[Rd] Milestone: 2000 packages on CRAN
Today, 2009-10-04, from http://cran.r-project.org/web/packages/ Currently, the CRAN package repository features 1997 objects including 1993 packages and 4 bundles containing 15 packages, for a total of 2008 available packages. It was 1.5 years ago (2007-04-12) we were at 1000 packages, cf. https://stat.ethz.ch/pipermail/r-devel/2007-April/045359.html From my previous in-house statistics there were ~500 packages in Oct 2004, and ~250 in April 2003. So, roughly, the number of packages doubles every 18 months. My daily procrastination /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] exTremes and ismev (PR#13981)
Greetings I am attempting to load exTremes and this is what I get... * utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- trying URL ' http://cran.uk.r-project.org/bin/windows/contrib/2.9/extRemes_1.60.zip' Content type 'application/zip' length 676182 bytes (660 Kb) opened URL downloaded 660 Kb package 'extRemes' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Mzukisi\AppData\Local\Temp\RtmpDk0EBq\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-29~1.2/doc/html/packages.html', reason 'Permission denied' *What could be the cause of this? Mzukisi Gwata Pretoria South Africa [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] exTremes and ismev (PR#13981)
mzukisi.gw...@gmail.com wrote: Greetings I am attempting to load exTremes and this is what I get... * utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- trying URL ' http://cran.uk.r-project.org/bin/windows/contrib/2.9/extRemes_1.60.zip' Content type 'application/zip' length 676182 bytes (660 Kb) opened URL downloaded 660 Kb package 'extRemes' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Mzukisi\AppData\Local\Temp\RtmpDk0EBq\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-29~1.2/doc/html/packages.html', reason 'Permission denied' *What could be the cause of this? This is not bug in R!!! Please read what a bug is in the FAQs. For questionsabout R, please ask on the R-help mailing list. In this case, there is not even an error anywhere, just a warning, that the given file that contains the list of installed packages could not be updated after the package's installatio, probably because auf limited permissions. Uwe Ligges Mzukisi Gwata Pretoria South Africa [[alternative HTML version deleted]] __ 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] suggest enhancement to segments and arrows to facilitate horizontal and vertical segments
This isn't a one-way street, as it means that some erroneous calls will not be detected, and code written to take advantage of this will only work under R = 2.10.0. I think we should probably insist that one of x1 and y1 is supplied: if both are omitted arrows() would give a warning, but segments() would not. On Fri, 2 Oct 2009, Tim Hesterberg wrote: I suggest a simple enhancement to segments() and arrows() to facilitate drawing horizontal and vertical segments -- set default values for the second x and y arguments equal to the first set. This is handy, especially when the expressions for coordinates are long. Compare: Segments: function (x0, y0, x1 = x0, y1 = y0, col = par(fg), lty = par(lty), --- function (x0, y0, x1, y1, col = par(fg), lty = par(lty), Arrows: function (x0, y0, x1 = x0, y1 = y0, length = 0.25, angle = 30, code = 2, --- function (x0, y0, x1, y1, length = 0.25, angle = 30, code = 2, Tim Hesterberg -- 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
Re: [Rd] R 2.9.2 crashes when sorting latin1-encoded strings
This was a missing PROTECT() in do_order.
But I'll echo what Simon Urbanek said: don't do that but rather use
the documented ways to re-encode the file as you read it. (Latin-1
used to be needed for collation on Mac OS X as C-level collation in
UTF-8 was completely broken -- but we have worked around that.)
We provided fileEncoding= in read.table for those who failed to RTFM
and thought encoding= was to set the file encoding, but it seems that
encodings are simply too hard a concept for some R users.
On Wed, 30 Sep 2009, Stefan Evert wrote:
Hi everyone!
I think I stumbled over a bug in the latest R 2.9.2 patched for OS X:
R version 2.9.2 Patched (2009-09-24 r49861)
i386-apple-darwin9.8.0
When I try to sort latin1-encoded character vectors, R sometimes crashes with
a segmentation fault. I'm running OS X 10.5.8 and have observed this
behaviour both with the i386 and x86_64 builds, in the R.app GUI as well as
on the command line.
Here's a minimal example that reliably triggers the crash on my machine:
=
print(sessionInfo())
words - c(aa, ab, a\xfc, a\xe4, b\xe4, b\xfc, \xe4\xfc)
str(words)
print(table(Encoding(words)))
Encoding(words) - latin1 # this is the correct encoding!
print(table(Encoding(words)))
N - 1000
words - rep(words, length.out=N)
print(N)
for (i in 1:N) {
x - words[1:i]
# the following line will crash for some i, depending on the particular
# strings in words and the subset selected for x above
order(x)
}
=
The output I get from this code is appended at the end of the mail. Note that
R incorrectly declares the latin1 strings in word to have UTF-8 encoding
(this seems wrong to me because the \x escapes insert raw bytes into the
string). The crash only occurs if the correct latin1 encoding (or
unknown) is explicitly specified. Otherwise the string handling code
appears to ignore everything after the first invalid multibyte character.
I haven't been able to trigger the bug without some kind of loop. The crash
always occurs at the same iteration, but this changes depending on the
contents of words and the specific subset selected in each loop iteration.
Also note that the 64-bit version of R gives a different error message. If I
omit the unrelated statement print(N), the 64-bit version segfaults and the
32-bit version just hangs with high CPU load. All this suggests to me that
there must be some insidious memory corruption or stack/range overflow in the
internal ordering code.
Can other people reproduce this problem on different platforms and possibly
with different versions of R?
BTW, I ran into the crash when trying to read.delim() a file in latin1
encoding, using either encoding=latin1 or fileEncoding=latin1, and then
converting it back and forth between a character vector and a factor. I
still don't understand what's going on there. The behaviour of read.delim()
seems to depend very much on my locale settings when running R, which is
rather unpleasant. Is there a way to find out how strings are stored
internally (i.e. getting the exact byte representation) and whether R
believes them to be in UTF-8 or latin1 encoding?
Best regards,
Stefan Evert
[ stefan.ev...@uos.de | http://purl.org/stefan.evert ]
Output of sample code on my machine:
print(sessionInfo())
R version 2.9.2 Patched (2009-09-24 r49861)
i386-apple-darwin9.8.0
locale:
en_GB/en_GB/C/C/en_GB/en_GB
attached base packages:
[1] stats graphics grDevices utils datasets methods base
words - c(aa, ab, a\xfc, a\xe4, b\xe4, b\xfc, \xe4\xfc)
str(words)
chr [1:7] aa ab a\xfc a\xe4 b\xe4 b\xfc ...
print(table(Encoding(words)))
unknown UTF-8
2 5
Encoding(words) - latin1 # this is the correct encoding!
print(table(Encoding(words)))
latin1 unknown
5 2
N - 1000
words - rep(words, length.out=N)
print(N)
[1] 1000
for (i in 1:N) {
+ x - words[1:i]
+ # the following line will crash for some i, depending on the particular
+ # strings in words and the subset selected for x above
+ order(x)
+ }
*** caught bus error ***
address 0x86, cause 'non-existent physical address'
Traceback:
1: order(x)
aborting ...
Bus error
64-bit version:
print(sessionInfo())
R version 2.9.2 Patched (2009-09-24 r49861)
x86_64-apple-darwin9.8.0
locale:
en_GB/en_GB/C/C/en_GB/en_GB
attached base packages:
[1] stats graphics grDevices utils datasets methods base
words - c(aa, ab, a\xfc, a\xe4, b\xe4, b\xfc, \xe4\xfc)
str(words)
chr [1:7] aa ab a\xfc a\xe4 b\xe4 b\xfc ...
print(table(Encoding(words)))
unknown UTF-8
2 5
Encoding(words) - latin1 # this is the correct encoding!
print(table(Encoding(words)))
latin1 unknown
5 2
N - 1000
words - rep(words, length.out=N)
print(N)
[1] 1000
for (i in 1:N) {
+ x - words[1:i]
+ # the following line will crash for some i, depending on the particular
+ # strings in words and the subset selected for x above
+ order(x)
+ }
Error in order(x) :
[Rd] how to document stuff most users don't want to see
The functions metrop and temper in the mcmc package have a debug = FALSE argument that when TRUE adds a lot of debugging information to the returned list. This is absolutely necessary to test the functions, because one generally knows nothing about the simulated distribution except what what one learns from MCMC samples. Hence you must expose all details of the simulation to have any hope of checking that it is doing what it is supposed to do. However, this information is of interested mostly (perhaps solely) to developers. So I didn't document it in the Rd files for these functions. But it has ocurred to me that people might be interested in how these functions are validated, and I would like to document the debug output somewhere, but I don't want to clutter up the documentation that ordinary users see. That suggests a separate help page for debugging. Looking at Writing R Extensions it doesn't seem like there is a type of Rd file for this purpose. I suppose it could be added in (fairly long) sections titled Debug Output in metrop.Rd and temper.Rd or it could be put in a package help page (although that's not what that kind of page is really for). Any other possibilities to consider? -- Charles Geyer Professor, School of Statistics University of Minnesota char...@stat.umn.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to document stuff most users don't want to see
On 10/5/2009 1:50 PM, Charles Geyer wrote:
The functions metrop and temper in the mcmc package have a debug = FALSE
argument that when TRUE adds a lot of debugging information to the returned
list. This is absolutely necessary to test the functions, because one
generally knows nothing about the simulated distribution except what what
one learns from MCMC samples. Hence you must expose all details of the
simulation to have any hope of checking that it is doing what it is supposed
to do. However, this information is of interested mostly (perhaps solely)
to developers. So I didn't document it in the Rd files for these functions.
But it has ocurred to me that people might be interested in how these functions
are validated, and I would like to document the debug output somewhere, but I
don't want to clutter up the documentation that ordinary users see. That
suggests a separate help page for debugging. Looking at Writing R Extensions
it doesn't seem like there is a type of Rd file for this purpose. I suppose
it could be added in (fairly long) sections titled Debug Output in metrop.Rd
and temper.Rd or it could be put in a package help page (although that's not
what that kind of page is really for). Any other possibilities to consider?
I think writing it up in a vignette would probably be most appropriate.
You can link directly to a vignette from a man page (though not,
unfortunately, vice versa). For example, if you look at
package?grid, you'll see a list that was generated by this code:
Further information is available in the following
\link{vignettes}:
\tabular{ll}{
\code{grid} \tab Introduction to \code{grid} (\url{../doc/grid.pdf})\cr
\code{displaylist} \tab Display Lists in \code{grid}
(\url{../doc/displaylist.pdf})\cr
...
Duncan Murdoch
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Re: [Rd] how to document stuff most users don't want to see
There are many arguments in many functions that are rarely used. I prefer to see it all documented in the help pages. If they are not documented in the help pages (and sometimes even if they are), a user who wants them can invent other ways to get similar information with much greater effort, and do so for years only to eventually find a much easier way buried in the documentation. Example: I was frustrated for years that nls would refuse to produce output if it did not converge. I often used optim instead of nls for that reason. However, the list returned by optim does not have the nice methods that one can use with an nls object. Eventually, I found the warnOnly option documented under nls.control, which has made nls easier for me to use. Spencer Graves William Dunlap wrote: There are several help files in the R sources that describe concepts and not particular R objects. E.g., help(Methods), help(Syntax), and help(regex). They don't have a docType entry and their alias entries do not refer to functions. Perhaps your debugging documentation could go into a similar *.Rd file. Does check balk at such help files in a package? Should it? Should there be a special docType for such help files? Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Charles Geyer Sent: Monday, October 05, 2009 10:51 AM To: r-devel@r-project.org Subject: [Rd] how to document stuff most users don't want to see The functions metrop and temper in the mcmc package have a debug = FALSE argument that when TRUE adds a lot of debugging information to the returned list. This is absolutely necessary to test the functions, because one generally knows nothing about the simulated distribution except what what one learns from MCMC samples. Hence you must expose all details of the simulation to have any hope of checking that it is doing what it is supposed to do. However, this information is of interested mostly (perhaps solely) to developers. So I didn't document it in the Rd files for these functions. But it has ocurred to me that people might be interested in how these functions are validated, and I would like to document the debug output somewhere, but I don't want to clutter up the documentation that ordinary users see. That suggests a separate help page for debugging. Looking at Writing R Extensions it doesn't seem like there is a type of Rd file for this purpose. I suppose it could be added in (fairly long) sections titled Debug Output in metrop.Rd and temper.Rd or it could be put in a package help page (although that's not what that kind of page is really for). Any other possibilities to consider? -- Charles Geyer Professor, School of Statistics University of Minnesota char...@stat.umn.edu __ 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 -- 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] unit testing for R packages?
On 10/5/2009 3:01 PM, Blair Christian wrote: Hi All, I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd unit test through the writing R extensions manual but didn't find anything. Are there any suggestions out there? Nothing very specific, but what there is is described in that manual in the discussion of the tests subdirectory. Duncan Murdoch Currently I have several (a lot?) classes/methods that I keep tinkering with, and I'd like to run a script frequently to check that I don't cause any unforeseen problems. Right now I'm writing the classes/methods, but will be packaging it up soon. Thx, Blair __ 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] unit testing for R packages?
Hi, On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian blair.christ...@gmail.com wrote: I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd unit test through the writing R extensions manual but didn't find anything. Are there any suggestions out there? Currently I have several (a lot?) classes/methods that I keep tinkering with, and I'd like to run a script frequently to check that I don't cause any unforeseen problems. I've had good experiences using RUnit. To date, I've mostly used RUnit by putting tests in inst/unitTests and creating a Makefile there to run the tests. You should also be able to use RUnit in a more interactive fashion inside an interactive R session in which you are doing development. The vignette in svUnit has an interesting approach for integrating unit testing into R CMD check via examples in an Rd file within the package. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unit testing for R packages?
Seth I should look at RUnit more carefully sometime, but having had my own system in place from much earlier, I've never made the move. Basically I just use files in the tests/ directory which are run by a makefile in the package directory above. Roughly, this just means that I can run the tests quickly before building and checking the package. Is there a (very short) explanation of the main things that RUnit gives beyond this? Thanks, Paul -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r- project.org] On Behalf Of Seth Falcon Sent: October 5, 2009 3:48 PM To: Blair Christian Cc: r-devel@r-project.org Subject: Re: [Rd] unit testing for R packages? Hi, On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian blair.christ...@gmail.com wrote: I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd unit test through the writing R extensions manual but didn't find anything. Are there any suggestions out there? Currently I have several (a lot?) classes/methods that I keep tinkering with, and I'd like to run a script frequently to check that I don't cause any unforeseen problems. I've had good experiences using RUnit. To date, I've mostly used RUnit by putting tests in inst/unitTests and creating a Makefile there to run the tests. You should also be able to use RUnit in a more interactive fashion inside an interactive R session in which you are doing development. The vignette in svUnit has an interesting approach for integrating unit testing into R CMD check via examples in an Rd file within the package. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel La version française suit le texte anglais. This email may contain privileged and/or confidential information, and the Bank of Canada does not waive any related rights. Any distribution, use, or copying of this email or the information it contains by other than the intended recipient is unauthorized. If you received this email in error please delete it immediately from your system and notify the sender promptly by email that you have done so. Le présent courriel peut contenir de l'information privilégiée ou confidentielle. La Banque du Canada ne renonce pas aux droits qui s'y rapportent. Toute diffusion, utilisation ou copie de ce courriel ou des renseignements qu'il contient par une personne autre que le ou les destinataires désignés est interdite. Si vous recevez ce courriel par erreur, veuillez le supprimer immédiatement et envoyer sans délai à l'expéditeur un message électronique pour l'aviser que vous avez éliminé de votre ordinateur toute copie du courriel reçu. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Wish for stripchart to handle pch %in% 21:25 with bg (PR#13984)
Full_Name: Jean Lobry Version: 2.9.0 OS: i386-apple-darwin8.11.1 Submission from: (NULL) (83.197.82.45) Dear R-core, I have posted a href=http://finzi.psych.upenn.edu/Rhelp08/2009-September/212688.html;this/a on R-help, and then a href=http://finzi.psych.upenn.edu/R/R-devel/2009-September/054929.html;that/a on R-Dev. Looks for me as a documentation bug for the naive user: the documentation for function stripchart() should state more explicitly that it does not handle colorized points (i.e. pch in 21:25). I agree that the documentation is perfectly correct for advanced users, but this is not cristal clear, under 2.9.0, try: ### x - round(rnorm(50)) stripchart(x, pch = 21, col = black, bg = pink, method = jitter) points(0.5, 1, pch = 21, col = black, bg = pink, cex = 2) ### My wish is either for stripchart() to handle this case or for the documentation of stripchart() to say more explicitly that it does not handle this case. Not very important, but this is a real end-user casework. Hope you enjoy how I was reluctant to submit a documentation bug report in this case. HTH, Best, Z. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R's --enable-threads does nothing?; gdb needs -lpthread
In the R-2-9-branch (svn revision 49914, 2009-09-24), R's configure script has an --enable-threads option. But, does it do anything useful? When I use --enable-threads=posix, some of the configure output changes slightly, but it seems to have no effect on the actual link commands used when building R. Is that a bug, or am I misunderstanding what it's supposed to do? Btw, ldd said that exactly these 4 objects are linked against libpthread.so.0, regardless of whether I use --enable-threads or not: ./lib/R/modules/x86_64/R_X11.so ./lib/R/library/tcltk/libs/x86_64/tcltk.so ./lib/R/site-library/bigmemory/libs/x86_64/bigmemory.so ./lib/R/site-library/Rmpi/libs/x86_64/Rmpi.so Next I tried setting the LIBS=-lpthread environment variable when calling configure - that works. (Perhaps I should have also set FLIBS, I'm not sure.) The generated Makeconf file now has this: LIBS = -ldl -lm -lpthread and building with that links my libR.so against libpthread.so.0, which fixes the gdb problem described below. Is there any reason you know of NOT to link R with -lpthread on Linux, any potential downside? Now, why do I care about this -lpthread stuff in the first place? It's to work around a gdb limitation. I have a custom library of C code which I use from R, and my library needs to be linked with -lpthread. I know that R isn't thread-safe, and my code is not itself using threads, but it in turn statically links in some lower level libraries which insist on having the -lpthread. That has worked fine for me for a long time, no problems, except that gdb won't work! When I run R under the debugger with R -d gdb, gdb only works if my own linked-with-pthread package is NOT loaded. As soon as I load it, gdb stops with this error: [Thread debugging using libthread_db enabled] Error while reading shared library symbols: Cannot find new threads: generic error Googling says that happens because the R binary starts out without thread support, and gdb doesn't know what to do when my *.so suddenly brings in the thread stuff. Since I can't stop using -lpthread in my library, the obvious fix is for me to build R itself with -lpthread, so gdb doesn't get confused. -- Andrew Piskorski a...@piskorski.com http://www.piskorski.com/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unit testing for R packages?
On 05/10/2009 4:39 PM, spencerg wrote:
I put unit test in the examples, using \dontshow to hide stopifnot.
Many help pages I've written contain code like the following:
A - functionDocumentedHere()
B - manuallyComputedAnswer
\dontshow{stopifnot(}
all.equal(A, B)
\dontshow{)}
This will fail in a future release of R, because those aren't valid
expressions within \dontshow{}, which expects R code. You can achieve
the same effect using the clearer
all.equal(A,B)
\dontshow{ stopifnot(isTrue(.Last.value)) }
Duncan Murdoch
I think it helps the documentation to include an example comparing
a special case computed using a function with a manual computation.
However, stopifnot contributes nothing to user understanding, so I
hide it. One could also use \dontshow to hide entire examples that
check trivial details you think would not interest users.
Spencer
Seth Falcon wrote:
Hi,
On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian
blair.christ...@gmail.com wrote:
I'm interested in putting some unit tests into an R package I'm
building. I have seen assorted things such as Runit library, svUnit
library, packages
with 'tests' directories, etc
I grep'd unit test through the writing R extensions manual but didn't find
anything. Are there any suggestions out there? Currently I have
several (a lot?) classes/methods that I keep tinkering with, and I'd
like to run a script frequently to check that I don't cause any
unforeseen problems.
I've had good experiences using RUnit. To date, I've mostly used
RUnit by putting tests in inst/unitTests and creating a Makefile there
to run the tests. You should also be able to use RUnit in a more
interactive fashion inside an interactive R session in which you are
doing development.
The vignette in svUnit has an interesting approach for integrating
unit testing into R CMD check via examples in an Rd file within the
package.
+ seth
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Re: [Rd] unit testing for R packages?
On 05/10/2009 6:06 PM, spencerg wrote:
Hi, Duncan:
Thanks for the warning. Can you give me a hint of which release
might require this? In particular, will it be R 2.10.0, coming quite
soon?
The alpha version of 2.10.0 lets this pass, and I can't see changing
that now. But 2.11.0 (due next spring) may well enforce the rules that
have been documented but unenforced since before the release of 2.9.0.
Duncan Murdoch
Thanks,
Spencer
Duncan Murdoch wrote:
On 05/10/2009 4:39 PM, spencerg wrote:
I put unit test in the examples, using \dontshow to hide
stopifnot. Many help pages I've written contain code like the
following:
A - functionDocumentedHere()
B - manuallyComputedAnswer
\dontshow{stopifnot(}
all.equal(A, B)
\dontshow{)}
This will fail in a future release of R, because those aren't valid
expressions within \dontshow{}, which expects R code. You can achieve
the same effect using the clearer
all.equal(A,B)
\dontshow{ stopifnot(isTrue(.Last.value)) }
Duncan Murdoch
I think it helps the documentation to include an example
comparing a special case computed using a function with a manual
computation. However, stopifnot contributes nothing to user
understanding, so I hide it. One could also use \dontshow to hide
entire examples that check trivial details you think would not
interest users.
Spencer
Seth Falcon wrote:
Hi,
On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian
blair.christ...@gmail.com wrote:
I'm interested in putting some unit tests into an R package I'm
building. I have seen assorted things such as Runit library, svUnit
library, packages
with 'tests' directories, etc
I grep'd unit test through the writing R extensions manual but
didn't find
anything. Are there any suggestions out there? Currently I have
several (a lot?) classes/methods that I keep tinkering with, and I'd
like to run a script frequently to check that I don't cause any
unforeseen problems.
I've had good experiences using RUnit. To date, I've mostly used
RUnit by putting tests in inst/unitTests and creating a Makefile there
to run the tests. You should also be able to use RUnit in a more
interactive fashion inside an interactive R session in which you are
doing development.
The vignette in svUnit has an interesting approach for integrating
unit testing into R CMD check via examples in an Rd file within the
package.
+ seth
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[Rd] str() gives odd looking output on complex vectors that are not purely imaginary (PR#13985)
Full_Name: Rich Calaway Version: R 2.9.2 OS: Windows Vista Submission from: (NULL) (65.47.30.18) Try this: x - rnorm(25) y - rnorm(25)*1i z - x+y str(z) str(y) When I try this, I see the following: str(z) cplx [1:25] 0.0102+ 0.9463-1 -1.+ ... str(y) cplx [1:25] 0+0.0975i 0-1.5060i 0+0.4071i ... I see this in 2.9.2 and in the alpha build of 2.10.0: sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-intel32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Revobase_0.2-1 loaded via a namespace (and not attached): [1] pkgXMLBuilder_1.0 XML_2.6-0 sessionInfo() R version 2.10.0 alpha (2009-10-04 r49926) i386-pc-mingw32 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Characters vs. factors
It seems like a recent trend in R has been to make character vectors and factors almost equivalent (apart from the way that factors always remember their original range). There are a few exceptions: * summary.character != summary.factor * table(x, exclude = NULL) != table(factor(x), exclude=NULL) when x includes missing values * strsplit on a factor strsplit(factor(c(a, a b)), ) Error in strsplit(factor(c(a, a b)), ) : non-character argument * nchar on a factor: nchar(factor(c(abc, d, defgh))) [1] 1 1 1 * : with two character strings a:b Error in a:b : NA/NaN argument In addition: Warning messages: 1: NAs introduced by coercion 2: NAs introduced by coercion factor(a):factor(b) [1] a:b Levels: a:b Regards, Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unit testing for R packages?
Hi, I am the writer of svUnit. My initial goal was to build functions on top of RUnit which is older, and certainly deserves all the credit for core test unit functions. Unfortunately, the way RUnit is working internally did not allowed me to build the extensions I needed. Now, as Seth already told, there are several functions in svUnit that ease interactive use of the tests in an R session. What he did not told is that RUnit has some nice code coverage functions that svUnit does not have. Thus, not easy to decide... The good news is that both RUnit and svUnit are almost completely compatible with test unit code, that is, the same code put in inst/unitTests should run with both packages. So, you could write your test units, try both approaches in practice, and finally decide after a little bit of experiment which one you prefer (at least, read the vignette of each packages). In case you use Komodo Edit as R code editor, there is a nice GUI interactive panel to svUnit available (see http://www.sciviews.org/SciViews-K). Best, Philippe Grosjean Seth Falcon wrote: Hi, On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian blair.christ...@gmail.com wrote: I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd unit test through the writing R extensions manual but didn't find anything. Are there any suggestions out there? Currently I have several (a lot?) classes/methods that I keep tinkering with, and I'd like to run a script frequently to check that I don't cause any unforeseen problems. I've had good experiences using RUnit. To date, I've mostly used RUnit by putting tests in inst/unitTests and creating a Makefile there to run the tests. You should also be able to use RUnit in a more interactive fashion inside an interactive R session in which you are doing development. The vignette in svUnit has an interesting approach for integrating unit testing into R CMD check via examples in an Rd file within the package. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unit testing for R packages?
On Mon, Oct 5, 2009 at 5:44 PM, hadley wickham h.wick...@gmail.com wrote: Now, as Seth already told, there are several functions in svUnit that ease interactive use of the tests in an R session. What he did not told is that RUnit has some nice code coverage functions that svUnit does not have. What are those? I've skimmed through the documentation and couldn't see anything? The R wiki has information about both RUnit and svUnit. I'm not sure that it details all of the differences. I have successfully used the methodology of the gdata package described there. http://wiki.r-project.org/rwiki/doku.php?id=developers:runit Peter Hadley -- http://had.co.nz/ __ 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] unit testing for R packages?
On Mon, Oct 5, 2009 at 8:48 PM, Peter Cowan cowan...@gmail.com wrote: On Mon, Oct 5, 2009 at 5:44 PM, hadley wickham h.wick...@gmail.com wrote: Now, as Seth already told, there are several functions in svUnit that ease interactive use of the tests in an R session. What he did not told is that RUnit has some nice code coverage functions that svUnit does not have. What are those? I've skimmed through the documentation and couldn't see anything? The R wiki has information about both RUnit and svUnit. I'm not sure that it details all of the differences. I have successfully used the methodology of the gdata package described there. Sorry, I should have been more explicit. I was interested particularly in the code coverage functions. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Characters vs. factors
On Mon, Oct 5, 2009 at 4:33 PM, hadley wickham h.wick...@gmail.com wrote: It seems like a recent trend in R has been to make character vectors and factors almost equivalent (apart from the way that factors always remember their original range). There are a few exceptions: A related issue is that modeling functions throw a warning when character objects are used in place of factors: shopping - read.csv(http://spreadsheets.google.com/pub?key=tE9pXlYLwTAeiDWxL8h_viAsingle=truegid=0range=A1%3AE37output=csv;, as.is=TRUE) shopping$seconds - as.numeric(as.difftime(shopping$Total.Time)) fit - lm(seconds ~ Number.of.Items + Payment - 1, shopping,subset=-8) Warning message: In model.matrix.default(mt, mf, contrasts) : variable 'Payment' converted to a factor The warning doesn't affect R's behaviour, of course, but it does make it difficult to sanction the otherwise sensible advice to R beginners to read in data files with as.it=TRUE. (The warning leads to difficult-to-answer questions.) For similar reasons I deleted the warning from this post: http://blog.revolution-computing.com/2009/09/is-the-express-line-really-faster-1.html In general the trend towards equivalence of factors and character vectors is welcome, though. # David On Mon, Oct 5, 2009 at 4:33 PM, hadley wickham h.wick...@gmail.com wrote: It seems like a recent trend in R has been to make character vectors and factors almost equivalent (apart from the way that factors always remember their original range). There are a few exceptions: * summary.character != summary.factor * table(x, exclude = NULL) != table(factor(x), exclude=NULL) when x includes missing values * strsplit on a factor strsplit(factor(c(a, a b)), ) Error in strsplit(factor(c(a, a b)), ) : non-character argument * nchar on a factor: nchar(factor(c(abc, d, defgh))) [1] 1 1 1 * : with two character strings a:b Error in a:b : NA/NaN argument In addition: Warning messages: 1: NAs introduced by coercion 2: NAs introduced by coercion factor(a):factor(b) [1] a:b Levels: a:b Regards, Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (San Francisco, USA) Check out our upcoming events schedule at www.revolution-computing.com/events __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
