[Rd] Inconsistency between rowMeans documentation and reality?
Dear List, I'm not even sure this is an issue or not, but ?rowMeans has: Value: A numeric or complex array of suitable size, or a vector if the result is one-dimensional. The ‘dimnames’ (or ‘names’ for a vector result) are taken from the original array. If there are no values in a range to be summed over (after removing missing values with ‘na.rm = TRUE’), that component of the output is set to ‘0’ (‘*Sums’) or ‘NA’ (‘*Means’), consistent with ‘sum’ and ‘mean’. However the output of mean() and rowMeans() is not exactly the same when all supplied values are missing. > mean(NA, na.rm = TRUE) [1] NaN > mean(rep(NA, 5), na.rm = TRUE) [1] NaN > rowMeans(matrix(rep(NA, 5), ncol = 5), na.rm = TRUE) [1] NA So in one sense, the outputs are not consistent: > is.nan(mean(rep(NA, 5), na.rm = TRUE)) [1] TRUE > is.nan(rowMeans(matrix(rep(NA, 5), ncol = 5), na.rm = TRUE)) [1] FALSE but in another they are: > is.na(mean(rep(NA, 5), na.rm = TRUE)) [1] TRUE > is.na(rowMeans(matrix(rep(NA, 5), ncol = 5), na.rm = TRUE)) [1] TRUE I'm not familiar enough with the details to know if this even matters, but wonder if something in the documentation needs a change or tweak to clarify what is returned. As I say, in one sense the outputs are not consistent. > sessionInfo() R version 2.13.0 beta (2011-04-04 r55298) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base loaded via a namespace (and not attached): [1] tools_2.13.0 Thanks, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug in as.data.frame.POSIXct?
Any comments on this? Otherwise I will just submit a bug report. Hadley On Thu, Mar 31, 2011 at 10:30 AM, Hadley Wickham wrote: >> a <- as.POSIXct(1:2, origin="2011-01-01") >> dim(a) <- c(1, 2) >> as.data.frame(a) > a > 1 2011-01-01 00:00:01 > 2 2011-01-01 00:00:02 >> >> dim(a) <- c(2, 1) >> as.data.frame(a) > a > 1 2011-01-01 00:00:01 > 2 2011-01-01 00:00:02 > > I think this is because in as.data.frame.POSIXct we have > > nrows <- length(x) > > instead of > > nrows <- NROW(x) > > Hadley > > > -- > Assistant Professor / Dobelman Family Junior Chair > Department of Statistics / Rice University > http://had.co.nz/ > -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Names of a data set in a package
For some reason I want to let one data set in a package be known under two different names. Is that possible, and if so, how? I do not want to have two copies of the data set in the package. Thanks, Göran -- Göran Broström Department of Statistics Umeå University SE-90187 Umeå, Sweden __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Names of a data set in a package
2011/4/5 Göran Broström :
> For some reason I want to let one data set in a package be known under two
> different names. Is that possible, and if so, how? I do not want to have
> two copies of the data set in the package.
>
This will allow you to read the data frame under a different name but
you won't be able to modify it under the different name. We make use
of the built in data frame BOD and create the alternate name BOD2:
> makeActiveBinding("BOD2", function() BOD, .GlobalEnv)
> BOD$Time
[1] 1 2 3 4 5 7
> BOD2$Time
[1] 1 2 3 4 5 7
> # changing BOD also changes BOD2
> BOD$Time[1] <- 99
> BOD2$Time
[1] 99 2 3 4 5 7
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Use keep.source for function in package with lazy loading
Prof. Ripley, Thanks for the explanation. I had set both keep.source and keep.source.packages to TRUE for my experiments, but had not realized that a new R process would be involved, so did not try the environmental variable approach. >From what you say below, I don't think I am going to accomplish what I wanted, >since I want the source to show for users other than myself and there does not >seem to be a reasonable way to change the users environment before installing >my package (that is getting a bit too big brother to even think about). I was >hoping that there might be some switch somewhere that I had missed that would >say keep the source for this function even though the default is not to. But, >it does not look like there is anything like that, and it is not worth >implementing just for my one little use. Hmm, maybe I can set the source manually using .onAttach, I'll have to experiment some more. Thanks, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] > Sent: Monday, April 04, 2011 3:41 PM > To: Greg Snow > Cc: R-devel@r-project.org > Subject: Re: [Rd] Use keep.source for function in package with lazy > loading > > On Mon, 4 Apr 2011, Greg Snow wrote: > > > I have a function in one of my packages that I would like to print > > using the original source rather than the deparse of the function. > > The package uses lazy loading and the help page for library (under > > keep.source) says that keep.source does not apply to packages that > > use lazy loading and that whether those functions keep the source > > depends on when they are installed. > > Not quite: it is says it is 'determined when it is installed'. > > For a package that does not use lazy loading, what is installed is a > file of R code. When library() loads such a package, it sources() the > R code, and at that point has the option to keep the source or not > (for that R session). > > For a package which uses lazy loading, the source()ing happens when > the package is installed: the objects created are then dumped into a > database. Whether the source attribute is retained at that point > depends on the setting of the option "keep.source.pkgs". So if you can > arrange to install the package with that option set to true, in > principle (and in my experiments) the source attributes are retained. > > The easiest way to do this would seem to be to set the environment > variable R_KEEP_PKG_SOURCE to "yes" whilst installing the package. > > > This package is on R-forge and is being built there (and will > > eventually be used to submit the next version of the package to > > CRAN). > > > > I am not sure what the help means by 'installed', I have set the > > options to keep the source to TRUE before calling install.package, > > but that does not seem to work. > > I presume you mean keep.source.pkgs, not keep.source? That needs to > be set in the process which is installing the package: > install.packages() calls R CMD INSTALL in a separate process. > > > Is there a way to "strongly encourage" the source to be kept for > > this function (or the entire package)? > > > > Thanks, > > > > -- > > Gregory (Greg) L. Snow Ph.D. > > Statistical Data Center > > Intermountain Healthcare > > greg.s...@imail.org > > 801.408.8111 > > -- > 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] super basic questions about S4 classes
Apologies for asking something that is probably super obvious, i just started with S4 classes and i guess i am not finding documentation that layout the grammar rules and give enough examples. Some questions i am having are these 1. I understand that main method of writing a member function is to write a generic function and setMethod for this particular object. This, however, presumes that there is "virtuality" for this function, i.e. it could be used with other inherited classes . Truth is, many, if not most of my functions don't have virtuality in mind. I want to write them inside classes to achieve incapsulaton only -- use class member data without passing it as parameters or making global to a bunch of functions and have some specific class member functions that don't pollute a global namespace and can be called only for a particular class. This is what i know how to do with enclosures in R. Is there some obvious way of setting this environment local to a class without writing generic functions that i am missing? 2. Is it possible to overload functions in other ways than having default parameter values and prototypes? For example, can i have two constructors with completely different sets of parameters? 3. Is there some good way to debug S4 classes? I am very fond of mtrace() from debug package, but the simple set of commands i normally use doesn't take me into class methods. Would appreciate any pointers on these.. -- View this message in context: http://r.789695.n4.nabble.com/super-basic-questions-about-S4-classes-tp3428591p3428591.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] question about assignment warnings for replacement methods
Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object 'marginalData-methods': marginalData(object) = value I assume that this is to prevent people from making assignments in their usage statements (which seems completely understandable). But what about the case above? This is a person who just wants to show the proper usage for a replacement method. IOW they just want to write something that looks like what you actually do when you use a replacement method. They just want to show users how to do something like this: replacementMethod(object) <- newValue So is that really something that should not be allowed in a usage statement? Marc __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] question about assignment warnings for replacement methods
On 05/04/2011 1:51 PM, Marc Carlson wrote:
Hi,
I have seen several packages that with the most recent version of R are
giving a warning like this:
Assignments in \usage in documentation object 'marginalData-methods':
marginalData(object) = value
I assume that this is to prevent people from making assignments in their
usage statements (which seems completely understandable). But what
about the case above? This is a person who just wants to show the
proper usage for a replacement method. IOW they just want to write
something that looks like what you actually do when you use a
replacement method. They just want to show users how to do something
like this:
replacementMethod(object)<- newValue
So is that really something that should not be allowed in a usage
statement?
If replacementMethod was a replacement function, then
replacementMethod(object)<- newValue
is supposed to be fine. But if it is an S3 method, it should be
\method{replacementMethod}{class}(object)<- newValue
and if it is an S4 method I think it should be
\S4method{replacementMethod}{signature_list}(object)<- newValue
(though the manual suggests using the S3 style, I'm not sure how literally to
take it).
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Names of a data set in a package
5 apr 2011 kl. 18.25 skrev Gabor Grothendieck:
> 2011/4/5 Göran Broström :
>> For some reason I want to let one data set in a package be known under two
>> different names. Is that possible, and if so, how? I do not want to have
>> two copies of the data set in the package.
>>
>
> This will allow you to read the data frame under a different name but
> you won't be able to modify it under the different name. We make use
> of the built in data frame BOD and create the alternate name BOD2:
>
>> makeActiveBinding("BOD2", function() BOD, .GlobalEnv)
>> BOD$Time
> [1] 1 2 3 4 5 7
>> BOD2$Time
> [1] 1 2 3 4 5 7
>> # changing BOD also changes BOD2
>> BOD$Time[1] <- 99
>> BOD2$Time
> [1] 99 2 3 4 5 7
>
Thanks Gabor, but where do I put this in my package? To clarify, I want
> data(B, package = "A")
and
> data(C, package = "A")
refer to the same data set.
Göran
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Names of a data set in a package
2011/4/5 Göran Broström :
>
> 5 apr 2011 kl. 18.25 skrev Gabor Grothendieck:
>
>> 2011/4/5 Göran Broström :
>>> For some reason I want to let one data set in a package be known under two
>>> different names. Is that possible, and if so, how? I do not want to have
>>> two copies of the data set in the package.
>>>
>>
>> This will allow you to read the data frame under a different name but
>> you won't be able to modify it under the different name. We make use
>> of the built in data frame BOD and create the alternate name BOD2:
>>
>>> makeActiveBinding("BOD2", function() BOD, .GlobalEnv)
>>> BOD$Time
>> [1] 1 2 3 4 5 7
>>> BOD2$Time
>> [1] 1 2 3 4 5 7
>>> # changing BOD also changes BOD2
>>> BOD$Time[1] <- 99
>>> BOD2$Time
>> [1] 99 2 3 4 5 7
>>
> Thanks Gabor, but where do I put this in my package? To clarify, I want
>
>> data(B, package = "A")
>
> and
>
>> data(C, package = "A")
>
> refer to the same data set.
>
Implement your datasets as .R files. See ?data and the source to the
quantreg package, say, as it uses .R files for its data.
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] question about assignment warnings for replacement methods
Thank you for the clarifications Duncan.
Marc
On 04/05/2011 11:15 AM, Duncan Murdoch wrote:
On 05/04/2011 1:51 PM, Marc Carlson wrote:
Hi,
I have seen several packages that with the most recent version of R are
giving a warning like this:
Assignments in \usage in documentation object 'marginalData-methods':
marginalData(object) = value
I assume that this is to prevent people from making assignments in their
usage statements (which seems completely understandable). But what
about the case above? This is a person who just wants to show the
proper usage for a replacement method. IOW they just want to write
something that looks like what you actually do when you use a
replacement method. They just want to show users how to do something
like this:
replacementMethod(object)<- newValue
So is that really something that should not be allowed in a usage
statement?
If replacementMethod was a replacement function, then
replacementMethod(object)<- newValue
is supposed to be fine. But if it is an S3 method, it should be
\method{replacementMethod}{class}(object)<- newValue
and if it is an S4 method I think it should be
\S4method{replacementMethod}{signature_list}(object)<- newValue
(though the manual suggests using the S3 style, I'm not sure how
literally to take it).
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rtools questions
Hello:
1. How can I tell when the development version of Rtools has
changed? For the past few years, I've installed the development version
of R tools with each new release of R. I encountered problems with this
a few days ago, so I rolled back to Rtools212.exe. Unfortunately, I
seem to have more problems with that version. My latest install was
under Windows 7 Home Edition. My previous problems were on Vista, but I
also have access to Fedora 13 Linux.
2. "R CMD check" ends with the following:
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
unable to run 'pdflatex' on 'Rd2.tex'
Error in running tools::texi2dvi
You may want to clean up by 'rm -rf
C:/Users/sgraves/AppData/Local/Temp/Rtmpr6z3
r6/Rd2pdf55b96c9a'
This is using Rtools213, downloaded April 4 from
"www.murdoch-sutherland.com/Rtools" with R installed as follows:
sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Thanks,
Spencer
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Names of a data set in a package
5 apr 2011 kl. 21.01 skrev Gabor Grothendieck:
> 2011/4/5 Göran Broström :
>>
>> 5 apr 2011 kl. 18.25 skrev Gabor Grothendieck:
>>
>>> 2011/4/5 Göran Broström :
For some reason I want to let one data set in a package be known under two
different names. Is that possible, and if so, how? I do not want to have
two copies of the data set in the package.
>>>
>>> This will allow you to read the data frame under a different name but
>>> you won't be able to modify it under the different name. We make use
>>> of the built in data frame BOD and create the alternate name BOD2:
>>>
makeActiveBinding("BOD2", function() BOD, .GlobalEnv)
BOD$Time
>>> [1] 1 2 3 4 5 7
BOD2$Time
>>> [1] 1 2 3 4 5 7
# changing BOD also changes BOD2
BOD$Time[1] <- 99
BOD2$Time
>>> [1] 99 2 3 4 5 7
>>>
>> Thanks Gabor, but where do I put this in my package? To clarify, I want
>>
>>> data(B, package = "A")
>>
>> and
>>
>>> data(C, package = "A")
>>
>> refer to the same data set.
>>
>
> Implement your datasets as .R files. See ?data and the source to the
> quantreg package, say, as it uses .R files for its data.
Gabor, thanks again, I got it! Note though that quantreg nowadays uses .rda
files for its data. But in an old version I found the way to do it.
Göran
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
Rtools don't provide TeX - that's entirely up to you - so I suspect it may not
have anything to do with the Rtools version but rather your TeX installation...
Cheers,
Simon
On Apr 5, 2011, at 6:22 PM, Spencer Graves wrote:
> Hello:
>
>
> 1. How can I tell when the development version of Rtools has changed?
> For the past few years, I've installed the development version of R tools
> with each new release of R. I encountered problems with this a few days ago,
> so I rolled back to Rtools212.exe. Unfortunately, I seem to have more
> problems with that version. My latest install was under Windows 7 Home
> Edition. My previous problems were on Vista, but I also have access to
> Fedora 13 Linux.
>
>
> 2. "R CMD check" ends with the following:
>
>
> * checking examples ... OK
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> Re-running with no redirection of stdout/stderr.
> Hmm ... looks like a package
> Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
> unable to run 'pdflatex' on 'Rd2.tex'
> Error in running tools::texi2dvi
> You may want to clean up by 'rm -rf
> C:/Users/sgraves/AppData/Local/Temp/Rtmpr6z3
> r6/Rd2pdf55b96c9a'
>
>
> This is using Rtools213, downloaded April 4 from
> "www.murdoch-sutherland.com/Rtools" with R installed as follows:
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
>
> Thanks,
> Spencer
>
>
> --
> Spencer Graves, PE, PhD
> President and Chief Operating Officer
> Structure Inspection and Monitoring, Inc.
> 751 Emerson Ct.
> San José, CA 95126
> ph: 408-655-4567
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On 11-04-05 6:22 PM, Spencer Graves wrote:
Hello:
1. How can I tell when the development version of Rtools has
changed?
I don't make announcements of the changes, you just need to check the
web site. There are online tools that can do this for you
automatically, but I don't know which one to recommend. Google suggests
lots of them.
For the past few years, I've installed the development version
of R tools with each new release of R. I encountered problems with this
a few days ago, so I rolled back to Rtools212.exe. Unfortunately, I
seem to have more problems with that version. My latest install was
under Windows 7 Home Edition. My previous problems were on Vista, but I
also have access to Fedora 13 Linux.
I know that Windows 7 64 bit has problems with Rtools. Brian Ripley has
had some luck using the tools (the bin directory) and Cygwin DLLs from
last summer, along with the current compilers. I'm reluctant to back
out the new versions, because I use Cygwin for other things (including
OpenSSH) and don't want to get locked out of updates.
I haven't heard of problems with other Windows 7 versions, but I haven't
tried them.
2. "R CMD check" ends with the following:
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
unable to run 'pdflatex' on 'Rd2.tex'
Error in running tools::texi2dvi
You may want to clean up by 'rm -rf
C:/Users/sgraves/AppData/Local/Temp/Rtmpr6z3
r6/Rd2pdf55b96c9a'
This is using Rtools213, downloaded April 4 from
"www.murdoch-sutherland.com/Rtools" with R installed as follows:
sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Do you have pdflatex? It's not part of Rtools, it's part of LaTeX, as
described in Rtools.txt.
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote:
> On 11-04-05 6:22 PM, Spencer Graves wrote:
>>
>> Hello:
>>
>>
>> 1. How can I tell when the development version of Rtools has
>> changed?
>
> I don't make announcements of the changes, you just need to check the web
> site. There are online tools that can do this for you automatically, but I
> don't know which one to recommend. Google suggests lots of them.
I also asked myself this before and I must admit it took me a while to
interpret the contents of the webpage. There are multiple sections,
e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes
since R 2.11.0', and so on. Then within each section there are some
dates mentioned. Given my current R version (say R 2.13.0 beta) and
Rtools (Rtools213.exe), it not fully clear to me which section to look
at, e.g. 'Changes since R 2.12.2'? It might be more clear if there
instead the sections would be 'Changes in Rtools213', 'Changes in
Rtools212' and so on, and within each maybe list updates by
dates/version. More like a NEWS file. Then it would be easier to see
if there is an updated available or not. Even a NEWS file only
available as part of the installation will help decide whether the
version you have installed differ from the one available online.
Something like the following:
== Changes in Rtools213 ==
[...]
== Changes in Rtools212 ==
2011-03-25:
- Rtools 2.12 has been frozen.
- We have updated all of the tools to current Cygwin versions as of
March 25, 2011. We added the "du" utility from Cygwin. We have dropped
Vanilla Perl. The libjpeg version has been updated to 8c, and libpng
has been updated to 1.5.1.
2010-10-18: [v2.12.0.1892] <== Is this an Rtools version?!?
- Prior to October 18, 2010, builds of Rtools212.exe did not correctly
install the "extras" required to build R. Version 2.12.0.1892 or later
should fix this.
- We have now updated all of the tools to current Cygwin versions, and
have updated the compilers, and included the 64 bit compilers into
Rtools. See Prof. Ripley's page for the details.
- Perl is rarely needed in R since R 2.12.0, so it is by default not installed.
2010-??-??:
- The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010)
will be built with gcc 4.5.x, so Rtools212 contains a completely new
MinGW toolchain based on gcc 4.5.0.
== Changes in Rtools211 ==
[...]
Just a suggestion ...and thanks for providing Rtools!
/Henrik
>
>
> For the past few years, I've installed the development version
>>
>> of R tools with each new release of R. I encountered problems with this
>> a few days ago, so I rolled back to Rtools212.exe. Unfortunately, I
>> seem to have more problems with that version. My latest install was
>> under Windows 7 Home Edition. My previous problems were on Vista, but I
>> also have access to Fedora 13 Linux.
>
> I know that Windows 7 64 bit has problems with Rtools. Brian Ripley has had
> some luck using the tools (the bin directory) and Cygwin DLLs from last
> summer, along with the current compilers. I'm reluctant to back out the new
> versions, because I use Cygwin for other things (including OpenSSH) and
> don't want to get locked out of updates.
>
> I haven't heard of problems with other Windows 7 versions, but I haven't
> tried them.
>
>>
>>
>> 2. "R CMD check" ends with the following:
>>
>>
>> * checking examples ... OK
>> * checking PDF version of manual ... WARNING
>> LaTeX errors when creating PDF version.
>> This typically indicates Rd problems.
>> * checking PDF version of manual without hyperrefs or index ... ERROR
>> Re-running with no redirection of stdout/stderr.
>> Hmm ... looks like a package
>> Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
>> unable to run 'pdflatex' on 'Rd2.tex'
>> Error in running tools::texi2dvi
>> You may want to clean up by 'rm -rf
>> C:/Users/sgraves/AppData/Local/Temp/Rtmpr6z3
>> r6/Rd2pdf55b96c9a'
>>
>>
>> This is using Rtools213, downloaded April 4 from
>> "www.murdoch-sutherland.com/Rtools" with R installed as follows:
>>
>>
>>> sessionInfo()
>>
>> R version 2.12.2 (2011-02-25)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>
>
> Do you have pdflatex? It's not part of Rtools, it's part of LaTeX, as
> described in Rtools.txt.
>
> Duncan Murdoch
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check for 2.13 rc
Hi,
I have a couple of new errors in our package when I check it on R 2.13-rc
(r55310). The first one that's mystifying me is
* checking R code for possible problems ... NOTE
Error : object normalizePath is not exported by 'namespace:utils'
Error : object normalizePath is not exported by 'namespace:utils'
Firstly, it's strange to see NOTE and Error being used interchangeably here.
The package is being developed by a couple of us, so I checked that there were
no calls to normalizePath in any of our code, and there aren't:
darstr@clark-lab:~/Repitools_github/pkg$ grep -r normalizePath .
./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported by
'namespace:utils'
./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported by
'namespace:utils'
./Repitools.Rcheck/tests/tests.Rout.fail:Error : object 'normlizePath' is not
exported by 'namespace:utils'
I haven't got a clue where to look next.
My second concern is that I have used the code:
setOldClass("AffymetrixCelSet")
to make an S3 class be S4 dispatchable on. But R 2.13 wants me to document this
class that I don't own:
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
AffymetrixCelSet
Is this truly necessary ?
--
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On Tue, Apr 5, 2011 at 7:51 PM, Henrik Bengtsson wrote: > On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch > wrote: >> On 11-04-05 6:22 PM, Spencer Graves wrote: >>> >>> Hello: >>> >>> >>> 1. How can I tell when the development version of Rtools has >>> changed? >> >> I don't make announcements of the changes, you just need to check the web >> site. There are online tools that can do this for you automatically, but I >> don't know which one to recommend. Google suggests lots of them. > > I also asked myself this before and I must admit it took me a while to > interpret the contents of the webpage. There are multiple sections, > e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes > since R 2.11.0', and so on. Then within each section there are some > dates mentioned. Given my current R version (say R 2.13.0 beta) and > Rtools (Rtools213.exe), it not fully clear to me which section to look > at, e.g. 'Changes since R 2.12.2'? It might be more clear if there > instead the sections would be 'Changes in Rtools213', 'Changes in > Rtools212' and so on, and within each maybe list updates by > dates/version. More like a NEWS file. Then it would be easier to see > if there is an updated available or not. Even a NEWS file only > available as part of the installation will help decide whether the > version you have installed differ from the one available online. > Something like the following: > > == Changes in Rtools213 == > > [...] > > > == Changes in Rtools212 == > > 2011-03-25: > - Rtools 2.12 has been frozen. > - We have updated all of the tools to current Cygwin versions as of > March 25, 2011. We added the "du" utility from Cygwin. We have dropped > Vanilla Perl. The libjpeg version has been updated to 8c, and libpng > has been updated to 1.5.1. > > 2010-10-18: [v2.12.0.1892] <== Is this an Rtools version?!? > - Prior to October 18, 2010, builds of Rtools212.exe did not correctly > install the "extras" required to build R. Version 2.12.0.1892 or later > should fix this. > - We have now updated all of the tools to current Cygwin versions, and > have updated the compilers, and included the 64 bit compilers into > Rtools. See Prof. Ripley's page for the details. > - Perl is rarely needed in R since R 2.12.0, so it is by default not > installed. > > 2010-??-??: > - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) > will be built with gcc 4.5.x, so Rtools212 contains a completely new > MinGW toolchain based on gcc 4.5.0. > > == Changes in Rtools211 == > > [...] > > > Just a suggestion ...and thanks for providing Rtools! > > /Henrik If a NEWS file were included in the Rtools distribution itself (and not just on the web site) it would be helpful since its not always clear which version you have on your system in the first place. -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check for 2.13 rc
I think normalizePath() has been moved to 'base' very++ recently. /H
On Tue, Apr 5, 2011 at 5:00 PM, Dario Strbenac wrote:
> Hi,
>
> I have a couple of new errors in our package when I check it on R 2.13-rc
> (r55310). The first one that's mystifying me is
>
> * checking R code for possible problems ... NOTE
> Error : object normalizePath is not exported by 'namespace:utils'
> Error : object normalizePath is not exported by 'namespace:utils'
>
> Firstly, it's strange to see NOTE and Error being used interchangeably here.
> The package is being developed by a couple of us, so I checked that there
> were no calls to normalizePath in any of our code, and there aren't:
>
> darstr@clark-lab:~/Repitools_github/pkg$ grep -r normalizePath .
> ./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported
> by 'namespace:utils'
> ./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported
> by 'namespace:utils'
> ./Repitools.Rcheck/tests/tests.Rout.fail:Error : object 'normlizePath' is not
> exported by 'namespace:utils'
>
> I haven't got a clue where to look next.
>
> My second concern is that I have used the code:
>
> setOldClass("AffymetrixCelSet")
>
> to make an S3 class be S4 dispatchable on. But R 2.13 wants me to document
> this class that I don't own:
>
> * checking for missing documentation entries ... WARNING
> Undocumented S4 classes:
> AffymetrixCelSet
>
> Is this truly necessary ?
>
> --
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On 4/5/2011 5:01 PM, Gabor Grothendieck wrote: On Tue, Apr 5, 2011 at 7:51 PM, Henrik Bengtsson wrote: On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? I don't make announcements of the changes, you just need to check the web site. There are online tools that can do this for you automatically, but I don't know which one to recommend. Google suggests lots of them. I also asked myself this before and I must admit it took me a while to interpret the contents of the webpage. There are multiple sections, e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes since R 2.11.0', and so on. Then within each section there are some dates mentioned. Given my current R version (say R 2.13.0 beta) and Rtools (Rtools213.exe), it not fully clear to me which section to look at, e.g. 'Changes since R 2.12.2'? It might be more clear if there instead the sections would be 'Changes in Rtools213', 'Changes in Rtools212' and so on, and within each maybe list updates by dates/version. More like a NEWS file. Then it would be easier to see if there is an updated available or not. Even a NEWS file only available as part of the installation will help decide whether the version you have installed differ from the one available online. Something like the following: == Changes in Rtools213 == [...] == Changes in Rtools212 == 2011-03-25: - Rtools 2.12 has been frozen. - We have updated all of the tools to current Cygwin versions as of March 25, 2011. We added the "du" utility from Cygwin. We have dropped Vanilla Perl. The libjpeg version has been updated to 8c, and libpng has been updated to 1.5.1. 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? - Prior to October 18, 2010, builds of Rtools212.exe did not correctly install the "extras" required to build R. Version 2.12.0.1892 or later should fix this. - We have now updated all of the tools to current Cygwin versions, and have updated the compilers, and included the 64 bit compilers into Rtools. See Prof. Ripley's page for the details. - Perl is rarely needed in R since R 2.12.0, so it is by default not installed. 2010-??-??: - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) will be built with gcc 4.5.x, so Rtools212 contains a completely new MinGW toolchain based on gcc 4.5.0. == Changes in Rtools211 == [...] Just a suggestion ...and thanks for providing Rtools! /Henrik If a NEWS file were included in the Rtools distribution itself (and not just on the web site) it would be helpful since its not always clear which version you have on your system in the first place. However, adding a NEWS file increases the labor, and I'd be happy letting Duncan and others continue doing what they do without asking them to take the time to tell the rest of us what they did. Something simpler would suffice for my needs, e.g., a revision number in the name of the download file, like Rtools213.5107.exe for SVN revision number 5107. Windows 7 gives me the date my copy was downloaded, not the date of the last patch. On March 31, I downloaded and installed basic-miktex-2.9.3972.exe from "http://miktex.org/2.9/setup";. Today, I downloaded basic-miktex-2.9.4106.exe and basic-miktex-2.9.4106-x64.exe. From comparing names, I inferred (a) the first was a newer version of what I had previously installed, and (b) that was 32 bit and the other is 64 bit. I installed the latter, and the problem with pdflatex disappeared. Spencer -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On Tue, Apr 5, 2011 at 8:58 PM, Spencer Graves wrote: > On 4/5/2011 5:01 PM, Gabor Grothendieck wrote: >> >> On Tue, Apr 5, 2011 at 7:51 PM, Henrik Bengtsson >> wrote: >>> >>> On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch >>> wrote: On 11-04-05 6:22 PM, Spencer Graves wrote: > > Hello: > > > 1. How can I tell when the development version of Rtools has > changed? I don't make announcements of the changes, you just need to check the web site. There are online tools that can do this for you automatically, but I don't know which one to recommend. Google suggests lots of them. >>> >>> I also asked myself this before and I must admit it took me a while to >>> interpret the contents of the webpage. There are multiple sections, >>> e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes >>> since R 2.11.0', and so on. Then within each section there are some >>> dates mentioned. Given my current R version (say R 2.13.0 beta) and >>> Rtools (Rtools213.exe), it not fully clear to me which section to look >>> at, e.g. 'Changes since R 2.12.2'? It might be more clear if there >>> instead the sections would be 'Changes in Rtools213', 'Changes in >>> Rtools212' and so on, and within each maybe list updates by >>> dates/version. More like a NEWS file. Then it would be easier to see >>> if there is an updated available or not. Even a NEWS file only >>> available as part of the installation will help decide whether the >>> version you have installed differ from the one available online. >>> Something like the following: >>> >>> == Changes in Rtools213 == >>> >>> [...] >>> >>> >>> == Changes in Rtools212 == >>> >>> 2011-03-25: >>> - Rtools 2.12 has been frozen. >>> - We have updated all of the tools to current Cygwin versions as of >>> March 25, 2011. We added the "du" utility from Cygwin. We have dropped >>> Vanilla Perl. The libjpeg version has been updated to 8c, and libpng >>> has been updated to 1.5.1. >>> >>> 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? >>> - Prior to October 18, 2010, builds of Rtools212.exe did not correctly >>> install the "extras" required to build R. Version 2.12.0.1892 or later >>> should fix this. >>> - We have now updated all of the tools to current Cygwin versions, and >>> have updated the compilers, and included the 64 bit compilers into >>> Rtools. See Prof. Ripley's page for the details. >>> - Perl is rarely needed in R since R 2.12.0, so it is by default not >>> installed. >>> >>> 2010-??-??: >>> - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) >>> will be built with gcc 4.5.x, so Rtools212 contains a completely new >>> MinGW toolchain based on gcc 4.5.0. >>> >>> == Changes in Rtools211 == >>> >>> [...] >>> >>> >>> Just a suggestion ...and thanks for providing Rtools! >>> >>> /Henrik >> >> If a NEWS file were included in the Rtools distribution itself (and >> not just on the web site) it would be helpful since its not always >> clear which version you have on your system in the first place. > > However, adding a NEWS file increases the labor, and I'd be happy > letting Duncan and others continue doing what they do without asking them to > take the time to tell the rest of us what they did. > > > Something simpler would suffice for my needs, e.g., a revision number That wouldn't let you know what version has been installed after installation. -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On 4/5/2011 6:03 PM, Gabor Grothendieck wrote: On Tue, Apr 5, 2011 at 8:58 PM, Spencer Graves wrote: On 4/5/2011 5:01 PM, Gabor Grothendieck wrote: On Tue, Apr 5, 2011 at 7:51 PM, Henrik Bengtsson wrote: On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? I don't make announcements of the changes, you just need to check the web site. There are online tools that can do this for you automatically, but I don't know which one to recommend. Google suggests lots of them. I also asked myself this before and I must admit it took me a while to interpret the contents of the webpage. There are multiple sections, e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes since R 2.11.0', and so on. Then within each section there are some dates mentioned. Given my current R version (say R 2.13.0 beta) and Rtools (Rtools213.exe), it not fully clear to me which section to look at, e.g. 'Changes since R 2.12.2'? It might be more clear if there instead the sections would be 'Changes in Rtools213', 'Changes in Rtools212' and so on, and within each maybe list updates by dates/version. More like a NEWS file. Then it would be easier to see if there is an updated available or not. Even a NEWS file only available as part of the installation will help decide whether the version you have installed differ from the one available online. Something like the following: == Changes in Rtools213 == [...] == Changes in Rtools212 == 2011-03-25: - Rtools 2.12 has been frozen. - We have updated all of the tools to current Cygwin versions as of March 25, 2011. We added the "du" utility from Cygwin. We have dropped Vanilla Perl. The libjpeg version has been updated to 8c, and libpng has been updated to 1.5.1. 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? - Prior to October 18, 2010, builds of Rtools212.exe did not correctly install the "extras" required to build R. Version 2.12.0.1892 or later should fix this. - We have now updated all of the tools to current Cygwin versions, and have updated the compilers, and included the 64 bit compilers into Rtools. See Prof. Ripley's page for the details. - Perl is rarely needed in R since R 2.12.0, so it is by default not installed. 2010-??-??: - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) will be built with gcc 4.5.x, so Rtools212 contains a completely new MinGW toolchain based on gcc 4.5.0. == Changes in Rtools211 == [...] Just a suggestion ...and thanks for providing Rtools! /Henrik If a NEWS file were included in the Rtools distribution itself (and not just on the web site) it would be helpful since its not always clear which version you have on your system in the first place. However, adding a NEWS file increases the labor, and I'd be happy letting Duncan and others continue doing what they do without asking them to take the time to tell the rest of us what they did. Something simpler would suffice for my needs, e.g., a revision number That wouldn't let you know what version has been installed after installation. It worked for me today with MiKTeX, because I kept the previous installer in a place where I could identify it with what I installed. That's not as user friendly as NEWS, but it doesn't ask Duncan and anyone else who works on Rtools to rearrange their priorities to document something that I rarely read. (Even if I RTFM 24/7, I can't read fast enough to keep up with the changes and additions to TFM.) Spencer __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rcheck Directory
Hello, There seems to be a minor conflict of interesting in R CMD check. It creates a log directory, then gives a WARNING about it being there: * using log directory /home/darstr/Repitools_github/pkg/Repitools.Rcheck * using R version 2.13.0 RC (2011-04-05 r55310) * using platform: x86_64-unknown-linux-gnu (64-bit) * using session charset: UTF-8 ...... * checking package subdirectories ... WARNING Found the following directory(s) with names of check directories: ./Repitools.Rcheck Most likely, these were included erroneously. ...... -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rcheck Directory
On 6 April 2011 at 12:00, Dario Strbenac wrote: | Hello, | | There seems to be a minor conflict of interesting in R CMD check. It creates a log directory, then gives a WARNING about it being there: | | * using log directory /home/darstr/Repitools_github/pkg/Repitools.Rcheck | * using R version 2.13.0 RC (2011-04-05 r55310) | * using platform: x86_64-unknown-linux-gnu (64-bit) | * using session charset: UTF-8 | ...... | | * checking package subdirectories ... WARNING | Found the following directory(s) with names of check directories: | ./Repitools.Rcheck | Most likely, these were included erroneously. | ...... It usually means that you ran 'R CMD check' once before _inside_ directory, which usually fails, and you then went up a directory and did it again. Folks used to upload archives like that to CRAN which is why this is now checked for. Warnings are your friends. And, just like good friends, they sometimes go in misterious ways... Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
