[Rd] update.formula simplify = FALSE
Dear R users,
I am building a packaged where I want to use the update.formula function,
but modifying the option simplify = TRUE to FALSE. Since this is not an
argument, I modified the code and created a new function as:
update.formula2 - function (old, new, ...) {
tmp - .Internal(update.formula(as.formula(old), as.formula(new)))
out - formula(terms.formula(tmp, simplify = FALSE))
return(out)
}
This works fine. But when creating and checking the package (R CMD check
--as-cran mypackage), I obtained a warning saying that .Internal function
cannot be used inside a package.
Does anyone know how to define an update.formula (or equivalent) setting
simplify = FALSE?
Thanks.
Isaac Subirana.
IMIM. Barcelona.
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[Rd] Package does not have a NAMESPACE and should be re-installed
I'm trying to load a package locally from a zip file. When I load the package, I first get this, which looks okay: package ?IBGEPesq? successfully unpacked and MD5 sums checked HOWEVER, when I try to use the package to use the data with library(IBGEPesq) I get this message: package ?IBGEPesq? does not have a NAMESPACE and should be re-installed I've tried re-installing it, and I've tried following suggestions on similar posts, but with no success. Help please. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package does not have a NAMESPACE and should be re-installed
On 12-05-14 2:37 PM, walco...@msu.edu wrote: I'm trying to load a package locally from a zip file. When I load the package, I first get this, which looks okay: package ?IBGEPesq? successfully unpacked and MD5 sums checked HOWEVER, when I try to use the package to use the data with library(IBGEPesq) I get this message: package ?IBGEPesq? does not have a NAMESPACE and should be re-installed I've tried re-installing it, and I've tried following suggestions on similar posts, but with no success. The .zip file was likely produced by an earlier version of R. It is essentially a copy of an installed version of the package. You need a new .zip file, produced by the same version of R as you are using. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package does not have a NAMESPACE and should be re-installed
Duncan Murdoch-2 wrote On 12-05-14 2:37 PM, walcott3@ wrote: I'm trying to load a package locally from a zip file. When I load the package, I first get this, which looks okay: package ?IBGEPesq? successfully unpacked and MD5 sums checked HOWEVER, when I try to use the package to use the data with library(IBGEPesq) I get this message: package ?IBGEPesq? does not have a NAMESPACE and should be re-installed I've tried re-installing it, and I've tried following suggestions on similar posts, but with no success. The .zip file was likely produced by an earlier version of R. It is essentially a copy of an installed version of the package. You need a new .zip file, produced by the same version of R as you are using. Duncan Murdoch __ R-devel@ mailing list https://stat.ethz.ch/mailman/listinfo/r-devel I'm not sure I can get the newer version (it's census data from another country). Is there a way to figure out which version of R was used and just install that temporarily? -- View this message in context: http://r.789695.n4.nabble.com/Package-does-not-have-a-NAMESPACE-and-should-be-re-installed-tp4630059p4630070.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
Re: [Rd] Vignette problem
Duncan,
Thanks for the ideas. I checked them out and none seem to be the
culprit. My original message was wrong in one detail BTW, as I was
already using graphicx not graphics.
I switched over to the central server machine (CENTOS) to finish up
the coxme submission until I could figure this out. Ran CMD check,
tidied up the NAMESPACE, DESCRIPTION, NEWS files, fixed a missing $ sign
in an Rnw, etc. Submitted the final to CRAN, then updated all the files
on the Linux box from which the error below came -- both boxes point to
the same Mercurial master --- and then tried again.
Now it works! And I have no idea what could have prompted the
change. It will remain a mystery, since I'm not going to try to bring
the error back. :-)
Terry T.
On 05/14/2012 01:19 PM, Duncan Murdoch wrote:
On 14/05/2012 1:28 PM, Terry Therneau wrote:
I'm having a problem rebuilding a package, new to me in R 2.15.0
(Linux) It hits all that contain the line
\usepackage[pdftex]{graphics}
and leads to the following when running R CMD check on the directory.
(I do this often; a final run on the tar.gz file will happen before
submission.)
Since I float and resize my figures, removing the line is fatal in other
ways.
* checking re-building of vignette PDFs ... NOTE
Error in re-building vignettes:
...
/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def:414: Package
pdftex.de
f Error: PDF mode expected, but DVI mode detected!
(pdftex.def)If you are using `latex', then call
`pdflatex'.
(pdftex.def)Otherwise check and correct the driver
options.
(pdftex.def)Error recovery by switching to PDF mode.
See the pdftex.def package documentation for explanation.
Type Hreturn for immediate help.
...
l.414 }\@ehc
?
/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def:414: Emergency
stop.
...
l.414 }\@ehc
No pages of output.
Transcript written on lmekin.log.
/usr/bin/texi2dvi: latex exited with bad status, quitting.
make: *** [lmekin.pdf] Error 1
Error in buildVignettes(dir =
/home/therneau/research/surv/Hg/coxme.Rcheck/vign_test/coxme) :
running 'make' failed
Execution halted
-
The resulting .tex file work just fine with pdflatex, however. I
haven't found any reference to this elsewhere, but my guess is that it
is something simple that I've missed.
Do you have an explicit \usepackage{Sweave} in your file? If not,
Sweave will add one, and that might explain the difference between
your two tests.
Another possibility is that you have a copy of Sweave.sty that is not
the same as the one being used in one run or the other. The checks
will try to tell pdflatex to use the one that comes with your R
version, but other local ones can sometimes have higher precedence in
pdflatex.
And one idea what the problem might be: Sweave.sty uses the graphicx
package, and it may conflict with the graphics package.
Duncan Murdoch
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[Rd] How to set up an object to share data across diverse functions
In the past 6 months I've been struggling with an issue that has been raised periodically on the lists. This is the need to share information across a group of functions, possibly from different packages. So far I've found solutions that are either quite clumsy or else don't work as have (likely incorrectly) read the manuals. I'll be writing up my experiences as a way to help others, but am wondering if there is an accepted way to establish an object that can be read and written by a number of functions. I'm currently using list2env to create a list under the umbrella function, and if necessary pass this to other functions by name through the dot arguments, though preferably I'd rather use a pre-arranged and fixed name (this does not seem to work unless the object is in the global environment, and then I've occasionally had locked bindings errors, which I'll freely admit I don't understand at all). I also have to be very careful with dot arguments, especially if they are matrices. I've a couple of examples, but they are pretty long, so I'll save for off-list transmission. JN __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package does not have a NAMESPACE and should be re-installed
If you do not have access to the package's source code, you can try unzipping the the zip file, adding a NAMESPACE file, and re-zipping the package. It's not ideal, but it should work. This post from Stack Overflow has some more details: http://stackoverflow.com/questions/8012596/error-with-asreml-d-package-in-r-2-14-0/8014357#8014357 . Jeremy Jeremy Hetzel Boston University walcotteric wrote I'm trying to load a package locally from a zip file. When I load the package, I first get this, which looks okay: package ?IBGEPesq? successfully unpacked and MD5 sums checked HOWEVER, when I try to use the package to use the data with library(IBGEPesq) I get this message: package ?IBGEPesq? does not have a NAMESPACE and should be re-installed I've tried re-installing it, and I've tried following suggestions on similar posts, but with no success. - Jeremy T. Hetzel Boston University -- View this message in context: http://r.789695.n4.nabble.com/Package-does-not-have-a-NAMESPACE-and-should-be-re-installed-tp4630059p4630093.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] Object-oriented programming (OOP)
Hello everybody, please excuse my bad English. I am Alfredo Naime and I'm from to Venezuela. I want to make a lib with tools for simulation (queues, inventories, factory, etc.) using object-oriented programming (OOP). You have any manuals on the handling of data types, classes, inheritance, etc. in R with examples and how to make a R lib. Thank you, very much. Alfredo __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Object-oriented programming (OOP)
R has multiple OO paradigms, but since you're starting from a point of I want object oriented, I'd guess you would be interested in the S4 paradigm which is stricter rather than the far more sane S3 system. If S4 is for you, there are some good links here: http://stackoverflow.com/questions/4143611/sources-on-s4-objects-methods-and-programming-in-r See also the relatively new Reference Classes -- I don't have much documentation on those, but you could start here: http://www.bioconductor.org/help/course-materials/2010/HeidelbergNovember2010/ReferenceClasses-Morgan.pdf Best, Michael On Tue, May 15, 2012 at 9:55 AM, Alfredo Naime alfredon...@gmail.com wrote: Hello everybody, please excuse my bad English. I am Alfredo Naime and I'm from to Venezuela. I want to make a lib with tools for simulation (queues, inventories, factory, etc.) using object-oriented programming (OOP). You have any manuals on the handling of data types, classes, inheritance, etc. in R with examples and how to make a R lib. Thank you, very much. Alfredo __ 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] Package does not have a NAMESPACE and should be re-installed
jthetzel wrote If you do not have access to the package's source code, you can try unzipping the the zip file, adding a NAMESPACE file, and re-zipping the package. It's not ideal, but it should work. This post from Stack Overflow has some more details: http://stackoverflow.com/questions/8012596/error-with-asreml-d-package-in-r-2-14-0/8014357#8014357 . Jeremy Jeremy Hetzel Boston University Thanks! That worked and the package and library are loaded, and it shows that there is data there when I used data() However, now when I try to load the data to work with it, I get the following: Error in data(ocupacao2005) : invalid 'setTime' argument In addition: Warning message: In data(ocupacao2005) : zipped data found for package ‘IBGEPesq’. That is defunct, so please re-install the package. I'm playing around with it trying to fix it, but not sure exactly what it means. Any suggestions? -- View this message in context: http://r.789695.n4.nabble.com/Package-does-not-have-a-NAMESPACE-and-should-be-re-installed-tp4630059p4630132.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] R-devel on FreeBSD: new C99 functions don't build
About April 25th, there had been some changes within R-devel's src/nmath/pnbeta.c (and probably some other relevant places) and now building R-devel on FreeBSD 10.0-CURRENT (amd64) with gcc-4.6.4 and math/R-devel (selfmade forked port from math/R) fails like this: [..snip..] mkdir /usr/ports/math/R-devel/work/R-devel/bin/exec gcc46 -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -c Rmain.c -o Rmain.o gcc46 -std=gnu99 -export-dynamic -fopenmp -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -o R.bin Rmain.o -L../../lib -lR -lRblas ../../lib/libR.so: undefined reference to `log1pl' collect2: ld returned 1 exit status *** [R.bin] Error code 1 Stop in /usr/ports/math/R-devel/work/R-devel/src/main. *** [R] Error code 1 Stop in /usr/ports/math/R-devel/work/R-devel/src/main. *** [R] Error code 1 Stop in /usr/ports/math/R-devel/work/R-devel/src. *** [R] Error code 1 Stop in /usr/ports/math/R-devel/work/R-devel. *** [do-build] Error code 1 Stop in /usr/ports/math/R-devel. *** [build] Error code 1 Stop in /usr/ports/math/R-devel. === make failed for math/R-devel It seems, that at least one new C99 function (log1pl) is introduced in R-devel, see src/nmath/pnbeta.c:l95 return (double) (log_p ? log1pl(-ans) : (1 - ans)); for which there is only a declaration in FreeBSDs math.h, but no full implementation in libm (see http://wiki.freebsd.org/MissingMathStuff). Is there any chance to get at least rudimentary replacement functions in R-devel for systems with missing or defective C99 math functions? (For example, in the similar case of log1p(), see the RMATH_HAVE_LOG1P and RMATH_HAVE_WORKING_LOG1P bits in the configure script, src/include/Rmath.h0.in, and src/nmath/log1p.c; thanks to b.f. for pointing me out to this). Thanks for any help, Rainer Hurling CC'ed to b.f. as the maintainer of the math/R port on FreeBSD. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package does not have a NAMESPACE and should be re-installed
Thanks! That worked and the package and library are loaded, and it shows that there is data there when I used data() However, now when I try to load the data to work with it, I get the following: Error in data(ocupacao2005) : invalid 'setTime' argument In addition: Warning message: In data(ocupacao2005) : zipped data found for package ‘IBGEPesq’. That is defunct, so please re-install the package. I'm playing around with it trying to fix it, but not sure exactly what it means. Any suggestions? 1) Does traceback() give any hints as to where the setTime error is coming from? 2) Zipping data sets in packages was made defunct in R 2.13.0. However, I believe R 2.15 will still load data sets that were zipped using older versions of R, albeit with the warning that you see. As you are not the package maintainer, you can ignore it. - Jeremy T. Hetzel Boston University -- View this message in context: http://r.789695.n4.nabble.com/Package-does-not-have-a-NAMESPACE-and-should-be-re-installed-tp4630059p4630162.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
Re: [Rd] R-devel on FreeBSD: new C99 functions don't build
On Tue, May 15, 2012 at 10:05 AM, Rainer Hurling rhur...@gwdg.de wrote: About April 25th, there had been some changes within R-devel's src/nmath/pnbeta.c (and probably some other relevant places) and now building R-devel on FreeBSD 10.0-CURRENT (amd64) with gcc-4.6.4 and math/R-devel (selfmade forked port from math/R) fails like this: It seems, that at least one new C99 function (log1pl) is introduced in R-devel, see src/nmath/pnbeta.c:l95 return (double) (log_p ? log1pl(-ans) : (1 - ans)); AFAIK, Bruce Evans is not happy with the numerical accuracy of other open-source implementations of log1pl and so has blocked their inclusion in FreeBSD pending work on a better implementation. Can you put a conditional FreeBSD check here and use log1p instead of log1pl instead as a workaround? I can admire the insistence on correctness from the FreeBSD libm maintainers for their technical purity, but it can be a bit of a pain for things like this. - Murray __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel on FreeBSD: new C99 functions don't build
On 15.05.2012 20:49 (UTC+1), Murray Stokely wrote:
On Tue, May 15, 2012 at 10:05 AM, Rainer Hurlingrhur...@gwdg.de wrote:
About April 25th, there had been some changes within R-devel's
src/nmath/pnbeta.c (and probably some other relevant places) and now
building R-devel on FreeBSD 10.0-CURRENT (amd64) with gcc-4.6.4 and
math/R-devel (selfmade forked port from math/R) fails like this:
It seems, that at least one new C99 function (log1pl) is introduced in
R-devel, see
src/nmath/pnbeta.c:l95
return (double) (log_p ? log1pl(-ans) : (1 - ans));
AFAIK, Bruce Evans is not happy with the numerical accuracy of other
open-source implementations of log1pl and so has blocked their
inclusion in FreeBSD pending work on a better implementation.
Can you put a conditional FreeBSD check here and use log1p instead of
log1pl instead as a workaround?
I can admire the insistence on correctness from the FreeBSD libm
maintainers for their technical purity, but it can be a bit of a pain
for things like this.
- Murray
I read about this discussion and in principle I concur with your
opinion. As a scientist I tend to expect greatest possible correctness
from a statistical routine, especially when it uses long double format.
As a quick and dirty workaround I applied the following patch:
--- src/nmath/pnbeta.c.orig 2012-04-25 17:55:14.0 +0200
+++ src/nmath/pnbeta.c 2012-05-15 20:58:26.0 +0200
@@ -92,7 +92,11 @@
else {
if(ans 1 - 1e-10) ML_ERROR(ME_PRECISION, pnbeta);
if (ans 1.0) ans = 1.0; /* Precaution */
+#if !defined(__FreeBSD__)
return (double) (log_p ? log1pl(-ans) : (1 - ans));
+#else
+return (double) (log_p ? log1p(-ans) : (1 - ans));
+#endif /* FreeBSD */
}
}
It builds and installs fine now and I hope there are no side effects ...
Thank you for the quick answer and your advice,
Rainer
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