Re: [Rd] [R] Continuation and parse

[this is from R-help, at the end of June] Jim Lemon asked about parsing syntactically incorrect versus incomplete lines, generating a couple of responses. Philippe's suggestion isn't robust (e.g., \nls). Prof. Ripley's comment lead me to R_ParseVector (the only exposed parse routine).

[Rd] Building Windows package .zip files

Section 1.3.3 of Writing R Extensions says The recommended method of building binary packages is to use R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in the usual .tar.gz format) or the location of the directory of the package source to be built. (a) vignettes

Re: [Rd] tar warnings in R-3.0.2 RC when R is installed by a different (non-root) user

On 09/23/2013 02:53 PM, Prof Brian Ripley wrote: The issue is not the ownership (uname) but the uid. A tarball can only store uids up to 'nobody' (usually 32767), and certainly larger ones cannot be unpacked portably. The many identical warnings can obscure useful messages, e.g., about

Re: [Rd] Undocumented S4 method Warning For Bracket

On 12/05/2013 07:00 PM, Dario Strbenac wrote: Hello, With R version 3.0.2 Patched (2013-10-30 r64123) I don't see warnings that I get in R Under development (unstable) (2013-11-03 r64145) The warnings are like : Undocumented S4 methods: generic '[' and siglist 'BayMethList,ANY,ANY' The

Re: [Rd] External pointers and changing SEXPTYPE

On 12/16/2013 09:18 AM, Krzysztof Mlynarczyk wrote: Yes, it turned out that using R_PreserveObject and R_ReleaseObject solved that problem. Instead I think you want to use the third argument to R_MakeExternalPtr to protect the SEXP's you'd like to persist for the duration of the object, maybe

Re: [Rd] reference class internals

On 01/09/2014 07:53 PM, Norm Matloff wrote: Thanks, Hadley and Simon. The reason I asked today was that when reference classes first came out, it had appeared to me that there is no peformance advantage to using reference classes, that it was mainly a style issue (encapsulation, etc.). Unless

[Rd] eapply duplicates elements unnecessarily

eapply duplicates the elements of the environment it is being applied to env = new.env(); x = 1; tracemem(x) [1] 0x1758cd18 env[[x]] = x xx - eapply(env, length) tracemem[0x1758cd18 - 0x1758cbc8]: eapply but duplication seems unnecessary. I think this is because of 'duplicate' in

Re: [Rd] $new cannot be accessed when running from Rscript and methods package is not loaded

On 02/11/2014 09:06 AM, Winston Chang wrote: To state the issue that Kirill raised in a different way... A package with S4 or reference classes and Depends:methods can throw an error when you do something as simple as this: Rscript -e mypackage::foo() But this will work: Rscript -e

[Rd] R CMD Sweave tmp.tex doesn't create figures with fig=TRUE, include=FALSE

With this file /tmp$ cat tmp.Rnw \documentclass{article} \begin{document} figureexample, fig=TRUE, include=FALSE, width=4.2, height=4.6= v = seq(0, 60i, length=1000) plot(abs(v)*exp(v), type=l, col=Royalblue) @ \includegraphics{tmp-figureexample} \end{document} This command /tmp$ R --vanilla

[Rd] instantiating a reference class with an initialize() method from .onLoad fails

classes Version: 0.0.1 Date: 2012-08-05 Author: Martin Morgan Maintainer: Martin Morgan mtmor...@fhcrc.org Description: This package implements a simple 'reference' class Depends: methods Imports: methods License: Apache License 2.0 Collate: binding.R R CMD INSTALL

[Rd] Sweave provides a misleading error when vignette engine not fully specified

Trying to Stangle / Sweave a file $ cat vignette.Rnw %\VignetteEngine{knitr} \documentclass{article} \begin{document} \end{document} results in a misleading error message: ~/tmp$ R CMD Stangle vignette.Rnw Error: Vignette engine package not specified Execution halted when what is missing is

[Rd] CXX_STD and configure.ac in packages

In C++ code for use in a R-3.1.0 package, my specific problem is that I would like to use unordered_map if it is available, or tr1/unordered_map if not, or map if all else fails. I (think I) can accomplish this with configure.ac as AC_INIT(DESCRIPTION) CXX=`${R_HOME}/bin/R CMD config CXX`

Re: [Rd] CXX_STD and configure.ac in packages

, with attendant trade-offs -- as a guiding principle and as a pragmatic solution avoid my complicated unordered_map configure dance for now. Thanks all for the various inputs. Martin Morgan The map and unordered_map classes are a corner case, as they offer the same functionality but latter has much

[Rd] Package vignettes share the same environment?

In a package 'vig' R CMD build vig (or tools::buildVignettes(dir=vig) with $ cat vig/vignettes/vig1.Rnw \documentclass{article} \begin{document} = x - 1 @ \end{document} $ cat vig/vignettes/vig2.Rnw \documentclass{article} \begin{document} = x @ \end{document} produces vig2.pdf where x is

[Rd] citEntry handling of encoded URLs

in the examples; if the list of supported tags is not easy to enumerate, perhaps some insight can be provided at this point as to how the supported tags are determined? Thanks Martin Morgan -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA

Re: [Rd] citEntry handling of encoded URLs

On 05/23/2014 05:35 AM, Achim Zeileis wrote: On Thu, 22 May 2014, Martin Morgan wrote: The following citEntry includes a url with %3A and other encodings citEntry(entry=article, title = Software for Computing and Annotating Genomic Ranges, author = personList( as.person

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

engines that ignore tangle. It is very valuable to all parties to write a vignette with code that is fully evaluated; otherwise, it is too easy for bit rot to seep in, or to 'fake' it in a way that seems innocent but is misleading. Martin Morgan is comfortable with vignettes that do not have

[Rd] Should a package that indirectly Suggests: a vignette engine pass R CMD check?

the BiocStyle package for their vignette, and the BiocStyle package suggests the appropriate builder. Martin Morgan -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

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

On 08/27/2014 08:33 PM, Gavin Simpson wrote: On Aug 27, 2014 5:24 PM, Hadley Wickham snip / I'd say: Depends is a historical artefact from ye old days before package namespaces. Apart from depending on a specific version of R, you should basically never use depends. (The one exception is, as

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

functionality without ever manipulating the object of PkgA. Martin Morgan Hadley -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

[Rd] install.packages misleads about package availability?

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns install.packages(RUVSeq, repos=http://bioconductor.org/packages/2.14/bioc;) Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is

Re: [Rd] mpi.h errors on Mavericks packages

On 10/03/2014 04:17 PM, Daniel Fuka wrote: Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent

Re: [Rd] mpi.h errors on Mavericks packages

On 10/03/2014 04:58 PM, Martin Morgan wrote: On 10/03/2014 04:17 PM, Daniel Fuka wrote: Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am

Re: [Rd] Options that are local to the package that sets them

On 10/31/2014 05:55 PM, Gábor Csárdi wrote: On Fri, Oct 31, 2014 at 8:16 PM, William Dunlap wdun...@tibco.com wrote: You can put the following 3 objects, an environment and 2 functions that access it, in any package that need some package-specific storage (say your pkgB1 and pkgB2).

[Rd] package vignettes build in the same R process?

If I understand correctly, all vignettes in a package are built in the same R process. Global options, loaded packages, etc., in an earlier vignette persist in later vignettes. This can introduce user confusion (e.g., when a later vignette builds successfully because a package is require()'ed

Re: [Rd] How to maintain memory in R extension

a finalizer that runs when there are no longer references to the R object, see ?reg.finalizer or the interface to R and C finalizers in Rinternals.h. If you return more than one reference to a key, then of course you'll have to manage these in your own C++ code. Martin Morgan Thanks, Da

Re: [Rd] Changing style for the Sweave vignettes

; see ?browseVignettes and ?vignette for installed packages, and ?Stangle in R and R CMD Stangle for extracting the R code from stand-alone vignettes to .R files. Martin Morgan Kind regards, j. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box

Re: [Rd] R string comparisons may vary with platform (plain text)

about setting the locale within a session. Martin Morgan On 11/23/2014 03:44 AM, Prof Brian Ripley wrote: On 23/11/2014 09:39, peter dalgaard wrote: On 23 Nov 2014, at 01:05 , Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Sat, Nov 22, 2014 at 12:42 PM, Duncan Murdoch murdoch.dun

Re: [Rd] vapply definition question

], ...) is evaluated in the frame of lapply. Martin Morgan So, essentially, my question is whether the vapply code should be changed or whether a .Internal implementation should always assume an implicit ... regardless of the code, if the semantics requires it. Thanks Mick

Re: [Rd] R-devel does not update the C++ returned variables

; }) or that Rcpp should become more careful (i.e., should not allow!) modifying arguments with NAMED != 0. Martin (Morgan) Dirk | | ## now test: | require(microbenchmark) | i - 1:10 | (mb - microbenchmark(doubleThis(i), i*2, 2*i, i*2L, 2L*i, i+i, times=2^12)) | ## Lynne (i7; FC 20), R Under

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

. Being able to easily flag non-imported, non-base symbols would definitely improve the robustness of package code, even if not helping the end user disambiguate duplicate symbols. Martin Morgan I think that for a better solution, either 1) the search path should not be used at all to resolve

[Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?

(file='b.Rda'); b Loading required package: PkgA A Martin Morgan -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-devel@r

Re: [Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?

On 05/10/2015 08:19 AM, Martin Morgan wrote: Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package

Re: [Rd] Creating a vignette which depends on a non-distributable file

On 05/14/2015 04:33 PM, Henrik Bengtsson wrote: On May 14, 2015 15:04, January Weiner january.wei...@gmail.com wrote: Dear all, I am writing a vignette that requires a file which I am not allowed to distribute, but which the user can easily download manually. Moreover, it is not possible to

Re: [Rd] example fails during R CMD CHECK but works interactively?

On 05/15/2015 05:05 AM, Charles Determan wrote: Does anyone else have any thoughts about troubleshooting the R CMD check environment? In the pkg.Rcheck directory there is a file pkg-Ex.R. LANGUAGE=en _R_CHECK_INTERNALS2_=1 $(R_HOME)/bin/R --vanilla pkge-Ex.R followed by the usual strategy of

Re: [Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?

On 05/12/2015 05:31 AM, Martin Maechler wrote: Martin Morgan mtmor...@fredhutch.org on Mon, 11 May 2015 10:18:07 -0700 writes: On 05/10/2015 08:19 AM, Martin Morgan wrote: Loading an S4 object from a file without first loading the library sometimes (?, the example below

Re: [Rd] S4 inheritance and old class

a $ method on A setMethod($, A, function(x, name) slot(x, name)) And then a = new(A) a$tab d = new(D) d$tab I don't know about the setOldClass problem; it seems like a bug. Martin Morgan setClass( Class = B, contains = A, slots = list(B = character), validity

Re: [Rd] List S3 methods and defining packages

plot.tskernel plot.TukeyHSD Also this is for loaded, rather than attached, namespaces. Martin Morgan Thank you. Bests, Renaud visible from generic isS4 print.abbrev FALSE registered S3method for print print

Re: [Rd] download.file() on ftp URL fails in windows with default download method

please let me know; Elliot Waingold (CC'd here) can provide access to the VM we used for testing if that's of any help. Thanks! I have just been looking at this issue with Martin Morgan. We found that if we or the additional flag INTERNET_FLAG_PASSIVE on line 1012 of src/modules/internet

Re: [Rd] Issues with libcurl + HTTP status codes (eg. 403, 404)

R-devel r69197 returns appropriate errors for the cases below; I know of a few rough edges - ftp error codes are not reported correctly - download.file creates destfile before discovering that http fails, leaving an empty file on disk and am happy to hear of more. Martin On 08/27/2015

Re: [Rd] Issues with libcurl + HTTP status codes (eg. 403, 404)

On 08/27/2015 08:16 AM, Martin Maechler wrote: DM == Duncan Murdoch murdoch.dun...@gmail.com on Wed, 26 Aug 2015 19:07:23 -0400 writes: DM On 26/08/2015 6:04 PM, Jeroen Ooms wrote: On Tue, Aug 25, 2015 at 10:33 PM, Martin Morgan mtmor...@fredhutch.org wrote

Re: [Rd] Issues with libcurl + HTTP status codes (eg. 403, 404)

On 08/25/2015 12:54 PM, Kevin Ushey wrote: Hi all, The following fails for me (on OS X, although I imagine it's the same on other platforms using libcurl): options(download.file.method = libcurl) options(repos = c(CRAN = https://cran.rstudio.com/;, CRANextra =

Re: [Rd] dowload.file(method="libcurl") and GET vs. HEAD requests

previously R would download the error page as though it were the content. I'll give this some thought. Martin Morgan -Winston __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel This email message may contain leg

Re: [Rd] Is it possible to increase MAX_NUM_DLLS in future R releases?

ormance cost (but the cost here is in small fractions of a second...) in terms of symbol look-up (and collision?), but would have no consequence for those of us with more sane use cases. Martin Morgan Patches to the R sources (development trunk in subversion at https://svn.r-project.org/R/trunk/ )

Re: [Rd] failed to assign RegisteredNativeSymbol for splitString

On 07/18/2016 03:45 PM, Andrew Piskorski wrote: I saw a warning from R that I don't fully understand. Here's one way to reproduce it: $ /usr/local/pkg/R-3.2-branch-20160718/bin/R --version | head -n 3 R version 3.2.5 Patched (2016-05-05 r70929) -- "Very, Very Secure Dishes" Copyright

Re: [Rd] On implementing zero-overhead code reuse

On 10/03/2016 01:51 PM, Kynn Jones wrote: Thank you all for your comments and suggestions. @Frederik, my reason for mucking with environments is that I want to minimize the number of names that import adds to my current environment. For instance, if module foo defines a function bar, I want my

Re: [Rd] methods(`|`) lists all functions?

r behavior is found in 3.4.0. It seems to include all functions and methods. I imagine something is being passed to "grep" without being escaped. Exactly; I've fixed this in r71763 (R-devel). Martin Morgan I hope I didn't miss something in the documentation, and that I'm good to report

Re: [Rd] different compilers and mzR build fails

mzR is a Bioconductor package, so better to ask on the Bioconductor support forum https://support.bioconductor.org Oh, I see you did, and then the advice is to avoid cross-posting! The missing .o files would have been produced in an earlier compilation step; they likely failed in some way,

Re: [Rd] different compilers and mzR build fails

o an email message, avoding attachments. Martin On 21/12/16 17:06, Martin Morgan wrote: mzR is a Bioconductor package, so better to ask on the Bioconductor support forum https://support.bioconductor.org Oh, I see you did, and then the advice is to avoid cross-posting! The missing .o f

Re: [Rd] R libcurl does not recognize server certs

t the bundle location is inferred when R is built from source, and somehow there has been a disconnect between your R installation and certificate location, e.g., moving the certificate location after R installation. Martin Morgan John Roman Linux System Administrator RAND Corporation j

Re: [Rd] [PATCH] Fix missing break

s $ R --vanilla -e "pl = pairlist(1, 2); length(pl) = 1; pl" > pl = pairlist(1, 2); length(pl) = 1; pl Error in length(pl) = 1 : SET_VECTOR_ELT() can only be applied to a 'list', not a 'pairlist' Execution halted fixed in r72936 (R-devel) / 72937 (R-3-4-branch). Martin Morgan Index:

Re: [Rd] [PATCH] Fix bad free in connections

format, ap); is successful and res >= 0. usedVasprintf is then set to TRUE, and free(b) called. It seems like the code is correct as written? Martin Morgan (the real other Martin M*) return res; } __ R-devel@r-project.org mailing list ht

Re: [Rd] [PATCH] Fix status in main

have consequence, since exit() reports NA & 0377 (i.e., 0) and the incorrect assignment to runLast is immediately over-written by the correct value. Martin Morgan Index: src/main/main.c === --- src/main/main.c (revision

Re: [Rd] Are Rprintf and REprintf thread-safe?

On 11/21/2017 04:12 PM, Winston Chang wrote: Thanks - I'll find another way to send messages to the main thread for printing. The CRAN synchronicity and Bioconductor BiocParallel packages provide inter-process locks that you could use to surround writes (instead of sending message to the

Re: [Rd] length of `...`

nargs() provides the number of arguments without evaluating them > f = function(x, ..., y) nargs() > f() [1] 0 > f(a=1, b=2) [1] 2 > f(1, a=1, b=2) [1] 3 > f(x=1, a=1, b=2) [1] 3 > f(stop()) [1] 1 On 05/03/2018 11:01 AM, William Dunlap via R-devel wrote: In R-3.5.0 you can use ...length():

Re: [Rd] download.file does not process gz files correctly (truncates them?)

On 05/03/2018 05:48 AM, Joris Meys wrote: Dear all, I've been diving a bit deeper into this per request of Tomas Kalibra, and found the following : - the lock on the file is only after trying to read it using oligo, so that's not a R problem in itself. The problem is independent of extrenal

Re: [Rd] download.file does not process gz files correctly (truncates them?)

On 05/02/2018 03:21 PM, Joris Meys wrote: Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try

Re: [Rd] R CMD check warning about compiler warning flags

annotate doc/manual/R-exts.texi | less A quick google search (svn diff visual display) lead me to svn diff --diff-cmd meld -c73909 for my platform, which pops up the diffs in a visual context. Martin Morgan And your description seems wrong: there is now an _optional_ check controlled

Re: [Rd] Why R should never move to git

rge ... a-pull-request git push ... Creating pull requests is a problem for the developer wanting to contribute to R, not for the R-core developer. As we've seen in this thread, R-core would not need to feel responsible for helping developers create pull requests. Martin Morgan Maybe Git

Re: [Rd] How to address the following: CRAN packages not using Suggests conditionally

. This means that the Bioconductor devel branch periodically (as recently and I suspect over the next several days) contains considerable carnage that propagates to CRAN devel builds, creating additional work for CRAN maintainers. Martin Morgan Bioconductor Best regards, Ulrich On 01/22/2018

Re: [Rd] Compiler + stopifnot bug

r packages https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014506.html and elsewhere Martin Morgan On 1/3/19, 7:05 PM, "R-devel on behalf of Duncan Murdoch" wrote: On 03/01/2019 3:37 p.m., Duncan Murdoch wrote: > I see this too; by bisection, it seems to have first ap

Re: [Rd] defining r audio connections

the version of the API, as advised in the header file!) Martin Morgan On 5/6/20, 2:26 PM, "R-devel on behalf of Duncan Murdoch" wrote: On 06/05/2020 1:09 p.m., frede...@ofb.net wrote: > Dear R Devel, > > Since Linux moved away from using a file-system interface

Re: [Rd] defining r audio connections

a connection. (I mistakenly thought this was a more specialized mailing list; I wouldn't have posted to R-devel on this topic otherwise) Martin Morgan On 5/6/20, 4:12 PM, "Gábor Csárdi" wrote: AFAIK that API is not allowed on CRAN. It triggers a NOTE or a WARNING, and yo

Re: [Rd] Garbage collection of seemingly PROTECTed pairlist

SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); but writes three elements (the 0th, 1st, and 2nd) at for (int i = 0; i != nr; ++i) { out_int[i] = int_mat_int[n - 1 + i * nr]; } Martin Morgan On 9/11/20, 9:30 PM, "R-devel on behalf of Rory Nolan" wrote:

Re: [Rd] Is it possible to simply the use of NULL slots (or at least improve the help files)?

uot;, "numeric")) Error in setOldClass(c("character", "numeric")) : inconsistent old-style class information for "character"; the class is defined but does not extend "numeric" and is not valid as the data part In addition: Warning message: In .validDat

Re: [Rd] Is it possible to simply the use of NULL slots (or at least improve the help files)?

te 'not yet initialized' and distinct from character(0) or NA_character_, but want to mention those often appropriate alternatives. With setClassUnion("maybeNumber", c("numeric", "logical")) every instance of numeric _is_ a maybeNumber, e.g., > is(1, &qu

Re: [Rd] lapply and vapply Primitive Documentation

(I don't see lapply / vapply referenced as primitive in the original text changed by the commit). Martin Morgan On 7/10/20, 3:52 AM, "R-devel on behalf of Martin Maechler" wrote: >>>>> Cole Miller >>>>> on Thu, 9 Jul 2020 20:38:10 -0

Re: [Rd] [External] Something is wrong with the unserialize function

(csym, psym); + UNPROTECT(1); } return class; } seems to remove the warning; I'm guessing that the other SEXP already exist so don't need protecting? Martin Morgan On 10/29/20, 12:47 PM, "R-devel on behalf of luke-tier...@uiowa.edu" wrote:

Re: [Rd] unicode in R documentation

I have options(useFancyQuotes = FALSE) in my ~/.Rprofile. Martin Morgan On 7/13/21, 11:37 AM, "R-devel on behalf of Frederick Eaton" wrote: Dear R Team, I am running R from the terminal command line (not RStudio). I've noticed that R has been using Unicode quo

[Rd] gsub() hex character range problems in R-devel?

_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.2.0 (I have built my own R on macOS; similar behavior is observed on a Linux machine) Any hints welcome, Martin Morgan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] gsub() hex character range problems in R-devel?

However, I think it is better to formulate regular expressions to cover all of Unicode, so do something like e.g. "only keep ASCII digits, ASCII space, ASCII underscore, but remove all other characters". Best Tomas On 1/4/22 8:35 PM, Martin Morgan wrote: >

Re: [Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB

at the R-SIG-mac mailing list might have been more appropriate, but I did not see the issue discussed there. Martin From: Prof Brian Ripley Date: Wednesday, May 31, 2023 at 3:46 AM To: Martin Morgan Cc: Tomas Kalibera , R-devel Subject: Re: [Rd] Building R from source always fails on tools:::sy

[Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB

I build my own R from source on an M1 mac. I have a clean svn checkout in one directory ~/src/R-devel. I switch to ~/bin/R-devel and the first time run cd ~/bin/R-devel ~/src/R-devel/configure --enable-R-shlib 'CFLAGS=-g -O0' CPPFLAGS=-I/opt/R/arm64/include 'CXXFLAGS=-g -O0' make -j At some

Re: [Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB

: Tuesday, May 30, 2023 at 4:54 PM To: Martin Morgan , R-devel Subject: Re: [Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB On 5/30/23 22:09, Martin Morgan wrote: > I build my own R from source on an M1 mac. I have a clean svn checkout in one > directory

Re: [Rd] [EXTERNAL] Re: NOTE: multiple local function definitions for ?fun? with different formal arguments

or (`n` partially matches `na.print`, and 2 is not a valid value); both methods silently ignore the typo print(m = 2). Martin Morgan From: R-devel on behalf of Henrik Bengtsson Date: Tuesday, February 6, 2024 at 4:34 PM To: Izmirlian, Grant (NIH/NCI) [E] Cc: r-devel@r-project.org Sub

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

' ... ? Martin Morgan Duncan Murdoch but without the importFrom, you see a number of NOTE's no visible global function definition for 'hasArg' I don't want to import all of 'methods', as I only need one function. What am I doing wrong? Regards, Brian

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

n("dS",dS,envir=environment(cev)) so that assignment is to the unlocked new.env(). Presumably the new code assigns to bar's original environment, which is the (locked, once the package is loaded) package name space. Martin Morgan Or maybe not. Duncan Murdoch Can anyone suggest

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

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: >> Dear All, >> >> Two recent

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission maGUI 2.3

I cannot tell whether this will be helpful or not. It looks to me like the warning occurs when one of your dependencies uses BiocInstaller. You could create a database of all available packages chooseCRANmirror() chooseBioCmirror() db = available.packages() find the installation

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

Add a tag to the DESCRIPTION file or configure.ac-like indicating the git (presumably) revision, perhaps like https://stackoverflow.com/a/11535358/547331 ? On 1/4/19, 1:42 PM, "R-package-devel on behalf of Dirk Eddelbuettel" wrote: On 4 January 2019 at 19:24, Iñaki Ucar wrote:

Re: [R-pkg-devel] Bioconductor dependencies => Windows checks failed

Bioconductor 3.8 is the current release version of Bioconductor, and should be used by CRAN for current release versions of R. This seems perhaps like a stale installation on the Windows machine. A link to the actual check report would be helpful. Martin On 2/27/19, 9:25 AM, "R-package-devel

Re: [R-pkg-devel] Regarding maGUI package error

to load BiocInstaller should simply fail. Martin Morgan On 2/20/19, 2:06 AM, "R-package-devel on behalf of dhamma pal" wrote: Hi. Following is the check results from CRAN server, though I didn't get any warning on my PC. package maGUI_2.3.tar.gz does not pass th

Re: [R-pkg-devel] Help with the warning : 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN

apparently uses 3.5.* package binaries (for both CRAN & Bioconductor) in R-devel. Martin Morgan On 3/6/19, 10:00 AM, "R-package-devel on behalf of Yonghui Dong" wrote: Dear all, I remember somebody has asked a similar question days ago, but the problem has not bee

Re: [R-pkg-devel] Use of assignInNamespace in package

into other languages so pattern matching is not robust. In one's own code one could signal and handle specific classes of objects withCallingHandlers({ cond <- simpleWarning("foo") class(cond) <- c("my_warning", class(cond)) warning(cond) warning("bar")

Re: [R-pkg-devel] define an environment in .onLoad

which is actually a fun test of one's understanding of R's assignment and symbol look-up rules. Martin Morgan On 1/29/19, 4:50 PM, "R-package-devel on behalf of Gábor Csárdi" wrote: You don't need .onLoad for this, just put the environment into the package

Re: [R-pkg-devel] Advice on setAs - issue of "in method for 'coerce' with signature / no definition for classes

Since ncdf4 (and emld) both use S3 class systems, it is sufficient to simply declare setOldClass("ncdf4") some time prior to using setAs() . Martin On 5/24/19, 6:41 PM, "R-package-devel on behalf of Emmanuel Blondel (GMAIL)" wrote: Dear all, I write here as i'm in process to

Re: [R-pkg-devel] Link compiled C object to internal package file

are below, specifically the unique circumstances of 'in tests only'. I would guess that a relative path would not work, in general, because the path would be relative to the current working directory, which of course changes, rather than relative to the path of the shared object... Martin Morgan

Re: [R-pkg-devel] CRAN student assistants

message() / warning() / stop() write to stderr whereas print() / cat() write (by default) to stdout. Even without being able to suppress messages, it is well-established practice (the story is that this is the reason why 'stderr' was introduced into unix,

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

RShowDoc("R-exts") setion 1.5.1 Specifying imports and exports indicates that imports() has an except= argument, so import(adegenet, except = plot) might do the trick. Use it in your package as `adegenet::plot()`. Martin Morgan On 11/6/19, 8:31 PM, "R-package-devel on b

Re: [R-pkg-devel] [External] Re: Packages required and available but unsuitable versions: Error

time to offer your help, and am really grateful for your suggestions. Sincerely, Divyansh On 9/23/19, 7:44 AM, "Martin Morgan" wrote: Probably the easiest 'solution' is to remove the version dependencies, e.g., 'org.Hs.eg.db, org.Mm.eg.db, ...'.

Re: [R-pkg-devel] Packages required and available but unsuitable versions: Error

of the package BiocVersion (it should be 3.10.1 in R-devel) is incorrect. Martin Morgan Bioconductor On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh" wrote: Dear R developers community, I’m trying to build and submit an R package to CRAN but ke

Re: [R-pkg-devel] CRAN cannot find libraries on Windows

what are the correct paths? On 1/27/20, 3:32 PM, "R-package-devel on behalf of Uwe Ligges" wrote: Thanks, one suspicious part from the log below is -LC:/extsoft/lib/i386 which is clearly not in any variable we define on CRAN. Looking close shows that >

Re: [R-pkg-devel] Unable to reproduce reported problems. Docker image?

by the builder, and the reason why you are not able to reproduce it. Martin Morgan On 1/31/20, 9:04 AM, "R-package-devel on behalf of Dirk Eddelbuettel" wrote: On 31 January 2020 at 09:11, Borini, Stefano wrote: | Thanks. What is the recommended strategy in this case? Keep

Re: [R-pkg-devel] R CMD build hanging for some but not all packages

path names or movement across volumes?) better. Martin Morgan On 2/11/20, 9:31 AM, "R-package-devel on behalf of Gábor Csárdi" wrote: It is actually rather complicated, because .Rbuildignore can have regular expressions, that refer to files or directories, and for the

Re: [R-pkg-devel] Fwd: Re: [CRAN-pretest-archived] CRAN submission SSLR 0.9.0

so apparently there is a generics package that defines 'fit'... if you're playing in the tidyverse then it seems like you should @importFrom generics fit and @export fit. Martin Morgan On 3/11/20, 1:50 PM, "R-package-devel on behalf of Henrik Bengtsson" wrote: 'fpalomares', it

Re: [R-pkg-devel] Windows specific install error

This is the same as https://stat.ethz.ch/pipermail/r-package-devel/2020q1/005256.html and due I believe to stale packages on the CRAN windows builder; the solution is I believe on the CRAN side. Martin Morgan On 4/7/20, 6:14 PM, "R-package-devel on behalf of Ryan Sartor&quo

Re: [R-pkg-devel] 'S4Vectors' Error - Bioconductor dependencies

::valid() returns TRUE and / or update all packages to the most recent available BiocManager::install(ask = FALSE) I'm not sure about CRAN, but am confident that it will eventually clear itself up... (not much comfort, I know...) Martin Morgan On 3/31/20, 11:42 AM, "R-package-devel on b

Re: [R-pkg-devel] Use of `:::` in a package for code run in a parallel cluster

uced errors; first error: could not find function "foo" Do you really need to use `:::`? Martin Morgan On 9/13/20, 3:52 PM, "R-package-devel on behalf of David Kepplinger" wrote: Dear list members, I submitted an update for my package and got automatically rejected

Re: [R-pkg-devel] bioconductor package required but not available

Here is the build report for KEGGgraph http://bioconductor.org/packages/release/bioc/html/KEGGgraph.html where it builds, and is available, across all platforms. This does not seem to be a Bioconductor problem, but rather a CRAN configuration issue. Martin Morgan Bioconductor On 9/1/20, 12

Re: [R-pkg-devel] [R] a question of etiquette

it is necessary to obey licensing terms of the prior work, and important to acknowledge, above and beyond the specific licensing terms, the contributions individuals make. Martin Morgan On 6/2/20, 5:57 AM, "R-package-devel on behalf of Adelchi Azzalini" wrote: The point in que

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