Re: [R-pkg-devel] sf subsetting with square bracket

2019-02-05 Thread Duncan Murdoch
They want to be able to operate even if the user chooses not to install "sf", and apparently all but one of their functions can do so. Duncan Murdoch Both approaches work fine. Thanks, Duncan, for digging into this! Btw: sf people are aware: https://github.com/r-spatial/sf/issues/9

Re: [R-pkg-devel] sf subsetting with square bracket

2019-02-04 Thread Duncan Murdoch
On 03/02/2019 8:26 p.m., Duncan Murdoch wrote: On 03/02/2019 5:21 p.m., Berry Boessenkool wrote: Hi, my package in question can only be online next week, but here's a script for a MWE: https://gist.github.com/brry/7728b9b2d35afad7f1fc5978c3315009 The script uses devtools and osmplo

Re: [R-pkg-devel] sf subsetting with square bracket

2019-02-03 Thread Duncan Murdoch
to me that if osmplotr is returning objects of class "sf", then it should probably make sure that the "sf" package is loaded so that methods can be found. Duncan Murdoch btw:  sf 0.7.2,   R 3.4.3,   x86_64-w64-mingw32/x64 (64-bit) * * Kind regards, Berry ------

Re: [R-pkg-devel] sf subsetting with square bracket

2019-02-03 Thread Duncan Murdoch
e on Github or some other public repository? Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] vignette problems: invisible

2019-02-01 Thread Duncan Murdoch
On 01/02/2019 9:23 a.m., Duncan Murdoch wrote: On 01/02/2019 8:22 a.m., Troels Ring wrote: devtools::install_github("troelsring/ABCharge",force=TRUE,build_vignettes = TRUE) That looks like an issue with install_github. The normal way to install a package is to build the tarball, th

Re: [R-pkg-devel] vignette problems: invisible

2019-02-01 Thread Duncan Murdoch
ur package, I get the vignette. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] package docu

2019-01-27 Thread Duncan Murdoch
earlier message and thought that kw was a function, not data. If it is data, use promptData() instead of prompt. Duncan Murdoch BW Troels -Oprindelig meddelelse- Fra: Duncan Murdoch Sendt: 26. januar 2019 22:08 Til: Troels Ring ; 'Michael Dewey' ; 'package-develop

Re: [R-pkg-devel] package docu

2019-01-26 Thread Duncan Murdoch
is really full og kw - That message is about the Rd file, not the code. Look for Kw in the \usage section. You haven't pushed this file to Github, so I can't offer any more advice. Duncan Murdoch I'm so sorry to bother BW Troels -Oprindelig meddelelse- Fra: Duncan M

Re: [R-pkg-devel] package docu

2019-01-26 Thread Duncan Murdoch
quot;) is wrong. Duncan Murdoch All best wishes Troels -Oprindelig meddelelse- Fra: Michael Dewey Sendt: 26. januar 2019 13:17 Til: Troels Ring ; package-develop Emne: Re: [R-pkg-devel] package docu Dear Troels What happens if you add \alias{TOTAL} Michael On 26/01/2019 08:15, Tr

Re: [R-pkg-devel] R CMD check --as-cran problem

2019-01-14 Thread Duncan Murdoch
in NAMESPACE. But I still had the same error: there is no package called 'Matrix'. I think we'd need to see at least the check log, and likely the whole package, to diagnose this. Duncan Murdoch Thanks, Zhu -Original Message- From: Dirk Eddelbuettel [mailto:dirk.e

Re: [R-pkg-devel] R CMD check --as-cran problem

2019-01-14 Thread Duncan Murdoch
checks requireNamespace("survival"), it just calls getFromNamespace('survfitKM','survival'). That will usually work (just about everyone has survival installed, since it's recommended), but is unsafe. Zhu should use survival::survfitKM, but only after checkin

Re: [R-pkg-devel] RData files with identical objects in package

2019-01-13 Thread Duncan Murdoch
g getAnywhere("x") For example, > x <- 2 > getAnywhere("x") A single object matching ‘x’ was found It was found in the following places .GlobalEnv with value [1] 2 Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] objects are masked _by_ '.GlobalEnv'

2019-01-10 Thread Duncan Murdoch
[,1] [,2] [,3] # [1,] 0.0267 0.0267 0.0267 # [2,] 0.0200 0.0200 0.0200 # which is wrong and belongs to another included dataset. How did that happen to be caught in globalenvironment, how can I avoid that and get rid # of it? I can see I need to know more about environ

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

2019-01-09 Thread Duncan Murdoch
On 09/01/2019 11:39 a.m., Dirk Eddelbuettel wrote: Hi Duncan and Iñaki, On 4 January 2019 at 14:13, Duncan Murdoch wrote: | If you want a total hack, the help system can run R code during a build, | e.g. \Sexpr[stage=build]{paste("Built at", Sys.time())}. Certainly it | could

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

2019-01-04 Thread Duncan Murdoch
tage=build]{paste("Built at", Sys.time())}. Certainly it could embed some information in a help page; perhaps it could do more. Similarly, vignettes are typically built during R CMD build, so they might be able to have useful side effects. But it seems likely that something less o

Re: [R-pkg-devel] R package development

2019-01-01 Thread Duncan Murdoch
he file, and that is not valid in an Rd file. It should perhaps be five lines, Spdf(r,rho,n) Fpdf(r,rho,n) Hpdf(r,rho,n) Fcdf(a,rho,n) Hcdf(r,rho,n) but without seeing the whole file we can't say for sure. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission vioplot 0.3.0

2018-12-26 Thread Duncan Murdoch
lly is compatible with CRAN. If it is not compatible with CRAN, then don't waste everyone's time by submitting it there: let interested people install it from Github. 2. Submit it again after Jan 2, following the instructions in https://cran.r-project.org/web/packages/policies.html.

Re: [R-pkg-devel] file35451f8cc152 found a top level

2018-12-18 Thread Duncan Murdoch
R, TMP, TEMP) set to ".", they could be created in the top level of your package. Alternatively, if you are using basename() on tempfile() you'll get the same sort of thing. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] In R package directory, where to put results for some long-taking simulations I want to use in README / vignette?

2018-12-17 Thread Duncan Murdoch
ting to compare current results with historical ones, and version control would let you do that. Duncan Murdoch Thank you, Marta [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/lis

Re: [R-pkg-devel] Suggested package relies on recent R

2018-12-08 Thread Duncan Murdoch
fully if the suggested package is not present, i.e. wrap uses of the suggested package in if (requireNamespace(...)) { ... } Duncan Murdoch Hadley On Fri, Dec 7, 2018 at 9:11 AM David Hugh-Jones wrote: Hi, My package Suggests a package that relies on R >= 3.5.0. My package works f

Re: [R-pkg-devel] Unexpected symbol when checking package examples

2018-11-12 Thread Duncan Murdoch
#' } Thanks everyone for the help. I never would have found this mistake without this list. Perhaps roxygen should try parsing the code it inserts as examples. It can probably give a better error message than R could, since it knows which .R file it's looking at when the problem h

Re: [R-pkg-devel] Unexpected symbol when checking package examples

2018-11-12 Thread Duncan Murdoch
On 11/11/2018 7:01 PM, Duncan Murdoch wrote: On 11/11/2018 6:53 PM, Duncan Murdoch wrote: On 11/11/2018 3:39 PM, Jared Knowles wrote: Hi! I have a bit of a weird issue when I'm trying to check my package merTools (source repo available here: https://github.com/jknowles/merTools On Wi

Re: [R-pkg-devel] Unexpected symbol when checking package examples

2018-11-11 Thread Duncan Murdoch
On 11/11/2018 6:53 PM, Duncan Murdoch wrote: On 11/11/2018 3:39 PM, Jared Knowles wrote: Hi! I have a bit of a weird issue when I'm trying to check my package merTools (source repo available here: https://github.com/jknowles/merTools On Windows and Linux builds for R-release and R-devel,

Re: [R-pkg-devel] Unexpected symbol when checking package examples

2018-11-11 Thread Duncan Murdoch
o longer exists. Perhaps when you say \donttest, no tests should be done. Duncan Murdoch The functions cleanEx() and nameEx() appear to be created as part of the checking process. I have not changed the examples in the code since the last time I ran R CMD CHECK so I am quite confident that the

Re: [R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio

2018-11-06 Thread Duncan Murdoch
es in R_init_secsse.c: void R_init_secsse(DllInfo *dll) {   R_registerRoutines(dll, NULL, NULL, FortranEntries, NULL);   R_useDynamicSymbols(dll, FALSE); } Any suggestions? Nope! Sounds like a bug in devtools/roxygen2, but I don't know either of those packages well. Duncan Murdoch

Re: [R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio

2018-11-06 Thread Duncan Murdoch
f you run "R CMD check" on the tarball of your package? If so, how comfortable are you with debugging R code? I can tell you how to debug the check process, but it's a little tricky. Duncan Murdoch Any other suggestions? Cheers, Rampal On 02-Nov-18 08:33, Georgi Boshnakov

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
On 08/10/2018 7:47 AM, Duncan Murdoch wrote: On 08/10/2018 7:37 AM, Gábor Csárdi wrote: The package versions are in the output: https://travis-ci.org/gdkrmr/coRanking/jobs/428661435#L2836 I would just try to purge the cache on Travis, that often helps with incompatible package versions. I

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
"R6" are out of date. There may be others; those are just from the ones that update.packages() updated on my system (so they are probably recent releases). Duncan Murdoch Gabor On Mon, Oct 8, 2018 at 12:34 PM Duncan Murdoch wrote: On 08/10/2018 7:08 AM, Guido Kraemer wrote: Hi all

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
rsion of some package. Can you see sessionInfo() on the two systems? It prints versions for R and for all used packages. Look for differences there. Duncan Murdoch Best Regards, Guido Kraemer On 09/17/2018 05:45 PM, Guido Kraemer wrote: Hi all, Since a couple of days travis-ci fails f

[R-pkg-devel] A bug in rgl caused S3 methods to fail to register

2018-09-21 Thread Duncan Murdoch
ey both printed as but identical(ns1, ns2) could tell that they were not the same.) Hopefully if anyone else is ever dumb enough to unload their own namespace, this message will help them to fix the bug. Duncan Murdoch __ R-package-devel@r-proje

Re: [R-pkg-devel] make: Nothing to be done for `all'.

2018-09-13 Thread Duncan Murdoch
changes aren't being seen. Duncan Murdoch Thanks. ==> R CMD INSTALL --no-multiarch --with-keep.source Simstudy Loading libraries ... (working on a package) Welcome back to R!!! Loading required package: grid * installing to library '/Library/Frameworks/R.framework/Versio

Re: [R-pkg-devel] Package Etiquette

2018-09-09 Thread Duncan Murdoch
mailing list. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-08 Thread Duncan Murdoch
s. But as the cheesy saying goes: "The best time to plant a tree was 20 years ago. The second best time is now." I agree with this. Duncan Murdoch Dirk Demo below runs off the _installed_ package which is a rather neat feature we could stress more for more complete regressi

Re: [R-pkg-devel] fatal error: 'ilcplex/ilocplex.h' file not found

2018-09-07 Thread Duncan Murdoch
typo: it should have been ilocplex/ilocplex.h - you didn't include the ilocplex.h file in your package - some other error Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-07 Thread Duncan Murdoch
On 07/09/2018 3:09 AM, Rainer Krug wrote: On 7 Sep 2018, at 02:16, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote: On 06/09/2018 10:32 AM, Hadley Wickham wrote: On Wed, Sep 5, 2018 at 3:03 PM Duncan Murdoch mailto:murdoch.dun...@gmail.com>> wrote: On 05/09/2018

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-07 Thread Duncan Murdoch
On 07/09/2018 4:27 AM, Gábor Csárdi wrote: On Fri, Sep 7, 2018 at 9:01 AM Duncan Murdoch wrote: [...] I think it's useful to think of 3 groups who might run tests: - authors - CRAN - other users of a package. What Hadley was arguing for is that CRAN should identify itself

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-07 Thread Duncan Murdoch
On 07/09/2018 2:18 AM, David Hugh-Jones wrote: On Fri, 7 Sep 2018 at 01:16, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote: When packages delete tests just for CRAN, the quality of the repository suffers.  Users should be able to check an install by running

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-06 Thread Duncan Murdoch
On 06/09/2018 10:32 AM, Hadley Wickham wrote: On Wed, Sep 5, 2018 at 3:03 PM Duncan Murdoch wrote: On 05/09/2018 2:20 PM, Henrik Bengtsson wrote: I take a complementary approach; I condition on, my home-made, R_TEST_ALL variable. Effectively, I do: if (as.logical(Sys.getenv("R_TES

Re: [R-pkg-devel] Vignette title problem

2018-09-06 Thread Duncan Murdoch
error: Quitting from lines 40-42 (Untitled.Rmd) Error: `x` must be a string or a R connection Execution halted This comes from the code chunk library(clusterlab) synthetic <- clusterlab(centers=1,numbervec=100) which generates that error on its own. Duncan

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-05 Thread Duncan Murdoch
N: they don't really run full tests by default. But the vast majority of packages should be able to live within the CRAN guidelines. Duncan Murdoch /Henrik On Wed, Sep 5, 2018 at 11:08 AM Spencer Graves wrote: On 2018-09-05 12:52, Gábor Csárdi wrote: On Wed, Sep 5, 2018 at 6

Re: [R-pkg-devel] Trying to work around missing functionality

2018-08-28 Thread Duncan Murdoch
age. But that execution can do other things too, and that's what the call to globalVariables() does. (The order of execution of the files in the R directory usually doesn't matter, but it is well defined: alphabetical order by filename in the C locale unless overridden by the Collate field i

Re: [R-pkg-devel] New test in R-devel causes existing packages to fail: "Error: connections left open"

2018-08-19 Thread Duncan Murdoch
amples run slower on CRAN, but won't affect most users who are doing their own stuff as well as running examples. Or, how about the startup code for the package opens the connection? Or perhaps CRAN will respond to this thread with another suggestion. Duncan Murdoch On Sun, Aug 19, 2018 a

Re: [R-pkg-devel] Proper way to document helper functions not accessible by user.

2018-08-13 Thread Duncan Murdoch
best to try one of the workarounds that someone else suggested. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Calling R's tempdir() from C

2018-08-10 Thread Duncan Murdoch
mpdir() in your call from R to your C++ function, or in an initialization call for your package? It won't change during a session. Duncan Murdoch I tried out giving a NULL dirname to R_tmpnam{,2}, hoping that even though it's not mentioned in the docs, they would internally use t

Re: [R-pkg-devel] [R] Submit your own R package - @examples

2018-08-08 Thread Duncan Murdoch
on for them. Please follow up in the r-package-devel list. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Can Submission Failure

2018-08-07 Thread Duncan Murdoch
actly what devtools::build_win() does to build the tarball, but it then sends it to WinBuilder: you don't need to do that for a CRAN submission. Duncan Murdoch From: CRAN submission m

Re: [R-pkg-devel] Building my R package: issue when importing two functions with the same name

2018-08-07 Thread Duncan Murdoch
tions you can use pROCroc() or spatstatroc() and they won't conflict. (I was going to point you to the documentation for this, but I am not sure it is properly documented anywhere.) Duncan Murdoch When checking the package via devtools::check(), I get the following warning: Warning:

Re: [R-pkg-devel] Correct way to set title for vignette?

2018-07-24 Thread Duncan Murdoch
aster/vignettes/ggpval.Rmd but is this the correct file to set the title? I think ggpval.Rmd is generated from another file? No, .Rmd files are one possible type of vignette source file. Duncan Murdoch __ R-package-devel@r-project.org mailing list https

Re: [R-pkg-devel] Running R CMD CHECK on different architectures

2018-07-19 Thread Duncan Murdoch
change in R or one of the compilers or other tools that something that worked before no longer works. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Getting error: Installation failed: Unknown username with my package

2018-07-13 Thread Duncan Murdoch
On 12/07/2018 11:10 PM, R. Mark Sharp wrote: I had a few week development hiatus with github.com/rmsharp/nprcmanager and when I tried to get a Travis build to work it failed. All of my local builds are working without errors or warnings, but the devtools::install_github(“rmsharp/nprcmanager”)

Re: [R-pkg-devel] structure of R package

2018-07-13 Thread Duncan Murdoch
elsewhere) add a configure script so that R can find them on a user's system, and note the requirement in the DESCRIPTION file SystemRequirements field. It's better if the .tar.gz file is self-contained. Duncan Murdoch __ R-package-devel@r-p

Re: [R-pkg-devel] Puzzled about "locked environments".

2018-07-08 Thread Duncan Murdoch
change in the .R file, processed before locking, and your new package does it in a function, executed by the user after locking. Or maybe not. Duncan Murdoch Can anyone suggest where I should start looking for differences in the nature of the two packages? I could possibly give more detail, but

Re: [R-pkg-devel] Determine subset from glm object

2018-07-08 Thread Duncan Murdoch
where (if anywhere) it is documented? Is there a better way? One more guaranteed to be correct in the future? I would trust evaluating the subset more than grabbing row labels from gout$x, but I don't know for sure it is likely to be more robust. Duncan Murdoch __

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-05 Thread Duncan Murdoch
On 05/07/2018 2:06 PM, Duncan Murdoch wrote: On 05/07/2018 9:11 AM, David Hugh-Jones wrote: Agreed. I fixed the roxygen2 and it works fine. But yet, the original v4.0.1 on CRAN has a namespace file which contains S3method(bold,huxtable) export(bold) export(bold.huxtable) and S3method("

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-05 Thread Duncan Murdoch
ironments. Given that the error is unrelated to the solution, it really looks like memory corruption somewhere or other. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-05 Thread Duncan Murdoch
processing, and manually build the NAMESPACE file as export(foo) S3method(foo, bar) then things are fine. I don't know roxygen2 well enough to know what else you should have done to get your NAMESPACE file to look like that. Duncan Murdoch Here is a brief test case that shows the

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-04 Thread Duncan Murdoch
On 04/07/2018 4:04 PM, Joris Meys wrote: On Wed, Jul 4, 2018 at 9:31 PM, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote: That shouldn't matter.  That function was created in a local environment whose parent is (probably by the huxtable:::make_setter_ge

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-04 Thread Duncan Murdoch
s like a harmless change for huxtable::align.huxtable, but it might mess up other methods if they make use of the objects in that environment. Duncan Murdoch Iñaki El mié., 4 jul. 2018 a las 21:34, Duncan Murdoch () escribió: On 04/07/2018 3:23 PM, Joris Meys wrote: I just took a look at

Re: [R-pkg-devel] Weird error on CRAN linux check

2018-07-04 Thread Duncan Murdoch
they get created in the wrong environment as far as I can tell. That's where I would start looking. That shouldn't matter. That function was created in a local environment whose parent is (probably by the huxtable:::make_setter_getters function, but I didn't check). Duncan Murdo

Re: [R-pkg-devel] Errors from Suggests or Enhances not in mainstream repositories

2018-07-03 Thread Duncan Murdoch
ble to run even if they're not installed Nowadays 'if (requireNamespace("citrus")) { ... }' would be preferred in tests and examples, along with a 'citrus::' prefix on the objects from that package that are needed. This has milder side effects than `require()`.

Re: [R-pkg-devel] Errors from Suggests or Enhances not in mainstream repositories

2018-07-03 Thread Duncan Murdoch
y. Probably the easiest way to create the right structure is to use the drat package; see https://github.com/eddelbuettel/drat for instructions. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] How to handle deprecated package dependency? 2 suggestions 1 question

2018-06-25 Thread Duncan Murdoch
ate an entirely new but fixed CRAN package from it myself stripped to only the functionality I need, which is not ideal of course, or (C) Kindly ask CRAN to put the deprecated package back online for a couple of months while we look out for a better solution? Given how easy the fixes are, I'd

Re: [R-pkg-devel] R Markdown and tables in Word

2018-06-13 Thread Duncan Murdoch
can find the mailing lists and their descriptions here: https://www.r-project.org/mail.html Shakeel was (incorrectly) sent here from there. Since then other advice has appeared: probably an RStudio forum or Stack Overflow is his best bet. Duncan Murdoch Regards, Jason On 13 Jun 2018

Re: [R-pkg-devel] pkg built with static vignette introduces dependency on R > = 3.5.0

2018-06-08 Thread Duncan Murdoch
our tarball in R 3.5.x or earlier, not in R-devel, or to add the dependency mentioned in the warning message. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

2018-06-07 Thread Duncan Murdoch
reaks and you don't fix it, that will cause lots of extra work for others. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] r-patched error

2018-06-04 Thread Duncan Murdoch
On 04/06/2018 8:56 AM, David Hugh-Jones wrote: Thank you very much for this thoughtful advice! I am guessing that getNamespace("huxtable") would be another more self-documenting way to do this. I will make the change. Yes! I didn't see that one.

Re: [R-pkg-devel] r-patched error

2018-06-04 Thread Duncan Murdoch
xtableNamespace) }) > Checks are passing fine on other platforms. Is this just a weirdness to do > with the changes in R 3.5.0 on Linux? Or does it indicate a real problem? A possibility is memory corruption at the C level. Since you don't have any C code in huxta

Re: [R-pkg-devel] trouble with R check

2018-05-31 Thread Duncan Murdoch
: rmpiFort (or even Suggests: rmpiFort, or LinkingTo: rmpiFort) in your DESCRIPTION file. You have importFrom(rmpiFort, ...) or import(rmpiFort) in your NAMESPACE file. You have requireNamespace("rmpiFort") (or require("rmpiFort"), or library("rmpiFort&qu

Re: [R-pkg-devel] Errors in R package - Updated

2018-05-25 Thread Duncan Murdoch
sing object$coefficients, and that fails when object is xy.freekt. Duncan Murdoch checking examples ... ERROR Running examples in ‘freeknotsplines-Ex.R’ failed The error most likely occurred in: base::assign(".ptime", proc.time(), pos = "CheckExEnv") ### Name: coef.

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

2018-05-25 Thread Duncan Murdoch
e to import the generic but not all the dependencies of that package, and that could change when the package holding the generic was updated. Examples of generics that do more than simply call UseMethod are rare, but they exist: as.data.frame() and sort() are a couple. Duncan Murdoch Right --

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

2018-05-25 Thread Duncan Murdoch
enerics that do more than simply call UseMethod are rare, but they exist: as.data.frame() and sort() are a couple. Duncan Murdoch Russ -Original Message- From: Martin Maechler [mailto:maech...@stat.math.ethz.ch] Sent: Friday, May 25, 2018 2:13 AM To: Lenth, Russell V Cc: r-pa

Re: [R-pkg-devel] Errors in my package

2018-05-24 Thread Duncan Murdoch
- function(object, ...) { xdat <- object@x ydat <- object@y That's normally something that you would do with an S4 object. We can't tell from your posting what xy.freekt really is; maybe it would help if you posted the result of str(xy.freekt) after creating it. Duncan Mu

Re: [R-pkg-devel] File link does not exist : how to get the correct one?

2018-05-18 Thread Duncan Murdoch
On 18/05/2018 11:37 AM, Duncan Murdoch wrote: On 18/05/2018 11:29 AM, Duncan Murdoch wrote: On 18/05/2018 11:06 AM, Joris Meys wrote: Hi all, The latest changes in R cause a lot of Rd warnings about file links that don't exist and are treated as a topic. One example is \code{\link[

Re: [R-pkg-devel] File link does not exist : how to get the correct one?

2018-05-18 Thread Duncan Murdoch
On 18/05/2018 11:29 AM, Duncan Murdoch wrote: On 18/05/2018 11:06 AM, Joris Meys wrote: Hi all, The latest changes in R cause a lot of Rd warnings about file links that don't exist and are treated as a topic. One example is \code{\link[stats]{fitted}} Now if I look at ?fitted , the na

Re: [R-pkg-devel] File link does not exist : how to get the correct one?

2018-05-18 Thread Duncan Murdoch
?fitted) [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/stats/help/fitted.values" attr(,"call") help(topic = "fitted", package = NULL) attr(,"topic") [1] "fitted" attr(,"tried_all_packages") [1] FALSE attr(,"

Re: [R-pkg-devel] mvrnorm, eigen, tests, and R CMD check

2018-05-17 Thread Duncan Murdoch
. [2] You can find out details of the current machine using the .Platform and version variables, and make tests conditional on particular values of those. I'd recommend limiting such tests to your own personal runs (using [1]) or not including saved output, because CRAN will run the tests on multiple platforms. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] why can't we importFrom 'methods' ?

2018-05-17 Thread Duncan Murdoch
rent treatment. If you try to use importFrom to import a single function (in this case 'hasArg') from methods, you receive an ERROR from R CMD check Namespace dependency not required : 'methods' That message usually means that you didn't list 'methods' in th

Re: [R-pkg-devel] How to write example results to a tempdir()?

2018-04-26 Thread Duncan Murdoch
On 26/04/2018 1:04 PM, Henrik Bengtsson wrote: On Thu, Apr 26, 2018 at 6:28 AM, Spencer Graves wrote: On 2018-04-26 07:11, Jose A Guijarro wrote: El 25/04/18 a las 20:21, Duncan Murdoch escribió: On 25/04/2018 1:32 PM, Sarah Goslee wrote: Don't change the working directory! Tha

Re: [R-pkg-devel] How to write example results to a tempdir()?

2018-04-26 Thread Duncan Murdoch
On 26/04/2018 9:28 AM, Spencer Graves wrote: On 2018-04-26 07:11, Jose A Guijarro wrote: El 25/04/18 a las 20:21, Duncan Murdoch escribió: On 25/04/2018 1:32 PM, Sarah Goslee wrote: Don't change the working directory! That has all kinds of unpleasant side effects for the unsuspecting

Re: [R-pkg-devel] How to write example results to a tempdir()?

2018-04-25 Thread Duncan Murdoch
ler than Sarah's suggestion. If it is likely, you can use tryCatch(..., finally = setwd(savedir)), but I think Sarah's solution would be preferable in most cases: many users will not understand what tryCatch() does. Duncan Murdoch Sarah On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guija

Re: [R-pkg-devel] some notes

2018-04-24 Thread Duncan Murdoch
true -- see the rgl vignettes, and the rglwidget() function. The main limitation is that the output needs to be HTML rather than LaTeX/PDF. (There are ways to incorporate interactive rgl graphics into PDF documents, but they are limited and fragile, so I don't recommend them.) Duncan Murdoch

Re: [R-pkg-devel] some notes

2018-04-24 Thread Duncan Murdoch
. Spencer Graves and I are not involved in running CRAN. We will give you advice that we think is good advice, but if it conflicts with Uwe's, follow his. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listi

Re: [R-pkg-devel] some notes

2018-04-24 Thread Duncan Murdoch
e other times are short, usually elapsed time will also be short. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object

2018-04-21 Thread Duncan Murdoch
ersions of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the check with R-devel. What should I do to fix this? getNamespaceExports() is described on its help page as an internal function, not intended for users. If you want to see the exports of a package, look at its NA

Re: [R-pkg-devel] CRAN pretest archived because of 2 NOTEs

2018-04-18 Thread Duncan Murdoch
27;ve been using in some form that pre-dates R and uses -M(M).D(D). e.g., NOTE "Version contains large components (2018-3.28)" Hadley was expressing some general advice, not a policy change. I think it's good advice: get rid of NOTEs if you can. You can't, so don't.

Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

2018-04-16 Thread Duncan Murdoch
On 16/04/2018 1:06 PM, Martin Morgan wrote: On 04/16/2018 12:31 PM, Duncan Murdoch wrote: On 16/04/2018 12:06 PM, Martin Maechler wrote: Duncan Murdoch on Mon, 16 Apr 2018 11:52:10 -0400 writes: > On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote: >>

Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

2018-04-16 Thread Duncan Murdoch
On 16/04/2018 12:06 PM, Martin Maechler wrote: Duncan Murdoch on Mon, 16 Apr 2018 11:52:10 -0400 writes: > On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote: >> Dear All, >> >> Two recent threads in the bioconductor devel mailing list >

Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

2018-04-16 Thread Duncan Murdoch
are major differences between the platforms) is to have two copies of the help file, one in man/unix, one in man/windows, but that doesn't seem appropriate from your description. Duncan Murdoch Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medic

Re: [R-pkg-devel] Cannot submit package due to misspell note

2018-04-06 Thread Duncan Murdoch
which would be Blah, Blah, Blah" Good point, I agree. Duncan Murdoch - Georgi Boshnakov From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf of Duncan Murdoch [murdoch.dun...@gmail.com] Sent: 07 April 2018 00:06 To: Ben Bolke

Re: [R-pkg-devel] Cannot submit package due to misspell note

2018-04-06 Thread Duncan Murdoch
unning tests for arch 'i386' ... [4s] OK Running 'testthat.R' [4s] ** running tests for arch 'x64' ... [5s] OK Running 'testthat.R' [5s] * checking PDF version of manual ... OK * DONE Status: 1 NOTE So I assume the rejection is due to misspelling note (

Re: [R-pkg-devel] Cannot submit package due to misspell note

2018-04-05 Thread Duncan Murdoch
to do. Duncan Murdoch On Thu, Apr 5, 2018 at 4:30 PM, Duncan Murdoch wrote: On 05/04/2018 4:17 PM, Dudek Andrzej wrote: CRAN maintainers rejected the package two times already due to this note But for previous version I've been asked to add the references in description field: Package

Re: [R-pkg-devel] Cannot submit package due to misspell note

2018-04-05 Thread Duncan Murdoch
ir, P. (2013) , De Leeuw, J., Mair, P. (2015) , Groenen, P.J.F., Winsberg, S., Rodriguez, O., Diday, E. (2006) , Walesiak, M. (2016) , Walesiak, M. (2017) ). are grammatically complete sentences, so I probably would have asked you to reword things. Duncan Murdoch ___

Re: [R-pkg-devel] R Internal data can not use

2018-03-31 Thread Duncan Murdoch
? How are you trying to reach it? The sysdata.rda data is not supposed to be accessible outside the package. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread Duncan Murdoch
'int' to itself [-Wself-assign] Take a look at that line (and the other similar ones) and see why the compiler thinks you've got something like i = i; in your code. Duncan Murdoch __ R-package-devel@r-project.org mailing list htt

Re: [R-pkg-devel] Warning: rBind is deprecated-- but I don't call it

2018-03-21 Thread Duncan Murdoch
put from running all the examples (and which should contain the warning at an informative spot), or foo-Ex.R if you want all the code that was run to get that output. Duncan Murdoch ++ Alex On 21 March 2018 at 19:36, William Revelle wrote: Dear friends, When testing my latest version of

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Rpolyhedra 0.2.2

2018-03-15 Thread Duncan Murdoch
the download. Probably the easiest fix for this is to stop your document from trying to download that file: just drop the link to it. Duncan Murdoch Best, Ale. -- Forwarded message -- From: Date: 2018-03-15 1:39 GMT-03:00 Subject: [CRAN-pretest-archived] CRAN submissi

Re: [R-pkg-devel] Weird error message during R CMD Check

2018-03-13 Thread Duncan Murdoch
ass it to a function. Duncan Murdoch even if it is parameter of get_DB_info(connectionString) function - see the function definition below error message. Please, can you help me to understand what should be fixed in the code so that I could successfully submit my package to CRAN? Tha

Re: [R-pkg-devel] Dealing with not so temporary files

2018-03-12 Thread Duncan Murdoch
find it. What is the proper etiquette for this? Even if I provide an argument for the user to specify the location to save the file, I should provide a default location. Why not provide an argument whose default is something given by tempfile()? Duncan Murdoch Any suggestions app

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

2018-02-24 Thread Duncan Murdoch
On 24/02/2018 7:56 PM, Marius Hofert wrote: On Sun, Feb 25, 2018 at 1:41 AM, Duncan Murdoch wrote: On 24/02/2018 7:26 PM, Marius Hofert wrote: On Sun, Feb 25, 2018 at 1:09 AM, Dirk Eddelbuettel wrote: On 25 February 2018 at 00:45, Marius Hofert wrote: | A package 'foo' uses a pa

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

2018-02-24 Thread Duncan Murdoch
f you have no alternative code, then don't test the "bar" code unless "bar" is installed. The basic idea is that your package should pass tests without errors even if "bar" is not available. I think Dirk is wrong saying that "bar" has to be availa

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