[Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo
Hi, Are there plans for the awesome git-svn bridge to allow the tracking of devel and releases in different branches of the same git repository? Currently, one has to create different repos for devel and release (see http://bioconductor.org/developers/how-to/git-svn/). Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo
- Original Message - From: Julian Gehring julian.gehr...@embl.de To: bioc-devel@r-project.org Sent: Wednesday, May 14, 2014 6:26:12 AM Subject: [Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo Hi, Are there plans for the awesome git-svn bridge to allow the tracking of devel and releases in different branches of the same git repository? Currently, one has to create different repos for devel and release (see http://bioconductor.org/developers/how-to/git-svn/). There are no plans to change this. Dan Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] legitimate use of :::
On Wed, May 14, 2014 at 12:29 AM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 13/05/2014 12:14 PM, Knut Krueger wrote:
Is there another new solution for this issue?
especially I would like to use:
utils:::.win32consoleCompletion
the use of this is suggested in the completion.r file of utils:
## test some typical completion attempts
library(utils)
testLine - function(line, cursor = nchar(line))
{
str(utils:::.win32consoleCompletion(line, cursor))
}
testLine()
I think you are misunderstanding the comments in that file. It's an
internal set of tests for the package, so test some typical completion
attempts is a description of the tests that follow, it's not a suggestion
that you should be able to run those lines
from your package.
If you do want access to the completion mechanism from a package, you should
write to its author (Deepayan Sarkar) and explain the kinds of things you
need to do. If you can convince him that giving you access is worth the
trouble of exposing some of it to user-level code, then he'll export a
function for you. (I think it's unlikely to be .win32consoleCompletion, but
who knows.)
Yes, .win32consoleCompletion() was meant for use by the Windows GUI,
but I can see a use-case for something similar elsewhere (for example,
ESS defines something analogous).
But I don't immediately see why another R package should need this. If
you have a legitimate use, we can discuss off-list and come up with a
solution.
-Deepayan
Duncan Murdoch
(full quote because of the age of the tread)
Kind regards Knut
Am 22.08.2013 20:57, schrieb Michael Friendly:
On 8/22/2013 7:45 AM, Uwe Ligges wrote:
On 22.08.2013 07:45, Yihui Xie wrote:
Hi,
So now R CMD check starts to warn against :::, but I believe sometimes
it is legitimate to use it when developing R packages. For example, I
have some utils functions that are not exported but I want to share
them across the packages that I maintain. I do not need to coordinate
with other authors about these internal functions since I'm the only
author and I know clearly what I'm doing, and I want to avoid copying
and pasting the code across packages just to avoid the NOTE in R CMD
check. What should I do in this case?
Nothing. The way you describe above seems to be a reasonable usage, iff
you are the same maintainer who knows what is going on. Other
maintainers should not use one of your not exported (hence non API)
functions, of course.
Uwe Ligges
Related to this is the use of other-package unexported utility functions
that don't pass Uwe's iff test, but I, as maintainer,
want to use in my package.
Cases in point: in heplots, I had used stats:::Pillai, stats:::Wilks,
stats:::Roy and stats:::LH for calculation in one of my functions.
Similarly, I had a need to use car:::df.terms, also unexported, but
don't want to ask John Fox to export it just for my use. Uwe's
reply suggests that I should not be using car:::df.terms, however.
To avoid the NOTEs (which often triggers a 'pls fix' upon submission to
CRAN), I simply copied/pasted these functions to my package, but this
seems wasteful.
-Michael
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[Rd] S3 - how to implement colnames-
Have a class for which I would like to provide a colnames-.myclass function so that colnames(myintsance) - c(a,b,c) can be called. Witold -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] legitimate use of :::
Am 14.05.2014 08:56, schrieb Deepayan Sarkar: On Wed, May 14, 2014 at 12:29 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: I think you are misunderstanding the comments in that file. It's an internal set of tests for the package, so test some typical completion attempts is a description of the tests that follow, it's not a suggestion that you should be able to run those lines from your package. If you do want access to the completion mechanism from a package, you should write to its author (Deepayan Sarkar) and explain the kinds of things you need to do. If you can convince him that giving you access is worth the trouble of exposing some of it to user-level code, then he'll export a function for you. (I think it's unlikely to be .win32consoleCompletion, but who knows.) Yes, .win32consoleCompletion() was meant for use by the Windows GUI, but I can see a use-case for something similar elsewhere (for example, ESS defines something analogous). But I don't immediately see why another R package should need this. If you have a legitimate use, we can discuss off-list and come up with a solution. As TinnR was used at the University I tried to update the TinnR package because it was removed from cran http://cran.rstudio.com/web/packages/TinnR/index.html I think they used the win32consoleCompletion to connect Tinnr (Windows) with R - I do not really know the reason. Actually I found that R-Studio is much better for R-beginner and available for all platforms. Thanks for your hints - but I will not solve this problem anymore Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] large integer values
Dear devels,
I need to create a (short) vector in C, which contains potentially very
large numbers, exponentially to the powers of 2.
This is my test example:
lgth = 35;
int power[lgth];
power[lgth - 1] = 1;
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
}
Everything works ok until it reaches the limit of 2^32:
power: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192,
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, 4194304,
8388608, 16777216, 33554432, 67108864, 134217728, 268435456, 536870912,
1073741824, -2147483648, 0, 0, 0
How should I declare the power vector, in order to accept integer values
larger then 2^32?
Thanks very much in advance,
Adrian
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
1, Schitu Magureanu Bd.
050025 Bucharest sector 5
Romania
Tel.:+40 21 3126618 \
+40 21 3120210 / int.101
Fax: +40 21 3158391
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Re: [Rd] [R] S3 - how to implement colnames-
Hi Witold, you should first of all redefine colnames to use UseMethod. Then you have to write a colnames.default that uses base::colnames (so that it does not interfere with existing code and other functions) and the you can define the method for your class. I would suggest, though, to use attributes for your object, rather than risking to mess up the default R function. Hope it helps, Cheers, Luca 2014-05-14 10:57 GMT+02:00 Witold E Wolski wewol...@gmail.com: Have a class for which I would like to provide a colnames-.myclass function so that colnames(myintsance) - c(a,b,c) can be called. Witold -- Witold Eryk Wolski [[alternative HTML version deleted]] __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luca Cerone Tel: +34 692 06 71 28 Skype: luca.cerone __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] large integer values
On 14/05/2014 10:37, Adrian Dușa wrote:
Dear devels,
I need to create a (short) vector in C, which contains potentially very
large numbers, exponentially to the powers of 2.
This isn't an R question, except in so far that R mandates the usual
convention of C int being 32-bit. However
1) You should use an unsigned integer type.
2) Most compilers have uint64_t but C99/C11 do not require it. They
require uint_fast64_t and uintmax_t (which is the widest unsigned int)
types.
3) double will hold much larger powers, and functions like pow_di (where
supported) or pow will compute them efficiently for you. And R has
R_pow_di in Rmath.h.
This is my test example:
lgth = 35;
int power[lgth];
power[lgth - 1] = 1;
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
}
Everything works ok until it reaches the limit of 2^32:
power: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192,
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, 4194304,
8388608, 16777216, 33554432, 67108864, 134217728, 268435456, 536870912,
1073741824, -2147483648, 0, 0, 0
How should I declare the power vector, in order to accept integer values
larger then 2^32?
Thanks very much in advance,
Adrian
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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
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Re: [Rd] large integer values
Dear Prof. Ripley,
Once again, thank you for your replies.
I must confess not being a genuine C programmer, having learned how to use
C only in connection to R (and the macros provided are almost a separate
language to learn).
I'll try to read more about the types you've indicated, and will keep
trying. So far, most certainly I am not doing it right, because all of them
have the same result. Tried declaring:
uint64_t power[lgth];
and
uint_fast64_t power[lgth];
and
uintmax_t power[lgth];
but still the top threshold appears at the limit of 32-bit in all cases.
Will keep reading about these...
Best wishes,
Adrian
On Wed, May 14, 2014 at 2:45 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote:
On 14/05/2014 10:37, Adrian DuÈa wrote:
Dear devels,
I need to create a (short) vector in C, which contains potentially very
large numbers, exponentially to the powers of 2.
This isn't an R question, except in so far that R mandates the usual
convention of C int being 32-bit. However
1) You should use an unsigned integer type.
2) Most compilers have uint64_t but C99/C11 do not require it. They
require uint_fast64_t and uintmax_t (which is the widest unsigned int)
types.
3) double will hold much larger powers, and functions like pow_di (where
supported) or pow will compute them efficiently for you. And R has
R_pow_di in Rmath.h.
This is my test example:
lgth = 35;
int power[lgth];
power[lgth - 1] = 1;
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
}
Everything works ok until it reaches the limit of 2^32:
power: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192,
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, 4194304,
8388608, 16777216, 33554432, 67108864, 134217728, 268435456, 536870912,
1073741824, -2147483648, 0, 0, 0
How should I declare the power vector, in order to accept integer values
larger then 2^32?
Thanks very much in advance,
Adrian
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
1, Schitu Magureanu Bd.
050025 Bucharest sector 5
Romania
Tel.:+40 21 3126618 \
+40 21 3120210 / int.101
Fax: +40 21 3158391
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Re: [Rd] large integer values
On May 14, 2014, at 8:41 AM, Adrian Dușa dusa.adr...@unibuc.ro wrote:
Dear Prof. Ripley,
Once again, thank you for your replies.
I must confess not being a genuine C programmer, having learned how to use
C only in connection to R (and the macros provided are almost a separate
language to learn).
I'll try to read more about the types you've indicated, and will keep
trying. So far, most certainly I am not doing it right, because all of them
have the same result. Tried declaring:
uint64_t power[lgth];
and
uint_fast64_t power[lgth];
and
uintmax_t power[lgth];
but still the top threshold appears at the limit of 32-bit in all cases.
How do you print them? It seems like you're printing 32-bit value instead ...
(powers of 2 are simply shifts of 1).
Cheers,
S
Will keep reading about these...
Best wishes,
Adrian
On Wed, May 14, 2014 at 2:45 PM, Prof Brian Ripley
rip...@stats.ox.ac.ukwrote:
On 14/05/2014 10:37, Adrian Dușa wrote:
Dear devels,
I need to create a (short) vector in C, which contains potentially very
large numbers, exponentially to the powers of 2.
This isn't an R question, except in so far that R mandates the usual
convention of C int being 32-bit. However
1) You should use an unsigned integer type.
2) Most compilers have uint64_t but C99/C11 do not require it. They
require uint_fast64_t and uintmax_t (which is the widest unsigned int)
types.
3) double will hold much larger powers, and functions like pow_di (where
supported) or pow will compute them efficiently for you. And R has
R_pow_di in Rmath.h.
This is my test example:
lgth = 35;
int power[lgth];
power[lgth - 1] = 1;
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
}
Everything works ok until it reaches the limit of 2^32:
power: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192,
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, 4194304,
8388608, 16777216, 33554432, 67108864, 134217728, 268435456, 536870912,
1073741824, -2147483648, 0, 0, 0
How should I declare the power vector, in order to accept integer values
larger then 2^32?
Thanks very much in advance,
Adrian
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
1, Schitu Magureanu Bd.
050025 Bucharest sector 5
Romania
Tel.:+40 21 3126618 \
+40 21 3120210 / int.101
Fax: +40 21 3158391
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Re: [Rd] large integer values
On Wed, May 14, 2014 at 5:35 PM, Simon Urbanek
simon.urba...@r-project.orgwrote:
[...]
How do you print them? It seems like you're printing 32-bit value instead
... (powers of 2 are simply shifts of 1).
I am simply using Rprintf():
long long int power[lgth];
power[lgth - 1] = 1;
Rprintf(power: %d, power[lgth - 1]);
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
Rprintf(, %d, power[lgth - j - 1]);
}
Basically, I need them in reversed order (hence the inverse indexing), but
the values are nonetheless the same.
Adrian
PS: also tried long long int, same result...
--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
1, Schitu Magureanu Bd.
050025 Bucharest sector 5
Romania
Tel.:+40 21 3126618 \
+40 21 3120210 / int.101
Fax: +40 21 3158391
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Re: [Rd] large integer values
On Wed, 2014-05-14 at 18:17 +0300, Adrian Dușa wrote:
On Wed, May 14, 2014 at 5:35 PM, Simon Urbanek
simon.urba...@r-project.orgwrote:
[...]
How do you print them? It seems like you're printing 32-bit value instead
... (powers of 2 are simply shifts of 1).
I am simply using Rprintf():
long long int power[lgth];
power[lgth - 1] = 1;
Rprintf(power: %d, power[lgth - 1]);
for (j = 1; j lgth; j++) {
power[lgth - j - 1] = 2*power[lgth - j];
Rprintf(, %d, power[lgth - j - 1]);
}
Basically, I need them in reversed order (hence the inverse indexing), but
the values are nonetheless the same.
Adrian
PS: also tried long long int, same result...
Your numbers are being coerced to int when you print them. Try the
format , %lld instead.
Martyn
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Re: [Rd] S3 - how to implement colnames-
Witold E Wolski wewolski at gmail.com writes: Have a class for which I would like to provide a colnames-.myclass function so that colnames(myintsance) - c(a,b,c) can be called. `colnames-` is not generic as Luca noted. But `dimnames-` is. If you write a suitable `dimnames-.myinstance`, then `colnames-` will find it. `dimnames-.data.frame` gives an example. I think you will want to either call NextMethod() or replace attr(x,dimnames) and return x. That is, you probably do not want to use `dimnames-`inside `dimnames-.myinstance`. HTH, Chuck __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug in read.dcf(all = TRUE)?
Hi,
read.dcf() can modify the locale variable LC_CTYPE, and here is a
minimal example:
Sys.getlocale('LC_CTYPE')
[1] en_US.UTF-8
read.dcf(textConnection('a: b'), all = TRUE)
a
1 b
Sys.getlocale('LC_CTYPE')
[1] C
After diagnosing the problem, it seems the on.exit() call in
read.dcf() is the culprit:
on.exit(Sys.setlocale(LC_CTYPE, Sys.getlocale(LC_CTYPE)), add = TRUE)
Sys.setlocale(LC_CTYPE, C)
https://github.com/wch/r-source/blob/96a2cc920/src/library/base/R/dcf.R#L68-L69
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.0
Regards,
Yihui
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Web: http://yihui.name
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Re: [Rd] large integer values
On Wed, May 14, 2014 at 6:24 PM, Martyn Plummer plumm...@iarc.fr wrote: [...] Your numbers are being coerced to int when you print them. Try the format , %lld instead. Oh my goodness, this was a printing issue...! (feeling embarrassed, but learned something new) Problem solved, thanks very much all, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive 1, Schitu Magureanu Bd. 050025 Bucharest sector 5 Romania Tel.:+40 21 3126618 \ +40 21 3120210 / int.101 Fax: +40 21 3158391 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
