maechler)
7. Re: potentially nasty interaction between R 1.8.0 and tetex
([EMAIL PROTECTED])
8. Re: potentially nasty interaction between R 1.8.0 and tetex
(Peter Dalgaard BSA)
9. Re: potentially nasty interaction between R 1.8.0 and tetex
([EMAIL PROTECTED])
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The countdown to R version 1.8.0 has begun. As a novelty, we now
make preliminary source tarballs available somewhat earlier in the
process. They will be found in
http://cran.us.r-project.org/src/base
with names of the form R-1.8.0alpha_2003-09-10.tar.gz
The first one was created a moment ago; subsequent ones will be
created by a cron job that runs at 05:00 local (Wisconsin) time.
There are still a couple of problems with these versions, but we
expect that there should be no major changes between now and release
time.
If you have "esoteric" platforms, it is particularly important that
you give us feedback about build issues as soon as you can. Much
better to fix problems before the release than to have to patch things
up immediately after release.
Daily snapshots are available as usual, but even if you check these,
it would be helpful if you could try building from the tarballs since
some potential packaging errors can only be caught that way.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Does anybody now of a ready-made ZIP/ZINB (zero inflated poisson model, zero
inflated negative binominal model) package for R?
-------------------------------------------------------
,///,
<')<:::>{
``
Maren Wellenreuther
Marine Biology Research Group
School of Biological Sciences
Level 1
University of Auckland
Private Bag 92019
Auckland, New Zealand
Phone: +64 9 3737599 ext 88483
Mobile 027 4804023
http://www2.auckland.ac.nz/leigh//Students/marenw/
http://www.adelaide.edu.au/sciences/env_biol/research/marine/marinepast.html
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I've been having problems building vignettes in bioconductor packages
with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants
Blue and Red predefined, when only blue and red are defined (as of
rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept
9th version). Might not apply to all other tetex systems. Seems to
have bitten the bioconductor build system, though.
Symptom:
512$ R CMD build --force Biobase
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking whether 'INDEX' is up-to-date ... OK
* creating vignettes ... ERROR
/usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/lib/R/bin/texi2dvi: see Bioconductor.log for errors.
Error in buildVignettes(dir = ".") : running texi2dvi on
Bioconductor.tex failed
Execution halted
Change produces:
517$ R CMD build --force Biobase
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking whether 'INDEX' is up-to-date ... OK
* creating vignettes ... OK
* removing junk files
* building 'Biobase_1.3.31.tar.gz'
YMMV.
best,
-tony
--
A.J. Rossini
[EMAIL PROTECTED] http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW : FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email
CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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[EMAIL PROTECTED] (A.J. Rossini) writes:
> I've been having problems building vignettes in bioconductor packages
> with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants
> Blue and Red predefined, when only blue and red are defined (as of
> rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept
> 9th version). Might not apply to all other tetex systems. Seems to
> have bitten the bioconductor build system, though.
>
> Symptom:
>
>
> 512$ R CMD build --force Biobase
> * checking for file 'Biobase/DESCRIPTION' ... OK
> * preparing 'Biobase':
> * checking whether 'INDEX' is up-to-date ... OK
> * creating vignettes ... ERROR
> /usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
> /usr/lib/R/bin/texi2dvi: see Bioconductor.log for errors.
> Error in buildVignettes(dir = ".") : running texi2dvi on
> Bioconductor.tex failed
> Execution halted
>
>
>
> Change produces:
>
> 517$ R CMD build --force Biobase
> * checking for file 'Biobase/DESCRIPTION' ... OK
> * preparing 'Biobase':
> * checking whether 'INDEX' is up-to-date ... OK
> * creating vignettes ... OK
> * removing junk files
> * building 'Biobase_1.3.31.tar.gz'
Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
"make pdf". Shouldn't the hyperlinks in the manuals have the same
problem?
BTW, this uncovered another problem in that "make pdf" didn't work
when srcdir != builddir because of
$(texinputs_BASE): FORCE $(top_srcdir)/share/perl/build-help.pl
but configure makes $(top_builddir)/share/perl/build-help.pl from a
.in file
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
> "make pdf". Shouldn't the hyperlinks in the manuals have the same
> problem?
I'm not sure what is called in the case you mention.
Note that this doesn't happen if one uses texi2dvi from the command
line, either, which is how I traced it down when comparing output in
the tex log files.
(i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
build" and not present when using RHOME/bin/texi2dvi).
best,
-tony
--
A.J. Rossini
[EMAIL PROTECTED] http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW : FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email
CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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In some contexts, I find the current behavior of rank() very
`suboptimal'.
We have the argument na.last = {TRUE | FALSE | NA }
where the first two cases treating NAs (almost) as if they were
== +Inf or == -Inf whereas the 3rd case just drops NAs.
For the typical ``Rank Transformation'' that is recommended in
EDA in several contexts, I would however want something else,
namely keep the NAs !
An example -- including the new option as I'm proposing it ---
makes things more clear :
> y <- c(2:1,NA,0)
> rank(y, na.last = TRUE)## ==== rank(y)
[1] 3 2 4 1
> rank(y, na.last = FALSE)
[1] 4 3 1 2
> rank(y, na.last = NA)
[1] 3 2 1
> rank(y, na.last = "keep") ### <<<<< NEW >>
[1] 3 2 NA 1
>
---
Alternatively to extending the possible values of `na.last' I
first thought of a new (boolean) argument, but found the current
solution less ugly.
Feedback welcome!
Martin Maechler <[EMAIL PROTECTED]> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
PS: Stumbled over this while implementing cor.test()s
method = c("pearson", "spearman", "kendall") for cor()
itself.
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>>>>> On Wed, 10 Sep 2003 16:21:03 -0700,
>>>>> A J Rossini (AJR) wrote:
> Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
>> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
>> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
>> "make pdf". Shouldn't the hyperlinks in the manuals have the same
>> problem?
> I'm not sure what is called in the case you mention.
> Note that this doesn't happen if one uses texi2dvi from the command
> line, either, which is how I traced it down when comparing output in
> the tex log files.
> (i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
> build" and not present when using RHOME/bin/texi2dvi).
Hmm, we have this definition of hyperref.cfg since 1.5.0, i.e., quite
some time now. I'm not sure if we really should change anything if
problems are only on Debian unstable machines. I have Debian testing
and that works fine.
.f
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[EMAIL PROTECTED] writes:
> >>>>> On Wed, 10 Sep 2003 16:21:03 -0700,
> >>>>> A J Rossini (AJR) wrote:
>
> > Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
> >> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
> >> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
> >> "make pdf". Shouldn't the hyperlinks in the manuals have the same
> >> problem?
>
> > I'm not sure what is called in the case you mention.
>
> > Note that this doesn't happen if one uses texi2dvi from the command
> > line, either, which is how I traced it down when comparing output in
> > the tex log files.
>
> > (i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
> > build" and not present when using RHOME/bin/texi2dvi).
>
> Hmm, we have this definition of hyperref.cfg since 1.5.0, i.e., quite
> some time now. I'm not sure if we really should change anything if
> problems are only on Debian unstable machines. I have Debian testing
> and that works fine.
We'd probably want to take a closer look at what the issue really is,
including teTeX version numbers. It could be a permanent change in
teTeX v2+ in which case we're going to see the effect all over the
place as it gets into major Linux distros, or it could be an
installation problem with Debian-unstable which should go away.
Then again, does "blue" and "Blue" really do different things? In a
"no-op or fix" situation, we might choose to do the change...
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
--- End Message ---
--- Begin Message ---
>>>>> On 11 Sep 2003 10:30:39 +0200,
>>>>> Peter Dalgaard BSA (PDB) wrote:
> [EMAIL PROTECTED] writes:
>> >>>>> On Wed, 10 Sep 2003 16:21:03 -0700,
>> >>>>> A J Rossini (AJR) wrote:
>>
>> > Peter Dalgaard BSA <[EMAIL PROTECTED]> writes:
>> >> Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
>> >> thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
>> >> "make pdf". Shouldn't the hyperlinks in the manuals have the same
>> >> problem?
>>
>> > I'm not sure what is called in the case you mention.
>>
>> > Note that this doesn't happen if one uses texi2dvi from the command
>> > line, either, which is how I traced it down when comparing output in
>> > the tex log files.
>>
>> > (i.e. the inclusion of the RHOME/share/texmf/hyperref.cfg from "R CMD
>> > build" and not present when using RHOME/bin/texi2dvi).
>>
>> Hmm, we have this definition of hyperref.cfg since 1.5.0, i.e., quite
>> some time now. I'm not sure if we really should change anything if
>> problems are only on Debian unstable machines. I have Debian testing
>> and that works fine.
> We'd probably want to take a closer look at what the issue really
> is,
yes, definitely
> including teTeX version numbers. It could be a permanent change in
> teTeX v2+ in which case we're going to see the effect all over the
> place as it gets into major Linux distros, or it could be an
> installation problem with Debian-unstable which should go away.
> Then again, does "blue" and "Blue" really do different things?
probably not
> In a
> "no-op or fix" situation, we might choose to do the change...
I don't know ... the problem is that it is the first time we see this,
and I'd like to avoid that "blue" works for us, we put it in and then
it doesn't work on a lot of other systems.
My system has:
galadriel:Leisch$ dpkg -l tetex*
ii tetex-base 2.0.2-4.1 basic teTeX library files
ii tetex-bin 2.0.2-4.2 teTeX binary files
ii tetex-doc 2.0.2-4.1 teTeX documentation
ii tetex-extra 2.0.2-4.1 extra teTeX library files
.f
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