[Rd] incorrect DLL path for Rbitmap.dll on Windows

Hello, I think there is a problem in recent devel builds of R on Windows with various devices from the grDevices package. For example: > capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE

[Rd] Problem with system2(), directing STDERR to a file

According to ?system2, I should be able to direct the output of STDERR to a file by giving the filename as a character vector to the "stderr" argument. But here is what happens. Given a ruby script test.rb (with its executable bit set): #!/usr/bin/env ruby STDOUT.puts "stdout" STDERR.puts "stder

Re: [Rd] Problem with system2(), directing STDERR to a file

er vector giving the names of possible > (temporary) files. Note that no files are generated by "tempfile". > > > try a file.create(t) after tempfile() > > cheers, > > Keith > > > Dan Tenenbaum wrote: > >> According to ?system2, I should be able to

Re: [Rd] Problem with system2(), directing STDERR to a file

ds base loaded via a namespace (and not attached): [1] tools_2.13.0 Thanks Dan On Wed, Nov 10, 2010 at 9:11 PM, Dan Tenenbaum wrote: > Hi Keith, > > The problem is not with tempfile(), and is not really a problem of whether > a file exists or not. The problem is that system

Re: [Rd] Problem with system2(), directing STDERR to a file

ided. If no stderr argument is supplied, I'd expect the stderr to appear in the R console, not be redirected to a file. Thanks! Dan On Thu, Nov 11, 2010 at 8:44 PM, Dan Tenenbaum wrote: > I notice that a fix for this issue was checked in. Thanks, much > appreciated! > >

Re: [Rd] diagnosing a CMD check failure

On Fri, Dec 17, 2010 at 12:38 PM, Vincent Carey wrote: > That got me a little further. system2() seems not to like my system. > > > system("date") > Fri Dec 17 15:35:21 EST 2010 > > system2("date") > sh: : No such file or directory > > This is with 2.13 r53555. > Hi Vince, There are some bugs i

[Rd] Problem building R-2.13 r54645 on Windows

I am building R-2.13 r54645 from source as described here: http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source The "make all recommended" command ends as follows on both 32 and 64-bit Windows (Windows Server 2003 R2 Enterprise Edition Service Pack 2 and Windows Server 2008 R2 E

Re: [Rd] Problem building R-2.13 r54645 on Windows

On Thu, Mar 3, 2011 at 10:50 AM, Dan Tenenbaum wrote: > I am building R-2.13 r54645 from source as described here: > http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source > The "make all recommended" command ends as follows on both 32 and 64-bit > Windows (

Re: [Rd] Problem building R-2.13 r54645 on Windows

On Fri, Mar 4, 2011 at 10:53 AM, Dan Tenenbaum wrote: > On Thu, Mar 3, 2011 at 10:50 AM, Dan Tenenbaum wrote: >> I am building R-2.13 r54645 from source as described here: >> http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source >> The "make all re

Re: [Rd] Problem building R-2.13 r54683 on Windows

rule to make target `Rzlib.def', needed by `Rzlib.dll'. Stop. make[3]: *** [rlibs] Error 1 make[2]: *** [../../bin/i386/R.dll] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Hope someone can have a look. Thanks Dan On Thu, Mar 3, 2011 at 10:50 AM, Dan Tenenbaum wro

Re: [Rd] Problem building R-2.13 r54683 on Windows

On Mon, Mar 7, 2011 at 11:00 AM, Dan Tenenbaum wrote: > Hi, Unfortunately it looks like this problem has somehow been reintroduced. > Looks like this has now been fixed. Many thanks! Dan > I am now trying to build R-devel 54683 from source, again following > the manual. I get the s

[Rd] tools::checkRd() output different from R CMD check

Hello, When running tools::checkRd() on a single .Rd file, should I expect the output to be the same as that generated by R CMD check when it checks .Rd files? R CMD check finds the following warning: * checking Rd \usage sections ... WARNING > Assignments in \usage in documentation object 'ilm'

[Rd] Feature request: display file name in R CMD check warning

Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method markup and not > their full name. > See the chapter 'Writing R documentation files' in manual 'Writing R > Extensions'. The package I'm looking at is on

Re: [Rd] Feature request: display file name in R CMD check warning

On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch wrote: > On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: >> >> Hi, >> >> I came across the following warning in R CMD check (it only occurred on >> Windows): >> >> The \usage entries for S3 methods should

Re: [Rd] Feature request: display file name in R CMD check warning

On Thu, Mar 17, 2011 at 9:33 AM, Dan Tenenbaum wrote: > On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch > wrote: >> On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: >>> >>> Hi, >>> >>> I came across the following warning in R CMD check (it only occurred

Re: [Rd] Feature request: display file name in R CMD check warning

On Thu, Mar 17, 2011 at 6:49 PM, Duncan Murdoch wrote: > On 11-03-17 12:33 PM, Dan Tenenbaum wrote: > >> On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch >> wrote: >> >>> On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: >>> >>>> >>>>

[Rd] R_HOME path getting munged in inst/doc/Makefile on Windows

Hello, I have come across two separate packages that have a Makefile in inst/doc which use the R_HOME variable. In both cases, the path to R_HOME gets munged in such a way that commands that include R_HOME fail on Windows: For example, one Makefile, for the xmapcore package ( https://hedgehog.fh

Re: [Rd] R_HOME path getting munged in inst/doc/Makefile on Windows

On Mon, Mar 21, 2011 at 7:22 PM, Simon Urbanek wrote: > > On Mar 21, 2011, at 9:07 PM, Dan Tenenbaum wrote: > > > Hello, > > > > I have come across two separate packages that have a Makefile in inst/doc > > which use the R_HOME variable. > > > > In

Re: [Rd] R_HOME path getting munged in inst/doc/Makefile on Windows

on Windows. Despite your perjorative comments, the > supplied value of R_HOME is valid. > > > Thanks, this did the trick. Dan > On Mon, 21 Mar 2011, Dan Tenenbaum wrote: > > Hello, >> >> I have come across two separate packages that have a Makefile in inst/doc

[Rd] problem with png() and large dimensions on some 32-bit Windows machines

Hello, I encountered this: > png(file=tempfile(), width=1165, height=12983) Error in png(file = tempfile(), width = 1165, height = 12983) : unable to start png() device In addition: Warning messages: 1: In png(file = tempfile(), width = 1165, height = 12983) : Unable to allocate bitmap 2: In

Re: [Rd] problem with png() and large dimensions on some 32-bit Windows machines

down some more, it works if I specify either height or width but not both. Thanks Dan On Tue, Mar 29, 2011 at 6:10 PM, Dan Tenenbaum wrote: > Hello, > > I encountered this: > > > png(file=tempfile(), width=1165, height=12983) > Error in png(file = tempfile(), width = 1165, h

[Rd] typo/bug in R-Beta

In r55204 src/library/tools/R/install.R, line 338. It says: shQUote(file.path(lockdir, pkg Should say: shQuote(file.path(lockdir, pkg Thanks Dan __ R-devel@r-project.org mailing list

Re: [Rd] typo/bug in R-Beta

On Thu, Mar 31, 2011 at 9:50 AM, Dan Tenenbaum wrote: > In r55204 > src/library/tools/R/install.R, line 338. > > It says: > >                             shQUote(file.path(lockdir, pkg > > Should say: > >                             shQuote(file.path(lockdir, pkg

[Rd] Problem running "make bitmapdll" with R-2.13 beta r55221 on Windows

Hello, I am building R r55221 according to http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source After I have done "make all && make recommended", "make bitmapdll" returns the following: E:\sandbox\R-2.13.r55221\src\gnuwin32>make bitmapdll make[1]: Entering directory `/cygdrive

Re: [Rd] Problem running "make bitmapdll" with R-2.13 beta r55221 on Windows

On Thu, Mar 31, 2011 at 2:01 PM, Dan Tenenbaum wrote: > Hello, > > I am building R r55221 according to > http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source > > After I have done "make all && make recommended", "make bitmapdll" &

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

On Wed, May 11, 2011 at 12:08 PM, Sean Robert McGuffee wrote: > Hi, > I¹m trying to figure out how to put images into my package¹s help > documentation. I¹ve gotten to the point where I can put the images in the > /inst/doc/ directory. I have also gotten to the point where I have package > checks

[Rd] R-devel (2.14 alpha) Windows binary

Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan

Re: [Rd] R-devel (2.14 alpha) Windows binary

10:45 >> R-2.14.0dev-win.exe >> ... >> >> so R-2.14.0dev-win.exe would be a pretty good surrogate for R 2.14.0 alpha >> until that is available. >> >>> >>> -pd >>> >>> On Oct 5, 2011, at 00:46 , Dan Tenenbaum wrote: >>>

Re: [Rd] MetaCran website v1.0.0-alpha

- Original Message - > From: "Gábor Csárdi" > To: "Gabriel Becker" > Cc: "Simon Urbanek" , "Rainer M Krug" > , r-devel@r-project.org > Sent: Tuesday, May 26, 2015 10:55:02 AM > Subject: Re: [Rd] MetaCran website v1.0.0-alpha > > On Tue, May 26, 2015 at 1:46 PM, Gabriel Becker > > wro

[Rd] system2() shortens R.home() to 8.3 form on windows

Hi, So in an interactive R session, R.home() returns the following: > R.home() [1] "D:/biocbld/bbs-3.2-bioc/R" However, if I call it from system2(), I get different results: > system2("R", "-q -e R.home()") > R.home() [1] "D:/biocbld/BBS-3~1.2-B/R" Similarly: > system2("R", "-q -e Sys.getenv(

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

Hi, > url <- > "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt"; > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL

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

- Original Message - > From: "Uwe Ligges" > To: "Dan Tenenbaum" , "R-devel@r-project.org" > > Sent: Saturday, August 8, 2015 3:57:34 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default > download method >

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

- Original Message - > From: "Dan Tenenbaum" > To: "Uwe Ligges" > Cc: "R-devel@r-project.org" > Sent: Saturday, August 8, 2015 4:02:54 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default > download method

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

Hi David, - Original Message - > From: "David Smith" > To: "Dan Tenenbaum" , "Uwe Ligges" > , "Elliot Waingold" > > Cc: "R-devel@r-project.org" > Sent: Wednesday, August 12, 2015 12:42:39 PM > Subject: RE: [R

Re: [Rd] Why not pthreads on Windows in 'parallel' package?

I'm confused; mclapply does not work on windows (at least with mc.cores > 1) because fork() is not available on windows. So the original question still seems relevant to me. Dan - Original Message - > From: "Henrik Bengtsson" > To: "Kasper Daniel Hansen" > Cc: "R-devel" > Sent: Frida

[Rd] require(..., quietly=TRUE) does not suppress warning

Hi, The `quietly` argument of `require` is documented as follows: quietly: a logical. If ‘TRUE’, no message confirming package attaching is printed, and most often, no errors/warnings are printed if package attaching fails. However: > require(foo, quietly=TRUE) Warning mes

Re: [Rd] require(..., quietly=TRUE) does not suppress warning

ve used the 'if (!require("pkg")) install.packages("pkg")' pattern before without seeing this warning, so I wondered if the behavior had changed, and that's what prompted me to write. I know I can squelch the warning by wrapping the require() in suppressWarnings()

Re: [Rd] R CMD INSTALL and file permission settings

On Sat, Jun 15, 2013 at 4:38 PM, Simon Urbanek wrote: > > On Jun 15, 2013, at 2:42 PM, Martin Maechler wrote: > >>> Dirk Eddelbuettel >>>on Sat, 15 Jun 2013 10:45:04 -0500 writes: >> >>> On 15 June 2013 at 07:00, Dirk Eddelbuettel wrote: >>> | >>> | On 15 June 2013 at 07:47, Simon Urb

Re: [Rd] packages with Sweave and knitr vignettes?

On Fri, Aug 23, 2013 at 1:24 PM, Michael Friendly wrote: > Now that R 3.0.0+ supports non-Sweave vignettes, R-exts \S 1.4.2 seems to > imply that > it is possible to include both Sweave and knitr vignettes in a single > package. > > I'm wondering > if anyone has tried this and/or if there are some

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

Hi, I created a package as follows: > a = 1 > package.skeleton() Then I got the following output when building the package: * checking for file ‘anRpackage/DESCRIPTION’ ... OK * preparing ‘anRpackage’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and m

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

the tarball produced could > cause > problems when unpacking with other tools. > > On 23/09/2013 20:55, Dan Tenenbaum wrote: > > Hi, > > > > I created a package as follows: > > > >> a = 1 > >> package.skeleton() > > > > Then I

[Rd] uninformative error message when building package: ‘x’ must be an atomic vector

Hi, When building this Bioconductor package with R-devel: http://www.bioconductor.org/packages/devel/bioc/src/contrib/ROntoTools_1.1.2.tar.gz I get the following: [...] Error: processing vignette ‘rontotools.Rnw’ failed with diagnostics: ‘x’ must be an atomic vector Execution halted If I insta

Re: [Rd] "Failed to locate the 'texi2pdf' output file"

t; completed in full when returning the control to R, then the PDF is not > there and you would get this error. I don't know if this can happen. > The reason why I came to think of this is because I recall that I've > seen this behavior when using bitmap() and Ghostscript to c

[Rd] install.packages() removes package on Windows

Hi, Starting with the XML package installed: > "XML" %in% rownames(installed.packages()) [1] TRUE > I ran the following script: pkgs <- c("XML") for (i in 1:100) { install.packages(pkgs, repos="http://cran.fhcrc.org";) if (!all(pkgs %in% rownames(installed.packages( { p

Re: [Rd] install.packages() removes package on Windows

Thanks Henrik and Jon, that's very helpful. Dan - Original Message - > From: "Jon Olav Skoien" > To: "Henrik Bengtsson" > Cc: "Dan Tenenbaum" , "R-devel" > Sent: Friday, October 11, 2013 1:38:26 AM > Subject: Re: [Rd] instal

[Rd] "size of shared memory region" messages show up with Rtools 3.1.0.1939

Hi, After installing Rtools 3.1.0.1939 into c:\rtools31, when I call any (most?) of the commands in c:\rtools31\bin, I see strange messages printed to stderr. Example: C:\Rtools31>bin\tar 0 [main] tar 6084 shared_info::initialize: size of shared memory region changed from 27984 to 21136

Re: [Rd] "size of shared memory region" messages show up with Rtools 3.1.0.1939

- Original Message - > From: "Dan Tenenbaum" > To: "R-devel" > Sent: Wednesday, November 20, 2013 2:41:36 PM > Subject: [Rd] "size of shared memory region" messages show up with Rtools > 3.1.0.1939 > > Hi, > > After insta

Re: [Rd] "size of shared memory region" messages show up with Rtools 3.1.0.1939

- Original Message - > From: "Dan Tenenbaum" > To: "R-devel" > Sent: Wednesday, November 20, 2013 2:49:24 PM > Subject: Re: [Rd] "size of shared memory region" messages show up with Rtools > 3.1.0.1939 > > > > - Original

[Rd] interpreting the output of getParseData()

Hi, I'm trying to make sense of the output of getParseData(). The "parent" column is supposed to refer to the "id" of the parent of the given item, but there are numbers in the parent column that do not exist in the id column. Example: > p <- parse(text="f<-function(){if(TRUE)1 else 2}") > df <

Re: [Rd] [RFC] A case for freezing CRAN

- Original Message - > From: "Joshua Ulrich" > To: "Jeroen Ooms" > Cc: "r-devel" > Sent: Wednesday, March 19, 2014 2:59:53 PM > Subject: Re: [Rd] [RFC] A case for freezing CRAN > > On Wed, Mar 19, 2014 at 4:28 PM, Jeroen Ooms > wrote: > > On Wed, Mar 19, 2014 at 11:50 AM, Joshua Ulri

Re: [Rd] [RFC] A case for freezing CRAN

- Original Message - > From: "David Winsemius" > To: "Jeroen Ooms" > Cc: "r-devel" > Sent: Wednesday, March 19, 2014 11:03:32 PM > Subject: Re: [Rd] [RFC] A case for freezing CRAN > > > On Mar 19, 2014, at 7:45 PM, Jeroen Ooms wrote: > > > On Wed, Mar 19, 2014 at 6:55 PM, Michael We

Re: [Rd] [RFC] A case for freezing CRAN

- Original Message - > From: "Gábor Csárdi" > To: "r-devel" > Sent: Thursday, March 20, 2014 6:23:33 PM > Subject: Re: [Rd] [RFC] A case for freezing CRAN > > Much of the discussion was about reproducibility so far. Let me > emphasize > another point from Jeroen's proposal. > > This i

Re: [Rd] inconsistent error messages on Mac OS X

- Original Message - > From: "Adam Welc" > To: r-devel@r-project.org > Sent: Wednesday, April 2, 2014 3:11:28 PM > Subject: [Rd] inconsistent error messages on Mac OS X > > Hi All, > > I am one of the contributors to the FastR project ( > https://bitbucket.org/allr

[Rd] minor issue with R CMD INSTALL --build

Hello, I created a trivial package like this: R --vanilla a = 1 package.skeleton("apkg") Then at the command prompt I removed apkg/man/* to avoid installation errors since those man pages are incomplete. Then: R CMD build apkg R CMD INSTALL --build apkg_1.0.tar.gz says: [...] packaged insta

Re: [Rd] R-3.1.0 OSX Snow Leopard installs old binary

- Original Message - > From: "Gábor Csárdi" > To: "Simon Urbanek" > Cc: r-devel@r-project.org > Sent: Thursday, April 17, 2014 4:42:50 PM > Subject: Re: [Rd] R-3.1.0 OSX Snow Leopard installs old binary > > On Thu, Apr 17, 2014 at 5:18 PM, Simon Urbanek > wrote: > > > > > On Apr 17, 2

Re: [Rd] R-3.1.0 OSX Snow Leopard installs old binary

- Original Message - > From: "Gábor Csárdi" > To: "Simon Urbanek" > Cc: r-devel@r-project.org > Sent: Thursday, April 17, 2014 6:52:33 PM > Subject: Re: [Rd] R-3.1.0 OSX Snow Leopard installs old binary > > On Thu, Apr 17, 2014 at 9:43 PM, Simon Urbanek > wrote: > [...] > > > The Sugg

[Rd] proposed change of check message when VIgnetteBuilder package is not declared as a dependency

Hi, I notice in R-3.1.1, if a package specifies a VignetteBuilder (such as knitr) in its DESCRIPTION file, but does not also depend on the specified package (in either Depends, Imports, or Suggests), that R CMD check will say: * checking package dependencies ... ERROR VignetteBuilder package no

Re: [Rd] how to list external dependencies (i.e., non-R packages)?

- Original Message - > From: "Kasper Daniel Hansen" > To: "Greg Minshall" > Cc: "r-devel" > Sent: Sunday, July 13, 2014 1:08:56 PM > Subject: Re: [Rd] how to list external dependencies (i.e., non-R packages)? > > Several packages in Bioconductor (and possibly CRAN) uses > SystemRequ

Re: [Rd] More than one package document with the same name

- Original Message - > From: "John McKown" > To: "Jerry Davison" > Cc: r-devel@r-project.org > Sent: Tuesday, August 5, 2014 5:10:28 PM > Subject: Re: [Rd] More than one package document with the same name > > On Tue, Aug 5, 2014 at 5:47 PM, Davison, Jerry > wrote: > > Hi, > > > > I s

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

- Original Message - > From: "Gavin Simpson" > To: "Hadley Wickham" > Cc: r-devel@r-project.org > Sent: Wednesday, August 27, 2014 3:01:53 PM > Subject: Re: [Rd] Re R CMD check checking in development version of R > > On 27 August 2014 15:24, Hadley Wickham wrote: > > > > Is that the

Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?

- Original Message - > From: "Henrik Bengtsson" > To: "R-devel" > Sent: Monday, October 27, 2014 11:16:10 AM > Subject: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX > Mavericks (10.9)? > > I'm trying to help someone to troubleshoot possible OSX Yosemite > issues

Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?

- Original Message - > From: "Dan Tenenbaum" > To: "Henrik Bengtsson" > Cc: "R-devel" > Sent: Monday, October 27, 2014 11:21:59 AM > Subject: Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for > OSX Mavericks (10.9)?

Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?

- Original Message - > From: "Henrik Bengtsson" > To: "Dan Tenenbaum" > Cc: "R-devel" > Sent: Monday, October 27, 2014 12:21:49 PM > Subject: Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for > OSX Mavericks (1

[Rd] proposed: minor change to error message

When checking a package (call it "A") that has "Enhances: B" in DESCRIPTION, I get the message: Package which this enhances but not available for checking: ‘B’ Can this be changed to: Package which enhances this but not available for checking: ‘B’ ? Because really, B is not enhanced by A, B d

[Rd] gsub with perl=TRUE results in 'this version of PCRE is not compiled with Unicode property support' in R-devel

The following code: res <- gsub("(*UCP)\\b(i)\\b", "", "nhgrimelanomaclass", perl = TRUE) results in: Error in gsub(sprintf("(*UCP)\\b(%s)\\b", "i"), "", "nhgrimelanomaclass", : invalid regular expression '(*UCP)\b(i)\b' In addition: Warning message: In gsub(sprintf("(*UCP)\\b(%s)\\b",

[Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK * clean

Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

- Original Message - > From: "Simon Urbanek" > To: "Dan Tenenbaum" > Cc: "R-devel" > Sent: Monday, January 12, 2015 5:50:35 PM > Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place > (R-devel) > > Dan, &g

Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

- Original Message - > From: "Duncan Murdoch" > To: "Dan Tenenbaum" , "Simon Urbanek" > > Cc: "R-devel" > Sent: Monday, January 12, 2015 8:40:07 PM > Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place &

Re: [Rd] Request for help with UBSAN and total absense of CRAN response

- Original Message - > From: "Dirk Eddelbuettel" > To: r-devel@r-project.org > Cc: "Erik Bernhardsson" , "Dirk Eddelbuettel" > > Sent: Tuesday, January 13, 2015 7:30:47 AM > Subject: [Rd] Request for help with UBSAN and total absense of CRAN response > > > CRAN has a package of mine

[Rd] issue with update.packages()

Hello, I see the following issue in R-devel since 'both' has become the default pkgType for binary platforms. update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac). To reproduce this you need

Re: [Rd] problem with update.packages() in R-Devel (3.2.0) on Windows

- Original Message - > From: "Henrik Bengtsson" > To: "John Fox" > Cc: "R-devel" > Sent: Monday, January 26, 2015 11:12:39 AM > Subject: Re: [Rd] problem with update.packages() in R-Devel (3.2.0) on > Windows > > We are several seeing this one. It's a known bug, cf. > https://

Re: [Rd] problem with update.packages() in R-Devel (3.2.0) on Windows

- Original Message - > From: "Henrik Bengtsson" > To: "John Fox" > Cc: "R-devel" > Sent: Tuesday, January 27, 2015 10:15:36 AM > Subject: Re: [Rd] problem with update.packages() in R-Devel (3.2.0) on > Windows > > It works again using: > > % R --version > R Under development

Re: [Rd] A good way to debug a c++ library embedded to R code

- Original Message - > From: "Gabriel Becker" > To: "Charles Novaes de Santana" > Cc: "r-devel" > Sent: Monday, February 2, 2015 12:02:27 PM > Subject: Re: [Rd] A good way to debug a c++ library embedded to R code > > Charles, > > Run R under gdb > > R -d gdb > > You can then set b

Re: [Rd] Notes on building a gcc toolchain for Rtools (but not multilib)

- Original Message - > From: "Duncan Murdoch" > To: "Hsiu-Khuern Tang" , r-devel@r-project.org > Sent: Monday, March 9, 2015 10:40:02 AM > Subject: Re: [Rd] Notes on building a gcc toolchain for Rtools (but not > multilib) > > On 09/03/2015 11:07 AM, Hsiu-Khuern Tang wrote: > > O

Re: [Rd] Notes on building a gcc toolchain for Rtools (but not multilib)

- Original Message - > From: "Duncan Murdoch" > To: "Dan Tenenbaum" > Cc: "Hsiu-Khuern Tang" , r-devel@r-project.org > Sent: Tuesday, March 10, 2015 11:37:12 AM > Subject: Re: [Rd] Notes on building a gcc toolchain for Rtools (but not

Re: [Rd] Notes on building a gcc toolchain for Rtools (but not multilib)

- Original Message - > From: "Duncan Murdoch" > To: "Dan Tenenbaum" > Cc: r-devel@r-project.org > Sent: Wednesday, March 11, 2015 12:06:48 PM > Subject: Re: [Rd] Notes on building a gcc toolchain for Rtools (but not > multilib) > > On 10/0

Re: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3

- Original Message - > From: "John Nash" > To: "Prof Brian Ripley" , r-devel@r-project.org > Sent: Thursday, March 12, 2015 8:15:42 AM > Subject: Re: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3 > > Thanks Brian. > > Indeed, the vignette is in markdown form. When I updated my system t

Re: [Rd] Notes on building a gcc toolchain for Rtools (but not multilib)

- Original Message - > From: "Duncan Murdoch" > Cc: r-devel@r-project.org > Sent: Thursday, March 12, 2015 10:17:23 AM > Subject: Re: [Rd] Notes on building a gcc toolchain for Rtools (but not > multilib) > > I've just uploaded a minor update (3.3.0.1957) to Rtools33, adding > th

Re: [Rd] [Rcpp-devel] Windows gcc toolchain for R 3.2.0

Duncan, - Original Message - > From: "Duncan Murdoch" > To: "R-devel@r-project.org" , > rcpp-de...@r-forge.wu-wien.ac.at > Sent: Wednesday, March 18, 2015 6:27:26 AM > Subject: [Rcpp-devel] Windows gcc toolchain for R 3.2.0 > > To anyone following the Windows toolchain saga: > > The gc

Re: [Rd] CRAN binary, but no source

- Original Message - > From: "Gábor Csárdi" > To: "John McKown" > Cc: r-devel@r-project.org > Sent: Thursday, March 19, 2015 9:03:37 AM > Subject: Re: [Rd] CRAN binary, but no source > > On Thu, Mar 19, 2015 at 11:59 AM, John McKown > > wrote: > [...] > > > > OOPS, I saw the 0.6 packa

Re: [Rd] CRAN binary, but no source

- Original Message - > From: "Gábor Csárdi" > To: "Dan Tenenbaum" > Cc: r-devel@r-project.org, "John McKown" > Sent: Thursday, March 19, 2015 11:15:47 AM > Subject: Re: [Rd] CRAN binary, but no source > > > > &

[Rd] request: check version requirements of Suggests package during R CMD build if install required

Hello, Say a package (call it pkgA) has this in its DESCRIPTION file: Suggests: foo (>= 1.2.3) And yet I only have version 1.2.2 of foo installed, which does not include coolFunction(). pkgA's vignette has this code chunk: library(foo) coolFunction() When I run R CMD build on my package, it w

Re: [Rd] Does (will) CRAN provide consistent integrity verification

- Original Message - > From: "Matt Younce" > To: r-devel@r-project.org > Sent: Thursday, April 16, 2015 9:32:04 AM > Subject: [Rd] Does (will) CRAN provide consistent integrity verification > > Intended Audience: CRAN administrators, maintainers and R Package > Developers. > Does anyon

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

- Original Message - > From: "Charles Determan" > To: r-devel@r-project.org > Sent: Wednesday, May 13, 2015 11:31:36 AM > Subject: [Rd] example fails during R CMD CHECK but works interactively? > > Greetings, > > I am collaborating with developing the bigmemory package and have run > i

[Rd] No R-2.14 beta executable for windows?

The link to the installer exe here: http://cran.fhcrc.org/bin/windows/base/rtest.html ...has been broken for a couple days? Thanks Dan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] No R-2.14 beta executable for windows?

Hi Peter, On Tue, Oct 18, 2011 at 11:24 PM, peter dalgaard wrote: > > On Oct 19, 2011, at 07:52 , Dan Tenenbaum wrote: > >> The link to the installer exe here: >> >> http://cran.fhcrc.org/bin/windows/base/rtest.html >> >> ...has been broken for a cou

Re: [Rd] No R-2.14 beta executable for windows?

On Wed, Oct 19, 2011 at 1:19 PM, Dan Tenenbaum wrote: > Hi Peter, > > On Tue, Oct 18, 2011 at 11:24 PM, peter dalgaard wrote: >> >> On Oct 19, 2011, at 07:52 , Dan Tenenbaum wrote: >> >>> The link to the installer exe here: >>> >>> http://cra

[Rd] Bug in Sys.which()?

At a Windows command prompt: C:\>which ls /cygdrive/c/Rtools215/bin/ls C:\>which perl /cygdrive/c/perl/bin/perl In R: > Sys.which(c("ls", "perl")) lsperl "c:\\RTOOLS~3\\bin\\ls.exe" "" Is this expected behavior? > session

Re: [Rd] Bug in Sys.which()?

On Mon, Nov 28, 2011 at 2:34 PM, Duncan Murdoch wrote: > On 11-11-28 5:20 PM, Dan Tenenbaum wrote: >> >> At a Windows command prompt: >> C:\>which ls >> /cygdrive/c/Rtools215/bin/ls >> >> C:\>which perl >> /cygdrive/c/perl/b

Re: [Rd] Vignette using parallel's makeCluster function has trouble building on Windows 7

Hi Rich, On Mon, Dec 5, 2011 at 4:19 PM, Rich Calaway wrote: > Hi, all-- > > I've been working on a doParallel package to provide a foreach > parallel backend for the new parallel package, but I am having trouble > building the vignette. On my system, if I use the following minimal > vignette (ca

[Rd] paste0 bug in install.packages() - leopard installer?

Hello, I get the following: > install.packages("abind", repos="http://cran.fhcrc.org";, type="source") trying URL 'http://cran.fhcrc.org/src/contrib/abind_1.4-0.tar.gz' Content type 'application/x-gzip' length 19642 bytes (19 Kb) opened URL == downl

[Rd] error starting R-devel with --arch ppc -- "an unusual circumstance has arisen"

When I try and start R-devel as follows: R --vanilla --arch ppc I see this, over and over again, ^C does not interrupt it and I have to close the terminal window: > Error in paste0(prefix, conditionMessage(e), "\n") : not a BUILTIN function In addition: Warning message: An unusual circumstance

Re: [Rd] error starting R-devel with --arch ppc -- "an unusual circumstance has arisen"

; > The really strange thing is that the build logs show success, but the build > directory is old and the resulting tar ball is not updated. I'll keep you > posted. It looks like this has been fixed. Thanks! Dan > > Cheers, > Simon > > > > On Dec 15, 201

Re: [Rd] Reference class finalize() fails with 'attempt to apply non-function'

On Thu, Dec 8, 2011 at 2:52 PM, Martin Morgan wrote: > This bug appears intermittently in R CMD check when reference classes have > finalize methods. The problem is that garbage collection can be run after > the methods package is no longer available. It affects (periodically) the > Bioconductor A

Re: [Rd] problem with R installation package

2012/1/9 Gallon Régis : > Dear, > > I have created my first package "G2Sd : Grain Size Statistiques and > Description". I submitted it to the CRAN after I have checked the tar.gz > file. All was ok, but since it is on the CRAN I can't install it : > > In getDependencies(pkgs, dependencies, availabl

Re: [Rd] Updated Windows toolchain

On Mon, Nov 28, 2011 at 11:56 PM, Prof Brian Ripley wrote: > An updated toolchain is now being used for Windows' builds of R-devel: > details are in the R-admin manual and at > http://www.murdoch-sutherland.com/Rtools/ and > http://www.stats.ox.ac.uk/pub/Rtools/ > Thanks for the update. I saw tha

Re: [Rd] Updated Windows toolchain

Hello, On Mon, Jan 9, 2012 at 12:28 AM, Prof Brian Ripley wrote: > CRAN Windows binary packages built for R-devel are now online, and Uwe's > winbuilder has gained the ability to check source packages under R-devel. > > Windows check results are available from > http://cran.r-project.org/bin/wind

Re: [Rd] Updated Windows toolchain

Hi Uwe, 2012/1/18 Uwe Ligges : > > > On 18.01.2012 01:09, Dan Tenenbaum wrote: >> >> Hello, >> >> On Mon, Jan 9, 2012 at 12:28 AM, Prof Brian Ripley >>  wrote: >>> >>> CRAN Windows binary packages built for R-devel are now online, and Uw

Re: [Rd] Updated Windows toolchain

2012/1/19 Uwe Ligges : > For the records: This rsync infelicity has been solved in the meantime. I can confirm that it works; just downloaded r58140. Thanks! Dan > > Uwe Ligges > > > On 19.01.2012 02:03, Dan Tenenbaum wrote: >> >> Hi Uwe, >> >> 2012/1/18

Re: [Rd] scan() doesn't like '1.#IND'

2012/2/8 Duncan Murdoch : > On 12-02-08 8:59 PM, Hervé Pagès wrote: >> >> Hi, >> >> Since C++ code compiled with g++ 4.6.3 on Windows (the version included >> in latest Rtools) now can produce things like '1.#IND' when writing >> doubles to a file (using the<<  operator), I wonder whether scan() >>

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