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()

[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] 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

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] 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

- 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 >

[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

[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(

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

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

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

[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] 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 > > > > &

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] [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] 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] 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" > 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] 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: "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] 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] 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] 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://

[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] 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

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] 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

[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

[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] 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

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

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: "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] 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] 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] 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

[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] 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

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

[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] 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

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] [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: "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

[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] "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

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

[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] 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] 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] "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] 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] 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] 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] 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

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] "Failed to locate the 'texi2pdf' output file"

m. Duncan's suggestion about a virus scanner is a good one, but there is no such software running on the machine in question. So it sounds maybe more like what Henrik describes above. Wondering if there are more insights to be had... Thanks, Dan >> >> Kasper >> >> &g

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

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "

[Rd] broken link to binary of R-3.0 RC

Hi, >From http://cran.r-project.org/bin/windows/base/rtest.html I clicked on: Download R-3.0.0 RC build for Windows and got Object not found for http://cran.r-project.org/bin/windows/base/R-3.0.0rc-win.exe Thanks, Dan __ R-devel@r-project.org mailin

Re: [Rd] Description depends line for windows only

On Fri, Mar 22, 2013 at 9:44 AM, Andrew Redd wrote: > I am developing a package that is only applicable on windows, is there a > line I can put in the depends field of the DESCRIPTION file to tell that > this should only be build for windows? > OS_type: windows See RShowDoc("R-exts") Section 1

Re: [Rd] missing space in R version specifier makes PACKAGES file unreadable by install.packages()

On Thu, Mar 21, 2013 at 10:28 AM, Duncan Murdoch wrote: > On 21/03/2013 12:59 PM, Dan Tenenbaum wrote: >> >> On Thu, Mar 21, 2013 at 9:52 AM, Dan Tenenbaum wrote: >> > Hi, >> > >> > After updating to R-3.0 beta r62328, I get the following: >>

Re: [Rd] missing space in R version specifier makes PACKAGES file unreadable by install.packages()

On Thu, Mar 21, 2013 at 9:52 AM, Dan Tenenbaum wrote: > Hi, > > After updating to R-3.0 beta r62328, I get the following: > >> install.packages("Biobase", type="source", >> repos="http://george2/BBS/2.12/bioc";) > Error in do.call(o

[Rd] missing space in R version specifier makes PACKAGES file unreadable by install.packages()

Hi, After updating to R-3.0 beta r62328, I get the following: > install.packages("Biobase", type="source", > repos="http://george2/BBS/2.12/bioc";) Error in do.call(op, list(v_c, v_t[[op]])) : could not find function "R (>=2.15.1)" The problem can be fixed by adding a space after >= in the of

[Rd] Failed to locate 'weave' output file / vignette product does not have a known filename extension

Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ’BitSeq.Rnw' failed with

Re: [Rd] question on why Rigroup package moved to Archive on CRAN

On Sat, Mar 9, 2013 at 2:17 PM, Kevin Hendricks wrote: > Hi, > One last quick question ... does anyone archive older CRAN package check > summaries? I searched the web but could not find any. My package was > archived in February of this year so any package check summary from earlier > than t

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

On Mon, Mar 4, 2013 at 2:15 PM, Steve Lianoglou wrote: > On Mon, Mar 4, 2013 at 4:28 PM, Aaron Mackey wrote: >> On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm wrote: >> >>> * where do the dragons lurk >>> >> >> webs of interconnected dynamically loaded libraries, identical versions of >> R compil

[Rd] png() problem with R-devel on Mac

> png(tempfile()) Error in .External(C_Quartz, "png", path.expand(filename), width, height, : Incorrect number of arguments (12), expecting 11 for 'Quartz' > sessionInfo() R Under development (unstable) (2013-02-24 r62054) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF

Re: [Rd] concurrent requests (Rook, but I think the question is more general)

On Thu, Oct 25, 2012 at 8:45 AM, Richard D. Morey wrote: > On 24/10/12 10:55 PM, Simon Urbanek wrote: >> >> >> The point is that you need a separate monitoring process or threads. That >> process can be R, Rserve or any thing else. >> >> >> > > Thanks for the tips. This is what I'm currently conte

Re: [Rd] concurrent requests (Rook, but I think the question is more general)

On Wed, Oct 24, 2012 at 11:13 AM, Richard D. Morey wrote: > This question involves Rook, but I think the answer will be general enough > that it pays to post here. At any rate, I don't know enough to know whether > this is a Rook only issue or a general R issue. > > Here's what I'd like to do (and

Re: [Rd] Straight-quotes for usage and examples sections in PDF docs?

On Mon, Aug 6, 2012 at 3:01 PM, Mike Lawrence wrote: > Is there any way to ensure that quotation marks are left as straight > quotes and not converted to curly quotes in the \usage and \examples > sections when the pdf versions of the docs are created? > Perhaps if the R session that builds the p

[Rd] 7 arguments passed to .Internal(identical) which requires 6

I know this has come up before on R-help (http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal-identical-which-requires-6-td4548460.html) but I have a concise reproducible case that I wanted to share. Also, please note the Bioconductor scenario which is potentially seriously impacted by th

Re: [Rd] Best way to locate R executable from within R?

On Tue, May 22, 2012 at 10:34 AM, Henrik Bengtsson wrote: > Hi, > > I'd like to spawn of a new R process from within R using system(), > e.g. system("R -f myScript.R").  However, just specifying "R" as in > that example is not guaranteed to work, because "R" may not be on the > OS's search path.

[Rd] Creating a reference manual during R CMD build

I'd like to have a way to create reference manuals during R CMD build (and have them go in the build/ directory of the resulting package tarball), whether or not any of my Rd files have \Sexpr macros in them. It seems like there are a couple of ways to suppress the building of manuals during R CMD

Re: [Rd] Missing Windows binary for R-2.15RC?

source. Dan > > On 27/03/2012 17:48, Dan Tenenbaum wrote: >> >> On Sat, Mar 24, 2012 at 1:07 PM, Duncan Murdoch >>  wrote: >>> >>> On 12-03-24 2:31 PM, Simon Urbanek wrote: >>>> >>>> >>>> >

Re: [Rd] Missing Windows binary for R-2.15RC?

gt;> >>>> >>>> On 24.03.2012 06:58, Daniel Nordlund wrote: >>>>>> >>>>>> -Original Message- >>>>>> From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] >>>>>> Sent: Friday, March 23, 2012 5:48 PM >>>>>> To:

Re: [Rd] Missing Windows binary for R-2.15RC?

On Fri, Mar 23, 2012 at 4:52 PM, Daniel Nordlund wrote: >> -Original Message- >> From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] >> On Behalf Of Dan Tenenbaum >> Sent: Friday, March 23, 2012 12:21 PM >> To: r-devel@r-project.org &g

[Rd] Missing Windows binary for R-2.15RC?

Hi, The page http://cran.r-project.org/bin/windows/base/rtest.html has a link to: http://cran.r-project.org/bin/windows/base/R-2.15.0rc-win.exe However, clicking on that link gives a 404 "Object not found' error. FYI. Dan __ R-devel@r-project.org mail

Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

On Tue, Mar 20, 2012 at 12:14 PM, Duncan Murdoch wrote: > This should now be fixed in R-devel, and shortly in the 2.15.0 beta. Thanks very much. Dan > > Duncan Murdoch > > > On 12-03-20 2:54 PM, Dan Tenenbaum wrote: >> >> On Tue, Mar 20, 2012 at 11:51 AM, Duncan

Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

On Tue, Mar 20, 2012 at 11:51 AM, Duncan Murdoch wrote: > On 12-03-20 1:46 PM, Dan Tenenbaum wrote: >> >> On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch >>  wrote: >>> >>> On 12-03-20 1:25 PM, Dan Tenenbaum wrote: >>>> >>>> >&

Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch wrote: > On 12-03-20 1:25 PM, Dan Tenenbaum wrote: >> >> On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch >>  wrote: >>> >>> On 12-03-19 10:27 PM, Dan Tenenbaum wrote: >>>> >>>> >&

Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch wrote: > On 12-03-19 10:27 PM, Dan Tenenbaum wrote: >> >> Hello, >> >> Sorry to repeat myself, but I was wondering if anyone had taken a look at >> this. > > > No.  Could you put together a simple self c

Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

On Wed, Mar 14, 2012 at 1:13 PM, Dan Tenenbaum wrote: > Hi, > > The following command: > R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd > run against this file: > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-pack

[Rd] issue with Rd2pdf and \Sexpr in Rd files

Hi, The following command: R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd run against this file: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd (username: readonly; password: readonly) produces a very verbose error (see below)

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() >>

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] 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

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

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] 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] 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] 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

[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

[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

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

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

[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] 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

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

[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] 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: >>>

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