[Rd] Lapack calls from fortran

2005-06-22 Thread Paul Gilbert
I am trying to call the lapack routine dgesv in the R distribution from the fortran code for a package, but when I dyn.load("dse1.so") I get an error about undefined symbol: dgesv_ I thought the proper incantation was MAKEFLAG="FLIBS=/path to/R-2.1.1/libRlapack.so" R CMD SHLIB dse1.f but appar

[Rd] simulate in stats

2005-09-14 Thread Paul Gilbert
arguments could be ignored, but it does not really make sense to introduce a new generic with that in mind. (I would also prefer that the "object" argument was called "model" but this is less important.) Paul Gilbert __ R-devel@r

[Rd] simulate in stats

2005-09-14 Thread Paul Gilbert
contexts where nsim and seed do not make sense. I realize that the default arguments could be ignored, but it does not really make sense to introduce a new generic with that in mind. (I would also prefer that the "object" argument was called "model" but this is less impor

Re: [Rd] simulate in stats

2005-09-15 Thread Paul Gilbert
ations and then do the analysis of them. In a Monte Carlo experiment the generated data set is just too big. A better approach is to do the analysis and save only necessary information after each simulation. That is the approach, for example, in dse2:::EstEval. Paul Paul Gilbert wrote: > Can th

[Rd] loadings() generic in R alpha

2005-09-15 Thread Paul Gilbert
Could loadings() in R-2.2.0 please be made generic? Thanks, Paul Gilbert __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] acf() generic in R alpha

2005-09-15 Thread Paul Gilbert
Could acf() in R-2.2.0 please be made generic? Thanks, Paul Gilbert __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] loadings() generic in R alpha

2005-09-16 Thread Paul Gilbert
re I can clearly see the reason for wanting to start consideration of this at an earlier point in the development cycle. Best, Paul Prof Brian Ripley wrote: > On Thu, 15 Sep 2005, Paul Gilbert wrote (in two separate messages) > >> Could loadings() in R-2.2.0 please be made generic? &g

Re: [Rd] loadings() generic in R alpha

2005-09-16 Thread Paul Gilbert
Gavin Simpson wrote: >On Fri, 2005-09-16 at 12:52 -0400, Paul Gilbert wrote: > > >>Brian >> >>It would help if I understood general principles. I thought one would >>want a case for NOT making functions generic, rather than a case for >>making them gen

Re: [Rd] loadings() generic in R alpha

2005-09-16 Thread Paul Gilbert
Brian Ok, lets leave this for now. When does the development cycle start for the next version that would allow making a function generic? Paul Prof Brian D Ripley wrote: >On Fri, 16 Sep 2005, Paul Gilbert wrote: > > > >>Brian >> >>It would help if I understood

Re: [Rd] automatically adding smooth to plot: options("plot.add.smooth")

2005-09-19 Thread Paul Gilbert
Martin Maechler wrote: > I've changed the subject in the hope some more people would > voice an opinion... ... > Now I even propose to have > > options(add.smooth = TRUE) > > as a new default. > > Do I get a reaction now? > Martin I think you may break a lot of things if you

Re: [Rd] automatically adding smooth to plot: options("plot.add.smooth")

2005-09-19 Thread Paul Gilbert
Duncan Murdoch wrote: > On 9/19/2005 10:01 AM, Paul Gilbert wrote: > >> Martin Maechler wrote: >> >>> I've changed the subject in the hope some more people would >>> voice an opinion... >> >> >> ... >> >>> Now I even

Re: [Rd] Shy Suggestion?

2005-09-20 Thread Paul Gilbert
Seth Falcon wrote: >On 20 Sep 2005, [EMAIL PROTECTED] wrote: > > >>As I said above, and will try to emphasize, I really do not want R >>CMD check to do any checking of Uses (unless asked to do >>so). Developers that use Uses need to make sure that their package >>works and passes R CMD check whe

Re: [Rd] Installing R-2.2.0 package

2005-10-13 Thread Paul Gilbert
round in the R build itself or the installation >>scripts? >> >> > >No, not a new feature in R-2.2.0, it has been there for some time now. > > I have the impression the feature behaves slightly differently as of R-2.2.0. Now the 00LOCK file is not removed in So

Re: [Rd] Installing R-2.2.0 package

2005-10-13 Thread Paul Gilbert
nu/R/SunOS-sparc32/R-2.2.0/bin/INSTALL: test: argument expected may be a clue. (BTW. If there is a simple answer to the libz problem then I would appreciate hearing.) Paul Gilbert > install.packages(c("RMySQL"), Sys.getenv("R_LIBS"), repos = "http://cran.

[Rd] checking S3 generic/method consistency

2005-10-14 Thread Paul Gilbert
methods to be checked consistently against one or the other. Is this deteremined by Depends in the DESCRIPTION file, the NAMESPACE, or something else? Paul Gilbert __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] checking S3 generic/method consistency

2005-10-17 Thread Paul Gilbert
will that override? This is all with a fairly "clean" test environment. What happens when other packages are attached? Where/how does it break when there are other packages attached that need conflicting generics (or can that actually work)? Thanks, Paul Kurt Hornik wrote: >&g

[Rd] proposal to make loadings() generic in R-devel

2005-11-03 Thread Paul Gilbert
alue must be a matrix, so I suggest sticking with the current non-specific structure for the return value. (For piecewise linear or other non-linear analysis there may be good reasons to allow more general structures for the loadings.) Paul Gilbert __

Re: [Rd] [R] ouml in an .Rd

2006-01-09 Thread Paul Gilbert
ions. > > On Fri, 6 Jan 2006, Paul Gilbert wrote: > >> I am trying to put an ouml in an .Rd file with no success. Writing R >> Extensions suggests: >> >> Text which might need to be represented differently in different >> encodings should be marked by |\enc|,

[Rd] typo in factanal.Rd

2006-01-11 Thread Paul Gilbert
In the file factanal.Rd the line then the first fit is started at the value suggested by J\ureskog should be then the first fit is started at the value suggested by \enc{J\ureskog}{Joreskog} or whatever that translates to on a system that does not mangle cut and paste of s

[Rd] package introductions

2006-02-01 Thread Paul Gilbert
TION file tag GettingStarted: foo.Intro probably as an optional tag to begin. Of course, the biggest simplification happens when things like this are done in a similar way by everyone. ( "configure ; make" is not

Re: [Rd] Bias in R's random integers?

2018-09-20 Thread Paul Gilbert
specified RNG to "buggy Kinderman-Ramage". Perhaps there does need to be a protocol for testing before release. When my package setRNG fails then many of my other packages will also fail because they depend on it. This is a simple fix but reverse dependencies may make it look like lots of

Re: [Rd] code for sum function

2019-02-19 Thread Paul Gilbert
ly and you 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/

Re: [Rd] survival changes

2019-06-02 Thread Paul Gilbert
, so don't 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

Re: [Rd] c.POSIXct

2010-08-19 Thread Paul Gilbert
I used to get caught by this c() behaviour often, but now I do expect it to drop attributes. I think it would break many things if you change it, and force people to write different code when they really do want to drop attributes. When you want new behaviour it is usually better to define a new

Re: [Rd] winbuilder warnings and errors

2010-09-08 Thread Paul Gilbert
Possibly you are using x11() or postscript() to open a graphics device? You need to use something generic like dev.new() or nothing (a device will open automatically). I would check that first, though it does not really explain the second problem. Paul >-Original Message- >From: r-devel-b

Re: [Rd] Non identical numerical results from R code vs C/C++ code?

2010-09-10 Thread Paul Gilbert
With fortran I have always managed to be able to get identical results on the same computer with the same OS. You will have trouble if you switch OS or hardware, or try the same hardware and OS with different math libraries. All the real calculations need to be double, even intermediate variables.

[Rd] FW: [R] same random numbers in different sessions

2010-10-12 Thread Paul Gilbert
From R-help ... >I notice that you have the IPSUR package loaded; you know, just a >shot in the dark here, but did you try not loading it? > >I ask because the vignette is built by making a special choice for >set.seed, and the workspace that ships with the package might be >interacting in an unex

[Rd] rc make error

2010-10-14 Thread Paul Gilbert
With R-rc_2010-10-11_r53297.tar.gz I am getting ... ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/mfa/gilp/toolchain/R/src/R-rc/library/cluster/libs/cluster.so': /home/mfa

Re: [Rd] Competing with one's own work

2010-12-03 Thread Paul Gilbert
At one time I lobbied for putting something in base or a required package, and it was suggested that the idea at the time was to remove things rather than add them. Generally, I agree that is a good idea, so I did not lobby more. When this question comes up it is always asked, and answered, in

[Rd] R-forge out?

2010-12-29 Thread Paul Gilbert
Is anyone else having trouble connecting to R-forge svn? (Perhaps I missed an outage announcement, or is it bad weather?) Paul La version française suit le texte anglais. -

Re: [Rd] R vs. C

2011-01-17 Thread Paul Gilbert
Spencer Would it not be easier to include this kind of test in a small file in the tests/ directory? Paul -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Spencer Graves Sent: January 17, 2011 3:58 PM To: Dominick Samperi Cc: Pa

[Rd] S3 method for S4 object

2011-02-03 Thread Paul Gilbert
code, is there an easy way to do this, or do I have to convert the generic to S4 and then make those methods deal with the S3 objects? (Using R 2.12.1 on Ubuntu 10.10.) Paul Gilbert La version française suit

[Rd] function call overhead

2011-02-16 Thread Paul Gilbert
(subject changed from: RE: [Rd] Avoiding name clashes: opinion on best practice naming conventions) Dominick Is this really true? Is there a speed advantage to defining a local function this way, say, within another function, and then calling it within a loop rather than the original? Do you

[Rd] S3/S4/NAMESPACE

2011-02-17 Thread Paul Gilbert
from pk2. This works, except when I try to use a function defined in pk1, Within the function the S4 method does not seem to be visible. Do I have to export an S4 generics and default methods from pk1 or am I doing something else wrong? Paul Gilbert

[Rd] fortan common block

2011-05-06 Thread Paul Gilbert
Is it possible in R to call a fortran routine that sets variables in a common block and expect the values to persist when a call is made from R to a second routine that uses the common block? If not (as I suspect), is it possible to use a common block in a group of routines that are used toget

Re: [Rd] fortan common block

2011-05-09 Thread Paul Gilbert
2011 3:44 AM > To: Paul Gilbert > Cc: r-devel@r-project. org > Subject: Re: [Rd] fortan common block > > On Fri, May 6, 2011 at 4:04 PM, Paul Gilbert > wrote: > > Is it possible in R to call a fortran routine that sets variables in > a common block and expect the values

Re: [Rd] fortan common block

2011-05-09 Thread Paul Gilbert
011 11:48 AM > To: Paul Gilbert > Cc: r-devel@r-project. org > Subject: Re: [Rd] fortan common block > > AFAIK it's all much simpler that you think. Technically common blocks > are just FORTRAN's slightly complicated way to declare and access > global variables.

Re: [Rd] How to document man/*.Rd pages with images?

2011-05-11 Thread Paul Gilbert
I thought the usual logic was that you might put graphs and images into a vignette, and you might refer to the vignette in an Rd help file, but you would not put the graphs into the help because ? access to the page cannot assume that you actual have a graphics device. Of course, examples in the

Re: [Rd] How to document man/*.Rd pages with images?

2011-05-11 Thread Paul Gilbert
> No one is > checking that there's not a function in ggplot2 that secretly sends me > all your code and data ;) Well, it is open source so we could check it. Hopefully you are checking this yourself, because it would be a criminal offense to do that. ;) Paul ===

Re: [Rd] Randomness not due to seed

2011-07-20 Thread Paul Gilbert
It does not look like your calculation is using the random number generator, so the other responses are probably more to the point. However, beware that setting the seed is not enough to guarantee the same random numbers. You need to also make sure you are using the same uniform RNG and any o

Re: [Rd] Best practices for writing R functions

2011-07-22 Thread Paul Gilbert
> -Original Message- > From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- > project.org] On Behalf Of Gabriel Becker > Sent: July 22, 2011 11:38 AM > To: Spencer Graves > Cc: Alireza Mahani; r-devel@r-project.org > Subject: Re: [Rd] Best practices for writing R functions > > On

[Rd] R DDD fortran

2011-07-29 Thread Paul Gilbert
Is there an easy way to compile a packages's fortran so that it has the information for ddd or gdb to follow the lines of the code? I seem to remember seeing something about this, but I cannot find it in Writing R Extensions. (I see about Valgrind, debugging a segfault, and some other tricks, bu

Re: [Rd] Building R package with precompiled shared library

2011-09-14 Thread Paul Gilbert
My understanding is that this cannot be done, for both licence and security reasons. The package build expects source code and removes binaries. You can link with binaries that are provided separately from the package, possibly coming from a vendor that sells non-open source code, but you cannot

Re: [Rd] R license for a derived data-only package

2011-09-16 Thread Paul Gilbert
Michael You might look at my TSzip package on CRAN. There are examples in the Guide: http://cran.at.r-project.org/web/packages/TSzip/vignettes/Guide.pdf. The package may not work directly, since it is designed for time series data (the example is daily market data.) But the general idea of just

Re: [Rd] using R as SHELL in gnu make

2011-09-20 Thread Paul Gilbert
Other than the RServe part, I do this all the time. It works well. Perhaps we can put together some notes off-line and then bring it back to the list. Paul > -Original Message- > From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- > project.org] On Behalf Of Cook, Malcolm > Se

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

2015-06-30 Thread Paul Gilbert
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 de

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

2015-10-22 Thread Paul Gilbert
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 th

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

2016-04-04 Thread Paul Gilbert
ble combinations of missing Suggested packages, but that's probably far too slow to be a default. But how do you 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 possibl

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

2016-08-31 Thread Paul Gilbert
And, 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: Wh

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

2016-09-08 Thread Paul Gilbert
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 a zero-length operan

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

2016-09-09 Thread Paul Gilbert
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 wrote: On 09/08/2016 01:22 PM, Gabriel Becker wrote: On Thu, Sep 8, 2016 at 10:05 AM, William Dunlap wrote:

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

2016-12-09 Thread Paul Gilbert
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 n

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

2017-11-05 Thread Paul Gilbert
om numbers 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 wrote: On 04/11/2017 10:20 PM, Daniel Nordlund wrote: Tirthankar, "random number generators" d

Re: [Rd] Apple M1 CRAN checks

2021-02-28 Thread Paul Gilbert
m a time when 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

Re: [Rd] Apple M1 CRAN checks

2021-02-28 Thread Paul Gilbert
.0658141036401502788e-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-b

[Rd] Depends vs Imports

2013-07-31 Thread Paul Gilbert
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 ‘Depends

Re: [Rd] Depends vs Imports

2013-07-31 Thread Paul Gilbert
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] Correct NAMESPACE approach when writing an S3 method for a generic in another package

2013-08-26 Thread Paul Gilbert
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 u

[Rd] ‘:::’ call

2013-08-28 Thread Paul Gilbert
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

2013-08-28 Thread Paul Gilbert
On 13-08-28 12:29 PM, Marc Schwartz wrote: On Aug 28, 2013, at 11:15 AM, Paul Gilbert 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 them to be exposed to

Re: [Rd] ‘:::’ call

2013-08-28 Thread Paul Gilbert
ol over our own test cases. IMHO, testing is the justification of CRAN's reputation and quality, and that is a part of what CRAN does. In God we trust, and everyone else should bring tests. Regards, Yihui -- Yihui Xie Web: http://yihui.name Department of Statistics, Iowa State University 2

Re: [Rd] ‘:::’ call

2013-08-28 Thread Paul Gilbert
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] "False" warning on "replacing previous import" when re-exporting identical object

2013-08-30 Thread Paul Gilbert
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 difficultly

Re: [Rd] declaring package dependencies

2013-09-12 Thread Paul Gilbert
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] declaring package dependencies

2013-09-13 Thread Paul Gilbert
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, | > | b

Re: [Rd] declaring package dependencies

2013-09-14 Thread Paul Gilbert
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 | >

Re: [Rd] declaring package dependencies

2013-09-15 Thread Paul Gilbert
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: | > I

[Rd] helping R-forge build

2013-09-16 Thread Paul Gilbert
(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 source

Re: [Rd] FOSS licence with BuildVignettes: false

2013-09-16 Thread Paul Gilbert
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 co

Re: [Rd] Design for classes with database connection

2013-09-19 Thread Paul Gilbert
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

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

2013-09-23 Thread Paul Gilbert
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

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

2013-09-27 Thread Paul Gilbert
On 13-09-27 06:05 PM, Peter Langfelder wrote: On Fri, Sep 27, 2013 at 2:50 PM, Kasper Daniel Hansen 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 of cleaning it up, as you ar

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

2013-10-20 Thread Paul Gilbert
On 13-10-20 04:58 PM, Gabor Grothendieck wrote: On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch 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 --as-cran: * checking CRAN

Re: [Rd] advise on Depends

2013-10-25 Thread Paul Gilbert
On 13-10-25 05:21 PM, Henrik Bengtsson wrote: On Fri, Oct 25, 2013 at 1:39 PM, John Chambers 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 necessary, rather than s

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

2013-10-30 Thread Paul Gilbert
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 insta

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

2013-10-31 Thread Paul Gilbert
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/. A

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

2013-10-31 Thread Paul Gilbert
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?

2013-11-01 Thread Paul Gilbert
pathto/python /pathto/python_version.py",intern=TRUE) call and post-process the one-line text output. --j On Thu, Oct 31, 2013 at 12:45 PM, Paul Gilbert mailto:pgilbert...@gmail.com>> wrote: On 13-10-31 01 :16 PM, Prof Brian Ripley wrote: On 31/10/2013 15:33, Paul Gilbert

Re: [Rd] Depending/Importing data only packages

2013-12-07 Thread Paul Gilbert
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

2013-12-07 Thread Paul Gilbert
o put the data that is used to calculate the prior into another package, because it will be larger than the code, and it does not change that often. Gabor On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert wrote: Would "Suggests" not work in this situation? I don't understand why you wo

Re: [Rd] Depending/Importing data only packages

2013-12-07 Thread Paul Gilbert
On 13-12-07 01:47 PM, Gabor Grothendieck wrote: On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert 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 a package that does Bay

Re: [Rd] Depending/Importing data only packages

2013-12-07 Thread Paul Gilbert
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 th

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

2014-01-26 Thread Paul Gilbert
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

2014-01-26 Thread Paul Gilbert
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?

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

2014-03-24 Thread Paul Gilbert
On 03/22/2014 01:32 PM, Radford Neal wrote: From: Philippe GROSJEAN ... 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 and disappear *without any vers

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

2014-03-26 Thread Paul Gilbert
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-Ex.Rout.save, this is compared to the output file for running the examples when the latter are ch

Re: [Rd] type.convert and doubles

2014-04-11 Thread Paul Gilbert
On 04/11/2014 01:43 PM, Simon Urbanek wrote: Greg, On Apr 11, 2014, at 11:50 AM, Gregory R. Warnes 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 as a double would

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

2014-04-13 Thread Paul Gilbert
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 fil

Re: [Rd] type.convert and doubles

2014-04-17 Thread Paul Gilbert
On 04/17/2014 02:21 PM, Murray Stokely wrote: On Thu, Apr 17, 2014 at 6:42 AM, McGehee, Robert 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 the web output as a text table. Th

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

2014-06-02 Thread Paul Gilbert
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] Re R CMD check checking in development version of R

2014-08-28 Thread Paul Gilbert
(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 wrote: On 27 August 2014 15:24, Hadley

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

2014-09-10 Thread Paul Gilbert
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

[Rd] requireNamespace() questions

2014-09-12 Thread Paul Gilbert
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 t

[Rd] extra package tests directory

2014-09-22 Thread Paul Gilbert
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 lik

Re: [Rd] Problem with build and check

2014-11-12 Thread Paul Gilbert
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 stri

Re: [Rd] Changing style for the Sweave vignettes

2014-11-13 Thread Paul Gilbert
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 accept

[Rd] testing dontrun examples

2014-11-26 Thread Paul Gilbert
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 the

Re: [Rd] testing dontrun examples

2014-11-26 Thread Paul Gilbert
they decided to do 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

Re: [Rd] testing dontrun examples

2014-11-27 Thread Paul Gilbert
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 if the

[Rd] unloadNamespace

2015-01-08 Thread Paul Gilbert
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 wo

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