Re: [Rd] Apple M1 CRAN checks

02788e-14 [4] -3.5527136788005009294e-15 I hope this helps you to track it down. Cheers, Simon On Mar 1, 2021, at 4:50 AM, Paul Gilbert wrote: If there was a response to the "how can I test it out" part of this question then I missed it. Can anyone point to a Win-builder like sit

Re: [Rd] Apple M1 CRAN checks

hen simple double precision was the norm, the tolerances are already fairly relaxed so I hesitate to adjust them with actually examining the results. Paul Gilbert On 2021-02-22 3:30 a.m., Travers Ching wrote: I noticed CRAN is now doing checks against Apple M1, and some packages are failing

Re: [R-pkg-devel] CRAN check texi2dvi failure

e. Maybe using \url in the vignette could fix the error? kind regards Enrico [*] R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.10 > On Sat, 09 Jan 2021, Paul Gilbert writes: I am trying to debug a problem that is appearing in the l

[R-pkg-devel] translation .mo files

looked there and many other places. I need a section or page reference.) Thanks, Paul Gilbert __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [Rd] survival changes

put in anything you are experimenting with. Good luck, Paul Gilbert On 6/1/19 8:02 PM, Therneau, Terry M., Ph.D. via R-devel wrote: On 6/1/19 1:32 PM, Marc Schwartz wrote: On Jun 1, 2019, at 12:59 PM, Peter Langfelder wrote: On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R

Re: [R-pkg-devel] Submitting a package whose unit tests sometimes fail because of server connections

from your package then it cannot be properly checked by other people. Paul Gilbert On 4/16/19 2:16 PM, Dirk Eddelbuettel wrote: On 16 April 2019 at 11:40, Will wrote: | Some things I have considered include: | |1. Skipping all unit tests on CRAN (using something like |*testtht::sk

Re: [Rd] code for sum function

have to specify it.) Then if you accidentally put singles, like a constant 0.0 rather than a constant 0.0D+0, into a double you will have small junk in the lower precision part. (I am assuming you are talking about a sum of reals, not integer or complex.) HTH, Paul Gilbert On 2/14/19 2:08 PM

Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?

(I didn't see an answer to this, so ...) I think using .NOTPARALLEL will usually get rid of the error but, in my experience, this problem is usually caused by an incorrect or incomplete Makefile. When not done in parallel this missing target is usually getting done first as a side-affect of

Re: [Rd] Extreme bunching of random values from runif with Mersenne-Twister seed

you need to keep track of both the starting seed and the number of nodes.) Paul Gilbert On 11/05/2017 10:58 AM, peter dalgaard wrote: On 5 Nov 2017, at 15:17 , Duncan Murdoch <murdoch.dun...@gmail.com> wrote: On 04/11/2017 10:20 PM, Daniel Nordlund wrote: Tirthankar, "ra

[Rd] parallel::detectCores() bug on Raspberry Pi B+

In R 3.3.2 detectCores() in package parallel reports 2 rather than 1 on Raspberry Pi B+ running Raspbian. (This report is just 'for the record'. The model is superseded and I think no longer produced.) The problem seems to be caused by grep processor /proc/cpuinfo processor : 0 model

Re: [Rd] R (development) changes in arith, logic, relop with (0-extent) arrays

it annoys me precisely when I need to be annoyed, that is, when I haven't thought through the consequences of sending zero-length arguments. On Fri, Sep 9, 2016 at 6:00 AM, Paul Gilbert <pgilbert...@gmail.com> wrote: On 09/08/2016 01:22 PM, Gabriel Becker wrote: On Thu, Sep 8, 2016 at 10:05

Re: [Rd] R (development) changes in arith, logic, relop with (0-extent) arrays

On 09/08/2016 01:22 PM, Gabriel Becker wrote: On Thu, Sep 8, 2016 at 10:05 AM, William Dunlap wrote: Shouldn't binary operators (arithmetic and logical) should throw an error when one operand is NULL (or other type that doesn't make sense)? This is a different case than

Re: [Rd] A bug in the R Mersenne Twister (RNG) code?

no I did not get burned by the R 1.7.0 change in the default generator. I got burned by a much earlier, unadvertised, and more subtle change in the Splus generator.) Paul Gilbert so it's not obvious that we would do it. Duncan Murdoch On 30/08/2016 5:45 PM, Mark Roberts wrote: Whomever, I

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies? - Part 2

On 08/04/2016 11:51 AM, Dirk Eddelbuettel wrote: On 4 August 2016 at 11:46, Paul Gilbert wrote: | If my package has a test that needs another package, but that package is | not needed in the /R code of my package, then I indicate it as | "Suggests", not as "Depends&q

[R-pkg-devel] Handling Not-Always-Needed Dependencies? - Part 2

(One question from the thread Handling Not-Always-Needed Dependencies?) I hope not to start another long tangled thread, but I have a basic confusion which I think has a yes/no answer and I would like to know if there is agreement on this point (or is it only me that is confused as usual).

Re: [Rd] Suggested dependencies in context of R CMD check

decide pass/fail when you do this? I think it will only pass when all the suggested packages are available? Paul Gilbert BTW, I'm not completely sure it needs to be possible to run vignettes without the Suggested packages they need. Vignettes are allowed to depend on things that aren't av

Re: [Rd] Best way to implement optional functions?

On 10/22/2015 03:55 PM, Duncan Murdoch wrote: I'm planning on adding some new WebGL functionality to the rgl package, but it will pull in a very large number of dependencies. Since many people won't need it, I'd like to make the new parts optional. The general idea I'm thinking of is to put

Re: [R-pkg-devel] download.file and https

behaviour still does not work. Paul /Henrik On Thu, Jul 2, 2015 at 7:46 PM, Paul Gilbert pgilbert...@gmail.com wrote: (This problem with download.file() affects quantmod, and possibly several other packages. e.g. getSymbols('M2',src='FRED') fails.) I think the St Louis Fed has moved to using https

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

On 06/30/2015 11:33 AM, Duncan Murdoch wrote: On 30/06/2015 5:27 PM, Lorenz, David wrote: There is something I'm really missing here. The function show is a standardGeneric function, so the correct way to write it as method like this: That describes methods::show. The problem is that the

Re: [R-pkg-devel] appropriate directory for data downloads in examples, demos and vignettes

Regarding alternative places for scripts, you can add a directory (eg inst/testLocalScripts) and then with a recently added R CMD feature you can do R CMD check --test-dir=inst/testLocalScripts your-package.tar.gz This will not (automatically) be checked on CRAN. Beware that you also need

Re: [Rd] Print output during long tests?

If your tests can be divided into multiple files in the tests/ directory then you will get lines like * checking tests ... Running ‘test1.R’ Running ‘test2.R’ Running ‘test3.R’ ... Paul On 05/04/2015 11:52 AM, Toby Hocking wrote: I am the author of R package animint which uses testthat

Re: [Rd] R CMD check and missing imports from base packages

in the popular 'dplyr' package masks the one that has been in the stats package forever, and they have nothing in common, so that may give you an example. As I recall, several packages mask the simulate generic in stats, if you are looking for examples. Paul Gilbert Bill Dunlap TIBCO Software wdunlap

Re: [Rd] Which function can change RNG state?

On 02/08/2015 09:33 AM, Dirk Eddelbuettel wrote: On 7 February 2015 at 19:52, otoomet wrote: | random numbers. For instance, can I be sure that | set.seed(0); print(runif(1)); print(rnorm(1)) | will always print the same numbers, also in the future version of R? There Yes, pretty much.

Re: [Rd] unloadNamespace

(tseries), it calls getNamespace(tseries), which has the side effect of loading that package (and its dependencies). One way to work around this is to check loadedNamespaces() before you try to unload a package. -Winston On Thu, Jan 8, 2015 at 9:45 AM, Paul Gilbert pgilbert...@gmail.com mailto:pgilbert

[Rd] unloadNamespace

In the documentation the closed thing I see to an explanation of this is that ?detach says Unloading some namespaces has undesirable side effects Can anyone explain why unloading tseries will load zoo? I don't think this behavior is specific to tseries, it's just an example. I realize one

Re: [Rd] testing dontrun examples

On 14-11-26 05:49 PM, Duncan Murdoch wrote: On 26/11/2014, 1:45 PM, Paul Gilbert wrote: Is there a good strategy for testing examples which should not be run by default? For instance, I have examples which get data from the Internet. If I wrap them in try() then they can be skipped

[Rd] testing dontrun examples

Is there a good strategy for testing examples which should not be run by default? For instance, I have examples which get data from the Internet. If I wrap them in try() then they can be skipped if the Internet is not available, but may not be tested in cases when I would like to know about

Re: [Rd] testing dontrun examples

that sometimes? Paul Hope this helps. Spencer On 11/26/2014 10:45 AM, Paul Gilbert wrote: Is there a good strategy for testing examples which should not be run by default? For instance, I have examples which get data from the Internet. If I wrap them in try() then they can be skipped

Re: [Rd] Changing style for the Sweave vignettes

You might also consider starting your vignettes with \begin{Scode}{echo=FALSE,results=hide} options(continue= ) \end{Scode} Then you get one prompt but it is still easy to cut and paste. This has been in many of my packages for many years, so I think it would be fair to assume it is

Re: [Rd] Problem with build and check

I certainly have longer argument lists with no problem. More likely the Rd file needs special consideration for %. Paul On 11/12/2014 02:11 PM, Therneau, Terry M., Ph.D. wrote: I am getting failure of build and check, for an Rd file that has a long argument list. Guess diagnosis: a quoted

[Rd] extra package tests directory

I am trying to decide on a name for a directory where I will put some extra package tests. The main motivation for this is the need to limit the package test time on CRAN. That is, these are tests that could be in the tests/ directory and could be run on CRAN, but will take longer than CRAN

[Rd] requireNamespace() questions

I am trying to follow directions at http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Suggested-packages regarding handling suggested packages with requireNamespace() rather than require(), and I have some questions. 1/ When I do requireNamespace() in a function is the loading of

Re: [Rd] How to test impact of candidate changes to package?

On 09/10/2014 06:12 AM, Kirill Müller wrote: If you don't intend to keep the old business logic in the long run, perhaps a version control system such as Git can help you. If you use it in single-user mode, you can think of it as a backup system where you manually create each snapshot and give

Re: [Rd] Re R CMD check checking in development version of R

(Please correct me if I'm wrong. I thought I mostly understood this, finally, but I've made the mistake of thinking I understood something too many times before.) On 08/28/2014 10:39 AM, Simon Urbanek wrote: On Aug 27, 2014, at 6:01 PM, Gavin Simpson ucfa...@gmail.com wrote: On 27 August

Re: [Rd] R CMD check for the R code from vignettes

On 06/02/2014 12:16 AM, Gabriel Becker wrote: Carl, I don't really have a horse in this race other than a strong feeling that whatever check does should be mandatory. That having been said, I think it can be argued that the fact that check does this means that it IS in the R package vignette

Re: [Rd] type.convert and doubles

On 04/17/2014 02:21 PM, Murray Stokely wrote: On Thu, Apr 17, 2014 at 6:42 AM, McGehee, Robert robert.mcge...@geodecapital.com wrote: Here's my use case: I have a function that pulls arbitrary financial data from a web service call such as a stock's industry, price, volume, etc. by reading

Re: [Rd] NOTE when detecting mismatch in output, and codes for NOTEs, WARNINGs and ERRORs

On 04/10/2014 04:34 AM, Kirill Müller wrote: On 03/26/2014 06:46 PM, Paul Gilbert wrote: On 03/26/2014 04:58 AM, Kirill Müller wrote: Dear list It is possible to store expected output for tests and examples. From the manual: If tests has a subdirectory Examples containing a file pkg

Re: [Rd] type.convert and doubles

On 04/11/2014 01:43 PM, Simon Urbanek wrote: Greg, On Apr 11, 2014, at 11:50 AM, Gregory R. Warnes g...@warnes.net wrote: Hi All, I see this in the NEWS for R 3.1.0: type.convert() (and hence by default read.table()) returns a character vector or factor when representing a numeric input

Re: [Rd] Varying results of package checks due to random seed

On 03/22/2014 01:32 PM, Radford Neal wrote: From: Philippe GROSJEAN philippe.grosj...@umons.ac.be ... for latest CRAN version, we have successfully installed 4999 packages among the 5321 CRAN package on our platform. ... It is strange that a large portion of R CMD check errors on CRAN occur

[Rd] No repository set, so cyclic dependency check skipped

When checking a package I am getting * checking package dependencies ... NOTE No repository set, so cyclic dependency check skipped How/where do I set the repository so I don't get this note? No doubt this is explained in Writing R Extension, but I have not found it. Paul

Re: [Rd] No repository set, so cyclic dependency check skipped

On 01/26/2014 12:31 PM, Uwe Ligges wrote: On 26.01.2014 17:52, Paul Gilbert wrote: When checking a package I am getting * checking package dependencies ... NOTE No repository set, so cyclic dependency check skipped How/where do I set the repository so I don't get this note? Set

Re: [Rd] Depending/Importing data only packages

Would Suggests not work in this situation? I don't understand why you would need Depends. In what sense do you rely on the data only package? Paul On 13-12-06 04:20 PM, Hadley Wickham wrote: Hi all, What should you do when you rely on a data only package. If you just Depend on it, you get

Re: [Rd] Depending/Importing data only packages

On 13-12-07 01:47 PM, Gabor Grothendieck wrote: On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert pgilbert...@gmail.com wrote: On 13-12-07 12:19 PM, Gábor Csárdi wrote: I don't know about this particular case, but in general it makes sense to rely on a data package. E.g. I am creating

Re: [Rd] Depending/Importing data only packages

On 13-12-07 05:21 PM, Hadley Wickham wrote: The Writing R Extensions manual says that Suggests is for packages which are required only for examples, which I believe matches Hadley's original question. Yes, but without this package they won't be able to run the majority of examples, which I

Re: [Rd] Where to drop a python script?

=TRUE) call and post-process the one-line text output. --j On Thu, Oct 31, 2013 at 12:45 PM, Paul Gilbert pgilbert...@gmail.com mailto:pgilbert...@gmail.com wrote: On 13-10-31 01 tel:13-10-31%2001:16 PM, Prof Brian Ripley wrote: On 31/10/2013 15:33, Paul Gilbert wrote

Re: [Rd] Where to drop a python script?

On 13-10-31 03:01 AM, Prof Brian Ripley wrote: On 31/10/2013 00:40, Paul Gilbert wrote: The old convention was that it went in the exec/ directory, but as you can see at http://cran.at.r-project.org/doc/manuals/r-devel/R-exts.html#Non_002dR-scripts-in-packages it can be in inst/anyName

Re: [Rd] Where to drop a python script?

On 13-10-31 01:16 PM, Prof Brian Ripley wrote: On 31/10/2013 15:33, Paul Gilbert wrote: On 13-10-31 03:01 AM, Prof Brian Ripley wrote: On 31/10/2013 00:40, Paul Gilbert wrote: The old convention was that it went in the exec/ directory, but as you can see at http://cran.at.r-project.org

Re: [Rd] Where to drop a python script?

The old convention was that it went in the exec/ directory, but as you can see at http://cran.at.r-project.org/doc/manuals/r-devel/R-exts.html#Non_002dR-scripts-in-packages it can be in inst/anyName/. A minor convenience of exec/ is that the directory has the same name in source and when

Re: [Rd] advise on Depends

On 13-10-25 05:21 PM, Henrik Bengtsson wrote: On Fri, Oct 25, 2013 at 1:39 PM, John Chambers j...@r-project.org wrote: One additional point to Michael's summary: The methods package itself should stay in Depends:, to be safe. It would be nice to have more detail about when this is

Re: [Rd] Question about selective importing of package functions...

On 13-10-20 04:58 PM, Gabor Grothendieck wrote: On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK

Re: [Rd] Problems when moving to Imports from Depends

On 13-09-27 06:05 PM, Peter Langfelder wrote: On Fri, Sep 27, 2013 at 2:50 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Peter, This is a relatively new warning from R CMD check (for some definition of new). The authors of Hmisc have clearly not yet gone through the process

Re: [Rd] Capture output of install.packages (pipe system2)

On 13-09-23 08:20 PM, Hadley Wickham wrote: Brian Ripley's reply describes how it is done in the tools package. For example, as I sent privately to Jeroen, x - system2(Rscript, -e \install.packages('MASS', repos='http://probability.ca/cran')\, stdout=TRUE, stderr=TRUE) captures all of the

Re: [Rd] Design for classes with database connection

Simon Your idea to use SQLite and the nature of some of the sorting and extracting you are suggesting makes me wonder why you are thinking of R data structures as the home for the data storage. I would be inclined to put the data in an SQL database as the prime repository, then extract parts

[Rd] helping R-forge build

(subject changed from Re: [Rd] declaring package dependencies ) ... Yes useful. But that includes a package build system (which is what breaks on R-Forge). If you could do that on a six-pack then could you fix R-Forge on a three-pack first please? The R-Forge build system is itself an open

Re: [Rd] FOSS licence with BuildVignettes: false

On 13-09-16 05:19 AM, Uwe Ligges wrote: ... Yes, and I could see really rare circumstances where vignette building takes a long time and the maintainer decides not to build vignettes as part of the daily checks. ... I thought 'BuildVignettes: FALSE' only turns of assembling the pdf, all the

Re: [Rd] declaring package dependencies

On 13-09-14 07:20 PM, Duncan Murdoch wrote: On 13-09-14 12:19 PM, Paul Gilbert wrote: On 13-09-14 09:04 AM, Duncan Murdoch wrote: On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote: On 13 September 2013 at 11:42, Paul Gilbert wrote: | On 13-09-13 11:02 AM, Dirk Eddelbuettel wrote: | It's

Re: [Rd] declaring package dependencies

On 13-09-14 09:04 AM, Duncan Murdoch wrote: On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote: On 13 September 2013 at 11:42, Paul Gilbert wrote: | On 13-09-13 11:02 AM, Dirk Eddelbuettel wrote: | It's not so much Rcpp itself or my 20-ish packages but the fact that we (as | in the Rcpp authors

Re: [Rd] declaring package dependencies

On 13-09-13 11:02 AM, Dirk Eddelbuettel wrote: On 13 September 2013 at 10:38, Duncan Murdoch wrote: | On 13/09/2013 10:18 AM, Dirk Eddelbuettel wrote: | On 13 September 2013 at 09:51, Duncan Murdoch wrote: | | Changes are generally announced in the NEWS.Rd file long before release, | | but

Re: [Rd] declaring package dependencies

Michael (Several of us are struggling with these changes, so my comments are from the newly initiated point of view, rather than the fully knowledgeable.) On 13-09-12 09:38 AM, Michael Friendly wrote: I received the following email note re: the vcdExtra package A vcd update has shown that

Re: [Rd] False warning on replacing previous import when re-exporting identical object

This is related to the recent thread on correct NAMESPACE approach when writing S3 methods. If your methods are S4 I think pkgB does not need to export the generic. Just export the method and everything works magically and your problem disappears. For S3 methods there seems to be the

[Rd] ‘:::’ call

I have a package (TSdbi) which provides end user functions that I export, and several utilities for plugin packages (e.g. TSMySQL) that I do not export because I do not intend them to be exposed to end users. I call these from the plugin packages using TSdbi::: but that now produces a note in

Re: [Rd] ‘:::’ call

On 13-08-28 12:29 PM, Marc Schwartz wrote: On Aug 28, 2013, at 11:15 AM, Paul Gilbert pgilbert...@gmail.com wrote: I have a package (TSdbi) which provides end user functions that I export, and several utilities for plugin packages (e.g. TSMySQL) that I do not export because I do not intend

Re: [Rd] ‘:::’ call

of what CRAN does. In God we trust, and everyone else should bring tests. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Aug 28, 2013 at 1:50 PM, Paul Gilbert pgilbert...@gmail.com wrote

Re: [Rd] ‘:::’ call

On 13-08-28 05:13 PM, Hadley Wickham wrote: 3/ Some functions are exported normally but hidden by using . in the beginning of their names. Other package maintainers would know they exist, but end users would not so easily find them. (Duncan's other suggestion of using \keyword{internal} in

Re: [Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

On 13-08-26 12:04 PM, Gavin Simpson wrote: Right Henrik, but then you have to document it or R CMD check raises a Warning, which is less likely to pass muster when submitting to CRAN. So you document that method on your existing method's Rd page (just via an \alias{}), which is fine until the

[Rd] Depends vs Imports

I am being asked to modernize the Depends line in the DESCRIPTION file of some packages. Writing R Extensions says: The general rules are Packages whose namespace only is needed to load the package using library(pkgname) must be listed in the ‘Imports’ field and not in the

Re: [Rd] Depends vs Imports

Simon Thanks, that helps a lot, but see below .. On 13-07-31 08:35 PM, Simon Urbanek wrote: On Jul 31, 2013, at 7:14 PM, Paul Gilbert wrote: I am being asked to modernize the Depends line in the DESCRIPTION file of some packages. Writing R Extensions says: The general rules are Packages

Re: [Rd] R-3.0.1 - transient make check failure in splines-EX.r

Avraham I resolved this only by switching to a different BLAS on the 32 bit machine.Since no one else seemed to be having problems, I considered it possible that there was a hardware issue on my old 32 bit machine. The R check test failed somewhat randomly, but often. most disconcertingly, it

Re: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony

Being generally uninformed about Windows, I have to admit to almost total confusion trying to follow this thread. However, since I have recently been trying to do something in Windows, I would appreciate a newbie friendly explanation of a few points: -Rtools is used to build R and to build

Re: [Rd] package file permissions problem R 3.0.0/Windows OS

On 13-04-15 03:19 PM, Prof Brian Ripley wrote: On 15/04/2013 14:11, John Fox wrote: Dear Brian, On Mon, 15 Apr 2013 06:56:26 +0100 Prof Brian Ripley rip...@stats.ox.ac.uk wrote: POSIX-style execute permission isn't a Windows concept, so it was fortuitous this ever worked. One possibility

[Rd] R-3.0.0 reg-tests-3.R / survival

make check is failing on reg-test3.R with a message that survival was built with an older version of R. (On my Ubuntu 32 bit and Ubuntu 64 bit machines). Why would make check be looking anywhere that it would find something built with an older version of R? ~/RoboAdmin/R-3.0.0/tests$ tail

Re: [Rd] R-3.0.0 reg-tests-3.R / survival

tcltk tools utils but the one in my development build tree of 3.0.0 has .libPaths() [1] /Users/pd/r-release-branch/BUILD-dist/library If I explicitly set R_LIBS, I can easily reproduce your error. On Apr 3, 2013, at 17:00 , Paul Gilbert wrote: make check is failing on reg-test3.R

Re: [Rd] [BioC] enabling reproducible research R package management install.package.version BiocLite

(More on the original question further below.) On 13-03-05 09:48 AM, Cook, Malcolm wrote: All, What got me started on this line of inquiry was my attempt at balancing the advantages of performing a periodic (daily or weekly) update to the 'release' version of locally installed R/Bioconductor

Re: [Rd] maintaining multiple R versions

and switch among them at the command line. Aaron On Fri, Jan 18, 2013 at 02:04:13PM -0500, Paul Gilbert wrote: (somewhat related to thread [Rd] R CMD check not reading R_LIBS ) For many years I have maintained R versions by building R (./configure ; make) in a directory indicating the version number

[Rd] maintaining multiple R versions

(somewhat related to thread [Rd] R CMD check not reading R_LIBS ) For many years I have maintained R versions by building R (./configure ; make) in a directory indicating the version number, putting the directory/bin on my path, and setting R_LIBS_SITE. It seems only one version can easily

Re: [Rd] R-forge, package dependencies

I'm surprised this works on Windows and Mac, since RMonetDB does not seem to be on CRAN. I thought it was still a requirement that dependencies need to be on CRAN (which makes development difficult for related packages like this). A related long standing request is that R-forge checking look

[Rd] SystemRequirements’ field

Am I correct in thinking that the ‘SystemRequirements’ field in a package DESCRIPTION file is purely descriptive, there are no standard elements that can be extracted by parsing it and used automatically? This field does not seem to be widely used, even for some obvious cases like backend

Re: [Rd] SystemRequirements’ field

On 12-12-12 02:19 PM, Prof Brian Ripley wrote: On 12/12/2012 18:33, Paul Gilbert wrote: Am I correct in thinking that the ‘SystemRequirements’ field in a package DESCRIPTION file is purely descriptive, there are no standard elements that can be extracted by parsing it and used automatically

Re: [Rd] An idea: Extend mclapply's mc.set.seed with an initial seed value?

I appreciate your problem, and getting reproducible random generator results on a parallel system is something to be careful about. However, I would avoid making it too easy to have a fixed seed. In earlier days there were mistakes too often made by users inadvertently using the same seed over

Re: [Rd] Retrieving data from aspx pages

) instead of examining in each web page the appropiate fields. 2012/10/30, Paul Gilbert pgilbert...@gmail.com: Jose As far as getting to the data, I think the best way to do this sort of thing would be if the site supports a SOAP or REST interface. When they don't (yet) then one is faced with clicking

Re: [Rd] Retrieving data from aspx pages

I don't know of an easy way to do this in R. I've been doing something similar with python scripts called from R. If anyone knows how to do this with just R, I would appreciate hearing too. Paul On 12-10-29 04:11 PM, jose ramon mazaira wrote: Hi. I'm trying to write an application to

Re: [Rd] Retrieving data from aspx pages

myself, and can't speak to it's current state but on quick inspection RHTMLForms seems worth a look for what you want. http://www.omegahat.org/RHTMLForms/ ~G On Tue, Oct 30, 2012 t 5:38 AM, Paul Gilbert pgilbert...@gmail.com mailto:pgilbert...@gmail.com wrote: I don't know of an easy way to do

Re: [Rd] Retrieving data from aspx pages

haven't used it extensively myself, and can't speak to it's current state but on quick inspection RHTMLForms seems worth a look for what you want. http://www.omegahat.org/RHTMLForms/ ~G On Tue, Oct 30, 2012 t 5:38 AM, Paul Gilbert pgilbert...@gmail.com mailto:pgilbert...@gmail.com wrote: I don't

[Rd] R 2.15.2 make check failure on 32-bit --with-blas=-lgoto2

Is --with-blas=-lgoto2 a known problem (other than possibly not being the preferred choice)? I thought I had been testing RC with the same setup I regularly use, but I now see there was a slight difference. I am now getting the following failure in make check on 32-bit Ubuntu 12.04,

Re: [Rd] R 2.15.2 make check failure on 32-bit --with-blas=-lgoto2

On 12-10-26 12:15 PM, Prof Brian Ripley wrote: On 26/10/2012 16:37, Paul Gilbert wrote: Is --with-blas=-lgoto2 a known problem (other than possibly not being the preferred choice)? And what precisely is it? And what chipset are you using? I thought I had been testing RC with the same

Re: [Rd] Is there an automatic method for updating an existing CRAN package from R-forge?

Yes, the button is still there if you are logged in and unhide it. (You probably also need the appropriate developer permission.) Beware that R-forge needs to indicate the package build status is current, but also, if you have just made svn updates it may falsely indicate current. Check the

[Rd] CRAN test / avoidance

( subject changed from Re: [Rd] R-devel Digest, Vol 115, Issue 18 ) I have the impression from this, and previous discussions on the subject, that package developers and CRAN maintainers are talking at cross-purposes. Many package maintainers are thinking that they should be responsible for

Re: [Rd] problem with vignettes when S4 classes in packages overlap

On 12-09-18 07:23 PM, Duncan Murdoch wrote: On 12-09-18 5:40 PM, Paul Gilbert wrote: ( A similar problem is also reported by Sebastian P. Luque with library(maptools) library(trip) in the vignette as below ). I am writing a vignette which loads RMySQL and RPostgreSQL. This produces

Re: [Rd] Requests for vignette clarification (re: Writing R Extensions)

be considered contrary to the spirit of what CRAN maintainers are attempting to do, and package maintainers should expect continuing problems as the loopholes are removed. Paul Gilbert I could learn how to do this from some examples of packages that manage vignettes the right way, if you

Re: [Rd] equivalent to source() inside a package

Is there a reason for not using a vignette or putting a file in the demo/ directory? This seems like the sort of thing for which they are intended. Paul On 12-05-25 03:33 PM, Wei Hao wrote: Hi all: I'm working on a project that I have packaged for ease of distribution. The different

Re: [Rd] Vignette questions

On 12-04-12 03:15 AM, Uwe Ligges wrote: On 12.04.2012 01:16, Paul Gilbert wrote: On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for Package vignette(s) without corresponding PDF: In this case the vignettes directory had both

Re: [Rd] Vignette questions

On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for Package vignette(s) without corresponding PDF: In this case the vignettes directory had both the pdf and Rnw; do I need to move the pdf to inst/doc? Yes, you need to put the pdf in

Re: [Rd] CRAN policies

Mark I would like to clarify two specific points. On 12-03-31 04:41 AM, mark.braving...@csiro.au wrote: ... Someone has subsequently decided that code should look a certain way, and has added a check that isn't in the language itself-- but they haven't thought of everything, and of course

[Rd] R-forge --as-cran

(Renamed from Re: [Rd] CRAN policies because the of the muli-threading of that subject.) Claudia Actually, my version numbers are year-month dates, eg 2012.3-1, although I don't set them automatically. I have had some additional off-line discussion on this. The problem is this: Now when I

Re: [Rd] CRAN policies

On 12-03-29 09:29 PM, mark.braving...@csiro.au wrote: I'm concerned this thread is heading the wrong way, towards techno-fixes for imaginary problems. R package-building is already encumbered with a huge set of complicated rules, and more instructions/rules eg for metadata would make things

[Rd] --as-cran / BuildVignettes: false

I have packages where I know CRAN and other test platforms do not have all the resources to build the vignettes, for example, access to databases. Previously I think putting BuildVignettes: false in the DESCRIPTION file resolved this, by preventing CRAN checks from attempting to run the

Re: [Rd] CRAN policies

One of the things I have noticed with the R 2.15.0 RC and --as-cran is that the I have to bump the version number of the working copy of my packages immediately after putting a version on CRAN, or I get an message about version suitability. This is probably a good thing for packages that I

Re: [Rd] CRAN policies

On 12-03-27 10:59 AM, Uwe Ligges wrote: On 27.03.2012 16:17, Paul Gilbert wrote: One of the things I have noticed with the R 2.15.0 RC and --as-cran is that the I have to bump the version number of the working copy of my packages immediately after putting a version on CRAN, or I get

Re: [Rd] CRAN policies

An associated problem, for the wish list, is that it would be nice for package developers to have a way to automatically distinguish between NOTEs that can usually be ignored (e.g. a package suggests a package that is not available for cross reference checks - I have several case where the

Re: [Rd] RC / methods package

On 12-03-25 05:29 PM, Paul Gilbert wrote: John Here is the definition of the TSMySQLConnection class, and a few other things. This is a simplified example that produces the message, but unfortunately will not work unless you have a MySQL database to connect to. (I do get the same problem

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