Re: [Rd] Error compiling 87283 on Windows 10 using Rtools4.4 6335-6327

2024-10-31 Thread Prof Brian Ripley via R-devel
On 31/10/2024 16:30, Avraham Adler wrote: When compiling R, the build fails after byte compiling grDevices with the following error: byte-compiling package 'grDevices' make[4]: *** [../../../share/make/lazycomp.mk:9: ../../../library/grDevices/R/grDevices.rdb] Error 139 make[3]: *** [Makefile.wi

Re: [Rd] Consider getNamespaceVersion() returning a numeric_version

2024-10-17 Thread Prof Brian Ripley via R-devel
On 17/10/2024 13:42, Tim Taylor wrote: I mean the `numeric_version` object not a numeric (double/int). Basically to protect me from myself I'd prefer not to have to remember to wrap `getNamespaceVersion()` with `as.package_version()`. I suspect a grep of CRAN may highlight others who are erron

Re: [Rd] config.site settings for M3 Mac typo in manual?

2024-05-20 Thread Prof Brian Ripley via R-devel
On 20/05/2024 09:06, Duncan Murdoch wrote: I've just upgraded to an M3 Mac laptop, and I'm working through getting the right configure settings to build R. The Installation and Administration manual says to have this in config.site: FFLAGS="-g -O2 -mmacos-version-min=11.0" FCFLAGS="-g -O2 -m

Re: [Rd] paths capability FALSE on devel?

2024-03-27 Thread Prof Brian Ripley via R-devel
On 27/03/2024 10:28, Alexandre Courtiol wrote: Hi all, I don't know if it is a local issue on my hands or not, but after installing R-devel the output of grDevices::dev.capabilities()$paths is FALSE, while it is TRUE for R 4.3.3. Relatedly, I have issues with plotting paths on devel. At this st

Re: [Rd] Advice debugging M1Mac check errors

2024-02-06 Thread Prof Brian Ripley via R-devel
On 04/02/2024 19:41, Holger Hoefling wrote: Hi, I wanted to ask if people have good advice on how to debug M1Mac package check errors when you don´t have a Mac? Is a cloud machine the best option or is there something else? I presumed this was about a CRAN package, possibly hdf5r which has a

Re: [Rd] system()/system2() using short paths of commands on Windows?

2023-10-30 Thread Prof Brian Ripley
On 30/10/2023 16:18, Yihui Xie wrote: Hi, It may have been so for 20+ years but I just discovered today that system() would always try to use the short path of a command on Windows: https://github.com/wch/r-source/blob/635a67/src/gnuwin32/run.c#L141 If that's true, I wonder if it could provide a

Re: [Rd] FYI: daily R source tarballs from ETH: *.xz instead of *.bz2)

2023-09-11 Thread Prof Brian Ripley
On 09/09/2023 01:56, Hervé Pagès wrote: Hi Martin, Sounds good. Are there any plans to support the xz compression for package source tarballs? What makes you think it is not supported? R CMD INSTALL happily installs .tar.xz files, and the name is not used to detect compression so .tar.gz fil

Re: [Rd] Installation of R-4.3.1 with intel 2022

2023-07-18 Thread Prof Brian Ripley
Note that 'intel 2022' is a bit vague. The current version is 2023.1.0, and that has both the 'classic' (icc/icpc/ifort which it seems you used) and new (icx/ixpx/ifx) compilers -- the former are said to be going to be discontinued later this year. R did not know about ifx so did not build wi

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

2023-05-31 Thread Prof Brian Ripley
On 30/05/2023 22:57, Martin Morgan wrote: Thanks Ivan & Tomas A simpler way to trigger the problem is library(tools) or library.dynam("tools", "tools", ".") so I guess it is loading src/tools.so Ivan, adding -d lldb I need to tell lldb where to find the R library (lldb) process launch --envir

Re: [Rd] R-4.2.3 build from source on Windows (w Rtools42) - lto1.exe error

2023-05-10 Thread Prof Brian Ripley
Initial comments - R 4.2.3 is not current - -flto does not seem to be the default in src/gnuwin32/MkRules. - LTO versions in GCC are tied to the compiler version, and in recent GCC are the same as the compiler version. The recommended toolchain for R 4.2.x is Rtools42 which according to NEWS

Re: [Rd] Let R compile for libcurl8 ?

2023-04-03 Thread Prof Brian Ripley
On 03/04/2023 15:24, Detlef Steuer wrote: Am Mon, 3 Apr 2023 15:13:58 +0100 schrieb Prof Brian Ripley : On 03/04/2023 14:07, Detlef Steuer wrote: Hi! The same Inar reported for rawhide (https://stat.ethz.ch/pipermail/r-devel/2023-March/082482.html) is true for SuSE's distros. Right

Re: [Rd] Let R compile for libcurl8 ?

2023-04-03 Thread Prof Brian Ripley
On 03/04/2023 14:07, Detlef Steuer wrote: Hi! The same Inar reported for rawhide (https://stat.ethz.ch/pipermail/r-devel/2023-March/082482.html) is true for SuSE's distros. Right now R does not compile with libcurl8, but SuSE Tumbleweed/Factory switched to 8 a week ago. Would be great, if the

Re: [Rd] CRAN package eaf

2023-03-14 Thread Prof Brian Ripley
it is the compiler and not your fault. We would like you to file a bug report specifically about your code and get agreement from the GCC developers that this is their bug. Best wishes, Manuel. On 01/03/2023 17:02, Prof Brian Ripley wrote: Dear maintainer, Please see the problems shown

Re: [Rd] Compiling R-devel on older Linux distributions, e.g. RHEL / CentOS 7

2023-02-07 Thread Prof Brian Ripley
On 08/02/2023 00:13, Gábor Csárdi wrote: As preparation for the next release, I am trying to compile R devel on RHEL / CentOS 7, which is still supported by RedHat until 2024 June. There are two issues. One is that the libcurl version in CentOS 7 is quite old, 7.29.0, and R devel now requires 7.

Re: [Rd] A potential POSIXlt->Date bug introduced in r-devel

2022-10-12 Thread Prof Brian Ripley
. Given that 2038 is not that far away, avoiding 32-bit time_t is generally a very good idea (not just for people working with dates in 5881580!). That test should not really be run on platforms with 32-bit time_t, but that is not currently known at R level. On 06/10/2022 13:38, Prof Brian

Re: [Rd] A potential POSIXlt->Date bug introduced in r-devel

2022-10-06 Thread Prof Brian Ripley
On 06/10/2022 09:41, Berwin A Turlach wrote: G'day all, On Thu, 6 Oct 2022 10:15:29 +0200 Martin Maechler wrote: Davis Vaughan on Wed, 5 Oct 2022 17:04:11 -0400 writes: > # Weird, where is the `NA`? > as.Date(x) > #> [1] "2013-01-31" "1970-01-01" "2013-03-31" > ```

Re: [Rd] Making CRAN memory access checks more accessible?

2022-03-02 Thread Prof Brian Ripley
On 28/02/2022 19:15, Bill Dunlap wrote: valgrind will detect some of the memory issues that UBSAN does. Only very few. None of the current 43 CRAN packages with UBSAN issues have them detected by valgrind ... the valgrind overlap is more with ASAN issues (see https://github.com/google/sani

Re: [Rd] minor CRAN issue

2022-02-28 Thread Prof Brian Ripley
On 28/02/2022 17:08, Therneau, Terry M., Ph.D. via R-devel wrote: I just bundled up and submitted the survival package, using R Under development (unstable) (2022-02-28 r81833) -- "Unsuffered Consequences" The 00-check.log file has a lot of lines like the following: 9a10 > > base::assign(".pt

Re: [Rd] build failure: 'hashtab' is not an exported object from 'namespace:utils'

2021-12-16 Thread Prof Brian Ripley
On 16/12/2021 09:13, Stephen Berman wrote: I just did `svn up' on the R development sources, switched to the build directory (I build R out of tree), ran make, and got this: Precisely which version of R-devel updating from which version? -- this is an area that has changed frequently in the la

Re: [Rd] Dropping RHS of a formula using NULL assignment

2021-12-14 Thread Prof Brian Ripley
On 14/12/2021 20:26, Blackwell, Matthew wrote: Hello all, In attempting to create a one-sided formula from a two-sided formula, I discovered that the following syntax will successfully complete this operation: f <- y ~ x + z f[2] <- NULL f ~x + z str(f) Class 'formula' language ~x + z .

Re: [Rd] [External] svd For Large Matrix

2021-08-13 Thread Prof Brian Ripley
On 13/08/2021 15:58, luke-tier...@uiowa.edu wrote: [copying the list] svd() does support matrices with long vector data. Your example works fine for me on a machine with enough memory with either the reference BLAS/LAPACK or the BLAS/LAPACK used on Fedora 33 (flexiblas backed, I believe, by a ve

Re: [Rd] Double to uint64_t on M1

2021-08-12 Thread Prof Brian Ripley
On 12/08/2021 04:52, Simon Urbanek wrote: Dipterix, this has nothing to do with R. 2^63 is too large to be represented as singed integer, so the behavior is undefined - to quote from the C99 specs (6.3.1.4): "If the value of the integral part cannot be represented by the integer type, the be

Re: [Rd] Bracketed paste issues on Linux

2021-06-15 Thread Prof Brian Ripley
I would have used source("clipboard") on systems which support it (Tomas has confirmed it works on Linux). See ?file. The macOS equivalent source(pipe("pbpaste")) also works. On 14/06/2021 11:06, Cesko Voeten wrote: Making it 1024 times larger gives: installing 'sysdata.rda' Error: segfault

Re: [Rd] Status of "**" operator

2021-05-22 Thread Prof Brian Ripley
On 21/05/2021 16:01, Marc Schwartz via R-devel wrote: Hi All, I was just sent some older R code from circa 2004, which contains the use of the "**" operator, which is parsed as "^". From looking at ?"**", I see the following in the Note section: "** is translated in the parser to ^, but thi

Re: [Rd] Apple M1 CRAN checks

2021-02-22 Thread Prof Brian Ripley
On 22/02/2021 08:30, Travers Ching wrote: I noticed CRAN is now doing checks against Apple M1, and some packages are failing including a dependency I use. I don't know what this refers to: M1 Mac CRAN checks are planned but AFAICS not yet included in the main results tables. OTOH, 'Additiona

Re: [Rd] Compression (really about LazyDate)

2021-02-19 Thread Prof Brian Ripley
On 18/02/2021 18:30, Therneau, Terry M., Ph.D. via R-devel wrote: This is a CRAN question: I have taken care to compress files in the data directory using "xz" (and checked that it is the best).  Is there then any impact or use for the LazyDataCompression option in the DESCRIPTION file? I h

Re: [Rd] issue with print()ing multibyte characters on R 4.0.4

2021-02-17 Thread Prof Brian Ripley
On 17/02/2021 04:58, Hiroaki Yutani wrote: Hi all, I saw several people on Japanese locale claim that, on R 4.0.4, print() doesn't display Japanese characters correctly. This seems to happen only on Windows and on macOS (I usually use Linux and I don't see this problem). For example, in the res

Re: [Rd] Does type raw really have no ordering?

2021-02-08 Thread Prof Brian Ripley
On 08/02/2021 13:25, Hugh Parsonage wrote: In the help for Extremes ?min Note that all versions fail for raw and complex vectors since these have no ordering. This makes sense for complex vectors, yet `raw` vectors seem to have a natural order. Indeed: which.min(as.raw(c(5L, 2L, 1L, 99L)))

Re: [Rd] Does parallel::mclapply work under emulation (Rosetta 2) on Apple Silicon?

2021-01-15 Thread Prof Brian Ripley
On 15/01/2021 05:53, Michael O'Dell via R-devel wrote: Setting aside the documented problems of running R natively on Apple's M1 machines (https://developer.r-project.org/Blog/public/2020/11/02/will-r-work-on-apple-silicon That's rather dated: see the more recent reports on this list. /index

Re: [Rd] Unicode characters in ISO8859-15 locale

2020-12-18 Thread Prof Brian Ripley
On 17/12/2020 12:28, Jeroen Ooms wrote: The hunspell package uses the code below to replace curly quotes (aka officially these are directional (or right/left) quotes. fancyquotes) with a regular ascii quotes that are needed for check spelling: chartr("\u2019", "'", input) As of last we

Re: [Rd] R-devel crash

2020-12-18 Thread Prof Brian Ripley
On 18/12/2020 13:39, Gábor Csárdi wrote: FYI. tolower, toupper and chartr with non-native chars is work in progress. (They were getting things wrong in a platform-dependent way, and it seems the replacement code is also flaky, if in general better than what went before.) sessionInfo()

Re: [Rd] UTF-8 characters in Rd files

2020-12-17 Thread Prof Brian Ripley
On 15/12/2020 23:57, Gábor Csárdi wrote: Dear list, I am trying to see if there is a way to expand the set of UTF-8 characters that we can use in Rd files. The main blocker is LaTeX when building the PDF manual. You need to explain why this is desirable. The other limiting factor is availabil

Re: [Rd] Specifying C Standard in Package's Makevars File

2020-09-29 Thread Prof Brian Ripley
On 28/09/2020 12:44, Andreas Kersting wrote: Hi, what is the correct way to specify a C standard in a package's Makevars file? Building a package with e.g. PKG_CFLAGS = -std=gnu11 does work but R CMD check issues a warning: for some unstated value of 'work' ... * checking compilation flags

Re: [Rd] Compilation error for R 4.0.2

2020-07-11 Thread Prof Brian Ripley
On 11/07/2020 11:47, Kurt Hornik wrote: Wim R Cardoen writes: Hello, I experienced a compiler error when I tried to compile the latest version of R i.e. R4.0.2 making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.

Re: [Rd] tcltk image reading problem (on a mac?): [tcl] encountered an unsupported criticial chunk type "eXIf"

2020-06-12 Thread Prof Brian Ripley
On 12/06/2020 03:49, Fox, John wrote: Dear Simon, On Jun 11, 2020, at 9:00 PM, Simon Urbanek wrote: Wayne, that one is unrelated, but interesting - you can fix it with sudo install_name_tool -change \ /usr/local/lib:/opt/X11/lib/libtk8.6.dylib \ /usr/local/lib/libtk8.6.dylib \ /usr/lo

Re: [Rd] CRAN checks and ASAN

2020-06-11 Thread Prof Brian Ripley
On 11/06/2020 15:57, Therneau, Terry M., Ph.D. via R-devel wrote: I have a version of R-devel on my development box that has the address sanitizer turned on.   This was instrumental in finding a pair of subtle memory issues.  (I had read, but never written, one element past the end of an array,

Re: [Rd] r-project.org SSL certificate issues

2020-06-09 Thread Prof Brian Ripley
On 10/06/2020 00:39, peter dalgaard wrote: Yes and no... At least as I understand it (Disclaimer: There are things I am pretty sure that I don't understand properly, somewhere in the Bermuda triangle beween CA bundles, TLS protocols, and Server-side settings), there are two sided to this: One

Re: [Rd] valgrind false positive on R startup?

2020-06-09 Thread Prof Brian Ripley
It is known, with a known workaround, see e.g. https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt . Set suppressions in ~/.valgrindrc, e.g. the CRAN check machine has --suppressions=/data/blackswan/ripley/wcsrtombs.supp It is an issue in your OS (glibc), not TRE nor R. On 10/06/2020 00:2

Re: [Rd] GCC warning

2020-05-23 Thread Prof Brian Ripley
On 23/05/2020 07:38, Simon Urbanek wrote: Adrian, newer compilers are better at finding bugs - you may want to read the full trace of the error, it tells you that you likely have a memory overflow when using strncpy() in your package. You should check whether it is right. Unfortunately we can

Re: [Rd] dbinom link

2020-05-18 Thread Prof Brian Ripley
On 18/05/2020 09:57, peter dalgaard wrote: In principle a good idea, but I'm not sure the whereabouts of Catherine Loader are known at this point. Last peeps from her on the net seem to be about a decade old. All attempts to contact Dr Loader re the locfit package failed, including those ear

Re: [Rd] Rtools and R 4.0.0?

2020-04-06 Thread Prof Brian Ripley
On 02/04/2020 05:35, Kevin Ushey wrote: Hello, Has a decision been made yet as to whether R 4.0.0 on Windows is going to be built using the new gcc8 toolchain (described at https://cran.r-project.org/bin/windows/testing/rtools40.html)? Short answer: 'no'. From the sidelines, I can see that t

Re: [Rd] status of Java & rJava?

2020-03-28 Thread Prof Brian Ripley
On 29/03/2020 04:07, Simon Urbanek wrote: Spencer, you could argue that Java is dead since Oracle effectively killed it by removing all public downloads, but if you manage to get hold of a Java installation then it works just fine with R. To my best knowledge there has never been an issue if

Re: [Rd] ASAN error with R-devel

2019-07-02 Thread Prof Brian Ripley
This is entirely within your OS's installation of Tcl/Tk and X11: the latter both allocated and freed. We've seen it before (even had it as bug report on R). Please check your OS is fully up-to-date and if so report it there. On 01/07/2019 15:55, Therneau, Terry M., Ph.D. via R-devel wrote:

Re: [Rd] r-project.org dns

2019-06-27 Thread Prof Brian Ripley
On 26/06/2019 21:13, Tim Keitt wrote: Sorry if this was already discussed. I notice that r-project.org is not found in dns lookups today. (At least for me -- I tried some online web look services as well.) THK We knew, but all the R listservers were also affected. The name servers in Vienna

Re: [Rd] rgl install for R 3.7

2019-06-02 Thread Prof Brian Ripley
On 02/06/2019 16:28, Koenker, Roger W wrote: I’ve installed R 3.7.0 on a new laptop running macos 10.14.5 and have managed to get most of my usual packages I presume 'R 3.7.0' is R-devel: it is not released and may never be released under that version. to compile from source with a ~/.R/Ma

Re: [Rd] Feature request: make file.exists interruptable

2019-04-16 Thread Prof Brian Ripley
The place for feature requests is bugs.r-project.org . On 15/04/2019 18:44, Christopher Hammill wrote: Hi R developers, On slow file systems with large lists of files, file.exists can take a long time to run. It would be nice if users could interrupt this function. I think it would be simple

Re: [Rd] Development version of R fails tests and is not installed

2019-03-05 Thread Prof Brian Ripley
On 05/03/2019 08:54, Berwin A Turlach wrote: G'day all, I have daily scripts running to install the patched version of the current R version and the development version of R on my linux box (Ubuntu 18.04.2 LTS). The last development version that was successfully compiled and installed was "R Un

Re: [Rd] svg ignores cex.axis in R3.5.1 on macOS

2018-09-06 Thread Prof Brian Ripley
On 06/09/2018 10:47, peter dalgaard wrote: I think this needs to be taken off the bug repository and continued here. By now it seems pretty clear that this is not an R bug, but a local problem on Spencer's machine, likely connected to font configurations. Or even on R-sig-Mac. I poked aroun

Re: [Rd] "utils::file.edit" does not understand "editor" with additional arguments

2018-08-29 Thread Prof Brian Ripley
We do not have the 'at a minimum' information requested by the posting guide, and I cannot reproduce anything like this on a Unix-alike. Both file.edit and edit.default call the same underlying C code, and that single-quotes the 'editor' argument to allow for spaces in its path/name so I would

Re: [Rd] longint

2018-08-16 Thread Prof Brian Ripley
On 16/08/2018 18:33, Hervé Pagès wrote: On 08/16/2018 05:12 AM, Dirk Eddelbuettel wrote: On 15 August 2018 at 20:32, Benjamin Tyner wrote: | Thanks for the replies and for confirming my suspicion. | | Interestingly, src/include/S.h uses a trick: | |     #define longint int | | and so does the n

Re: [Rd] CRAN: Update protocol buffers on macOS? (for RProtoBuf)

2018-07-07 Thread Prof Brian Ripley
On 06/07/2018 04:32, Jonathon Love wrote: Hi, I notice that the CRAN binary for the macOS version of RProtoBuf is built against quite an old version of protocol buffers (from 2014, before v3 format support was added). the windows version is (blessedly) kept up-to-date, but I'd like to float

Re: [Rd] Building R from source with the PGI compiler

2017-12-21 Thread Prof Brian Ripley
On 21/12/2017 01:03, Erin Hodgess wrote: Hello I would like to build R from source and use the PGI compiler, rather than the GCC compiler. On what platform? AFAIK we have only ever had reports on Linux. I saw the instructions for the Intel compiler in the R Installation Manual, but I didn't

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

2017-12-20 Thread Prof Brian Ripley
On 20/12/2017 17:42, Winston Chang wrote: On recent builds of R-devel, R CMD check gives a WARNING when some compiler warning flags are detected, such as -Werror, because they are non-portable. This appears to have been added in this commit: https://github.com/wch/r-source/commit/2e80059 Tha

Re: [Rd] javareconf issue

2017-10-27 Thread Prof Brian Ripley
On 27/10/2017 04:13, rosseji wrote: Using a real name and a signature are regarded as polite here. Hi, Wasn't able to see a bug report on this issue yet... Hope I'm not doublng up. This is a problem on your system. Also, macOS issues should be reported to R-sig-mac ... and you should give

Re: [Rd] Incorrect Import by Data for CSV File

2017-09-25 Thread Prof Brian Ripley
On 25/09/2017 08:00, Dario Strbenac wrote: Good day, The data function can import a variety of file formats, one of them being C.S.V. That isn't its documented purpose. It was the original way for packages to provide datasets as needed (before lazy data was added). Problematically, all of

Re: [Rd] configure.ac

2017-08-01 Thread Prof Brian Ripley
On 01/08/2017 17:26, peter dalgaard wrote: If you check developer.r-project.org, you'll find links to the scripts that we use for building releases and pre-releases of R. These are usually run on a Mac, but shouldn't require much change for Linux. In particular, notice this lead-in in the prer

Re: [Rd] special latin1 do not print as glyphs in current devel on windows

2017-08-01 Thread Prof Brian Ripley
You seem confused about Latin-1: those characters are not in Latin-1. (MicroSoft code pages are a proprietary encoding, some code pages such as CP1252 being extensions to Latin-1.) You have not given the 'at a minimum information' asked for in the posting guide so we have no way to reproduce t

Re: [Rd] Solaris SPARC testbed

2017-07-11 Thread Prof Brian Ripley
On 11/07/2017 16:48, Avraham Adler wrote: I've looked at some package testing results and I'm not seeing Solaris SPARC. Has that test-bed been deprecated for package testing? Are you talking about CRAN's check results? The Sparc hardware used for CRAN died during an unplanned power outage, an

Re: [Rd] LC_TIME not set correctly by Sys.setlocale() ?

2017-06-23 Thread Prof Brian Ripley
On 23/06/2017 15:35, Joris Meys wrote: Related to the following question on Stackoverflow: https://stackoverflow.com/questions/44723690/unexpected-behavior-of-sys-setlocale#44723690 It appears as if Sys.setlocale() does not update LC_TIME correctly for use in date formatting. Although R reports

Re: [Rd] v3.4.0-2 incompatible with gcc 7.1

2017-06-23 Thread Prof Brian Ripley
R is compatible with GCC 7.1 ! New compiler versions are tested, as well as those under development for the major compilers. (A few packages still fail with GCC 7.1, but that was reported to their maintainers months ago.) Just follow the instructions in the R-admin manual to install from sou

Re: [Rd] R history: Why 'L; in suffix character ‘L’ for integer constants?

2017-06-16 Thread Prof Brian Ripley
On 16/06/2017 20:37, Jim Hester wrote: The relevant sections of the C standard are http://c0x.coding-guidelines.com/5.2.4.2.1.html, which specifies that C There is more than one C standard, but that is none of them. ints are only guaranteed to be 16 bits, C long ints at least 32 bits in size,

Re: [Rd] Creating a private CRAN with webpages

2017-06-09 Thread Prof Brian Ripley
On 09/06/2017 07:44, Joshua Bradley wrote: I'm not trying to create a mirror of the CRAN. I also do not want to create a "subset" of CRAN packages. Sorry if my explanation was confusing. There are internal proprietary R packages that I would like to host on a private repo. I like the CRAN web pag

Re: [Rd] [R] Somewhat obscure bug in R 3.4.0 building from source

2017-05-22 Thread Prof Brian Ripley
On 22/05/2017 18:16, Peter Carbonetto wrote: Hi Peter, Duncan & Bert, Thank you kindly for the responses. Indeed, doc/NEWS.pdf is included in the source distribution, and then removed upon "make clean". I thought that it might be useful to report this for your benefit, but on closer inspection

Re: [Rd] tempdir() may be deleted during long-running R session

2017-04-21 Thread Prof Brian Ripley
From the R-admin manual §5: 'Various environment variables can be set to determine where R creates its per-session temporary directory. The environment variables TMPDIR, TMP and TEMP are searched in turn and the first one which is set and points to a writable area is used. If none do, the fina

Re: [Rd] Intel MKL compiling issue

2017-04-20 Thread Prof Brian Ripley
There is nothing here indicating any kind of error, so no way to give any insights And please do follow the posting guide, including not posting HTML. FWIW, I have tested R 3.4.0 RC (sic) with MKL 11.3, which is later than your 2013 ... (on x86_64 Fedora 24). On 20/04/2017 10:39, jing

Re: [Rd] Q: Windows/readline: missing history search

2017-04-18 Thread Prof Brian Ripley
Your error is in your subject line: getline rather than readline is used on Windows. (readline was not written for Windows and depends on a 'curses' library not available for Windows terminals let alone RGui. A considerable amount of time was spent trying to use it, unsuccessfully.) On 13/0

Re: [Rd] mean(x) != mean(rev(x)) different with x <- c(NA, NaN) for some builds

2017-03-31 Thread Prof Brian Ripley
From ?NA Numerical computations using ‘NA’ will normally result in ‘NA’: a possible exception is where ‘NaN’ is also involved, in which case either might result. and ?NaN Computations involving ‘NaN’ will return ‘NaN’ or perhaps ‘NA’: which of those two is not guarantee

Re: [Rd] Error "Warning in read_symbols_from_dll(so, rarch): this requires 'objdump.exe' to be on the PATH

2017-03-21 Thread Prof Brian Ripley
On 21/03/2017 17:12, Uwe Ligges wrote: On 19.03.2017 23:50, Christophe Genolini wrote: Hi all, I try to compile my package kml and I get the message [That will not be 'compiling': it may be from R CMD check, e.g. from wuth --as-cran in R-devel.] Warning in read_symbols_from_dll(so,rarch

Re: [Rd] Incompatible change in R-devel

2017-03-21 Thread Prof Brian Ripley
On 21/03/2017 16:38, Dirk Eddelbuettel wrote: Hi Brian, On 21 March 2017 at 07:29, Prof Brian Ripley wrote: | As of today's commit r72375 all packages with native-routine | registration of C or Fortran routines need to be reinstalled in R-devel | (and that include some of the recomm

[Rd] Incompatible change in R-devel

2017-03-21 Thread Prof Brian Ripley
As of today's commit r72375 all packages with native-routine registration of C or Fortran routines need to be reinstalled in R-devel (and that include some of the recommended packages in R itself which will not be reinstalled via make dependencies, so we advise a clean rebuild of R). We try t

Re: [Rd] Test suite failures in R-devel_2017-02-25_r72256

2017-02-28 Thread Prof Brian Ripley
On 27/02/2017 09:30, Peter Simons wrote: Hi, I tried compiling the latest pre-release for R 3.3.3 for the NixOS Linux distribution [1], but the build fails during the "make check" phase because of the following 2 issues: Hmm, R-devel (your subject line) is not a pre-release of R 3.3.3: it is

Re: [Rd] Registration of native routines

2017-02-19 Thread Prof Brian Ripley
On 14/02/2017 16:25, Prof Brian Ripley wrote: Registration of 'native routines' (entry points in compiled code loaded into R) has been available for over 14 years, ... (There are reports that the check in 'R CMD check' on Windows sometimes fails to detect use of registra

Re: [Rd] Registration of native routines

2017-02-14 Thread Prof Brian Ripley
On 14/02/2017 17:28, Avraham Adler wrote: On Tue, Feb 14, 2017 at 11:25 AM, Prof Brian Ripley wrote: Registration of 'native routines' (entry points in compiled code loaded into R) has been available for over 14 years, but few packages make use of it (less than 10% of those on

[Rd] Registration of native routines

2017-02-14 Thread Prof Brian Ripley
Registration of 'native routines' (entry points in compiled code loaded into R) has been available for over 14 years, but few packages make use of it (less than 10% of those on CRAN with compiled code). Registration has similar benefits to name spaces in R code: - it ensures that the routines

Re: [Rd] Grapics Device Resolution Limits

2017-02-10 Thread Prof Brian Ripley
On 10/02/2017 19:27, Prof Brian Ripley wrote: Note that there are at least 5 separate png() devices, so Linux was not using the (default) device used on Windows. In general, the device-limits info is not on the help page because we do not know it. On Windows the default device limits depend on

Re: [Rd] Grapics Device Resolution Limits

2017-02-10 Thread Prof Brian Ripley
Note that there are at least 5 separate png() devices, so Linux was not using the (default) device used on Windows. In general, the device-limits info is not on the help page because we do not know it. On Windows the default device limits depend on the OS version, 32/64-bit, RAM and the graph

Re: [Rd] changes in src/unix/system.c break builds on FreeBSD

2017-02-09 Thread Prof Brian Ripley
On 09/02/2017 11:44, Rainer Hurling wrote: Dear R devs, For some days now (~ February, 4th), I am not able to build the recent tarballs of R-devel on a FreeBSD test box anymore. The breakage seems to be related to the newest overhaul of src/unix/system.c: [..snip..] gcc49 -std=gnu99 -I. -I../.

Re: [Rd] Subject: Milestone: 10000 packages on CRAN

2017-01-29 Thread Prof Brian Ripley
On 28/01/2017 02:52, Henrik Bengtsson wrote: Continuing the tradition to post millennia milestones on CRAN: So, it happened. Today (January 27, 2017 PCT) CRAN reached 10,000 packages [1]. I predicted (rather tongue-in-check) at UseR! 2011 that we would have this 'for Christmas 2016', at a tim

Re: [Rd] Definition of uintptr_t in Rinterface.h

2017-01-01 Thread Prof Brian Ripley
On 29/12/2016 15:55, Simon Urbanek wrote: The problem is elsewhere - Rinterface.h guards the ultima-ratio fallback with HAVE_UINTPTR_T but that config flag is not exported in Rconfig.h. Should be now fixed in R-devel - please check if that works for you. Rconfig.h would be appropriate if Rint

Re: [Rd] syntax difference clusterExport in parallel and snow

2016-12-13 Thread Prof Brian Ripley
On 13/12/2016 17:05, Paul Johnson wrote: We got some errors and eventually figured out that parallel::clusterExport second argument is "varlist" while in snow::clusterExport it is "list". The user had loaded parallel first, but did something else which inadvertently loaded snow, then clusterExpo

Re: [Rd] Different results for cos,sin,tan and cospi,sinpi,tanpi

2016-12-01 Thread Prof Brian Ripley
Please note that you need to report your platforms (as per the posting guide), as the C function starts #ifdef HAVE_COSPI #elif defined HAVE___COSPI double cospi(double x) { return __cospi(x); } And AFAICS the system versions on Solaris and OS X behave the same way as R's substitute. O

Re: [Rd] [parallel-package] feature request: set default cluster type via environment variable

2016-11-24 Thread Prof Brian Ripley
On 24/11/2016 07:30, Christian Krause wrote: Dear all, I’m working as an administrator of a High-Performance Computing (HPC) Cluster which runs on Linux. A lot of people are using R on this Linux cluster and, of course, the *parallel* package to speed up their computations. It has been our co

Re: [Rd] grep

2016-10-03 Thread Prof Brian Ripley
On 02/10/2016 17:54, Pi wrote: Hello. It would be great if the grep function in R had the option to use the -m parameter as the linux command does. I guess you mean the non-standard flag of the GNU version of grep (probably but not necessarily as used by Linux). That the POSIX standard for

Re: [Rd] library() asks user to accept license of some built-in packages

2016-10-02 Thread Prof Brian Ripley
On 27/09/2016 10:49, Mikko Korpela wrote: When 'getOption("checkPackageLicense")' is 'TRUE' and the user calls 'library(grid)' for the first time, R asks the user to either accept or decline the package license. This should not be necessary as the package license is "Part of R ..." with "..." den

Re: [Rd] R without graphics

2016-05-23 Thread Prof Brian Ripley
On 24/05/2016 00:54, Simon Urbanek wrote: Um... any reason why you don't simply disable aqua? That file is only compiled if you enable aqua - it has really nothing to do with grDevices ... Also, you can specify a compiler for Objective-C separately and the manual advises you to do so (to spec

Re: [Rd] Submitting an updated package version to CRAN (Warning: non-ASCII characters)

2016-05-23 Thread Prof Brian Ripley
On 21/05/2016 21:25, Luck Buttered wrote: Dear all: I am updating the version of an R package I submitted last year on CRAN and came across two questions that I would be grateful to seek any input about: 1) In the updated version of the package, I am adding a second example dataset. This exampl

Re: [Rd] Max OSX 3.3.0 and lzma

2016-05-05 Thread Prof Brian Ripley
On 05/05/2016 19:40, Mick Jordan wrote: I have lzma installed (in /usr/local) but R-3.3.0 configure doesn't like something about it: checking for lzma_version_number in -llzma... yes checking lzma.h usability... no checking lzma.h presence... no checking for lzma.h... no configure: error: "liblz

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

2016-05-05 Thread Prof Brian Ripley
On 05/05/2016 10:11, Uwe Ligges wrote: On 05.05.2016 04:25, Marius Hofert wrote: Hi Simon, ... all interesting (but quite a bit above my head). I only read 'Linux' and want to throw in that this problem does not appear on Linux (it seems). I talked about this with Martin Maechler and he repor

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

2016-05-04 Thread Prof Brian Ripley
On 04/05/2016 08:44, Martin Maechler wrote: Qin Zhu on Mon, 2 May 2016 16:19:44 -0400 writes: > Hi, > I’m working on a Shiny app for statistical analysis. I ran into this "maximal number of DLLs reached" issue recently because my app requires importing many other packages.

Re: [Rd] R-exts update for new *check* argument in R 3.3.0

2016-04-20 Thread Prof Brian Ripley
On 19/04/2016 23:53, Jan Górecki wrote: Hello dear dev team, In the recent devel R-exts manual I cannot find any information about new option `--ignore-vignettes` to `R CMD check`. I would expect it to be mentioned somewhere in "1.4.2 Non-Sweave vignettes". Which is a subsection of §1.4 'Writi

Re: [Rd] Building R-patched and R-devel fails

2016-04-17 Thread Prof Brian Ripley
On 17/04/2016 07:25, Berwin A Turlach wrote: G'day all, probably you have noticed this by now, but I thought I ought to report it. :) Already fixed for Unix by the time this reached me. Since that version of Survival has been put into 3.2 patched, that also needed its Makefile.in updated.

[Rd] Avoid texinfo 6.1

2016-02-22 Thread Prof Brian Ripley
There are problems with the texi2dvi in the recently released texinfo 6.1. (The bug has been reported.) Avoid 6.1 if you can, but if not setting the environment variable R_TEXI2DVICMD=emulation will enable R to build, including NEWS.pdf and all the vignettes. We are working on a more comple

Re: [Rd] R Package Installation Ignores libPaths Setting

2016-02-18 Thread Prof Brian Ripley
You misunderstand what .libPaths does: it changes the path in the current session only. Installation uses a different R process. Set R_LIBS to change the library path for new sessions: see ?.libPath . On 18/02/2016 07:00, Dario Strbenac wrote: Good day, If the library path is changed with .

Re: [Rd] R-devel no longer supports Ubuntu 14.04 LTS (insufficient PCRE version)

2015-11-20 Thread Prof Brian Ripley
I think you have it backwards: Ubuntu 14.04 does not support R-devel PCRE 8.32 is 3 years old, so Ubuntu 14.04 shipped an already quite old version 19 months ago. R has long said that its requirement was PCRE (version 8.10 or later, preferably 8.32 or later) and 8.32 is indeed prefer

Re: [Rd] Building R for AIX in 64-bit mode

2015-10-15 Thread Prof Brian Ripley
On 15/10/2015 13:32, Michael Felt wrote: Hi. Just wanted to let you know I am getting close to packaging R for AIX in 64.bit mode. Which version? (You mentioned 3.1.3 and 3.2.2 far below.) There is little value in reporting on frozen branches, and most value in reporting on R-devel where al

Re: [Rd] gcc ubsan alignement test --minimal gcc version?

2015-10-14 Thread Prof Brian Ripley
On 13/10/2015 14:46, kaveh wrote: Dear All, I'm trying to implement the section of the manual pertaining to the gcc-ubsan test carried by CRAN on my local computer (ubuntu 14.04): http://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/README.txt I was wondering whether someone cou

[Rd] MiKTeX's withdrawal of texi2dvi.exe

2015-10-09 Thread Prof Brian Ripley
MiKTeX has abruptly removed texi2dvi.exe from its distribution. (MiKTeX broke its updating process earlier and an attempted update trashed the updater on my installation so I was forced to make a fresh install of the current distribution. I do not know if updates remove a currently installed

Re: [Rd] Building manuals are failing now that MikTex 2.9 has removed texi2dvi.exe

2015-10-08 Thread Prof Brian Ripley
Hmm, look in MkRules.dist for the setting you failed to make Obviously available in R-patched and R-devel only as we cannot foretell such changes. On 09/10/2015 06:24, Avraham Adler wrote: According to the MikTex bug reports [1], MikTex 2.9 has removed texi2dvi.exe last week (on 2015-09-2

Re: [Rd] authorship and citation

2015-10-08 Thread Prof Brian Ripley
S Ellison posted: (quoting someone else, it appears) I read the CRAN policies twice, and there is no official guideline on how to compile the citation. And once again Dr Ellison is not attributing quotes: that is clearly covered by the posting guide. Including: Take care when you quote ot

Re: [Rd] read.table reads "i" as NA_complex_

2015-10-07 Thread Prof Brian Ripley
On 07/10/2015 21:22, William Dunlap wrote: I just noticed that read.table() and type.convert() interpret the string "i" as a missing value of type complex. > str(read.table(text=c("i\ni\ni\ni\n"))) 'data.frame': 4 obs. of 1 variable: $ V1: cplx NA NA NA ... > str(type.convert

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