[Rd] Problem installing R-devel data 4 March 2016.

I am trying to install the latest development version of R so as to be able to perform a package check according the rules specified for CRAN. I performed the following steps: (1) Downloaded R-devel.tar.gz, dated 04-Mar-2016 03:21, from CRAN (2) Upacked. (3) Created directory "BldDir" next

Re: [Bioc-devel] Imports, depends and warnings

So a preliminary diagnosis is that some packages are not building even though they build in the nightly builds. The problem could be a newer compiler, newer R-devel, slightly different OS (debian vs ubuntu) or something else. Investigating further. However, in the meantime,

Re: [Bioc-devel] Imports, depends and warnings

Can you be more specific about which docker image you pulled? Dan - Original Message - > From: "Federico Marini" > To: "Martin Morgan" , "bioc-devel" > > Sent: Thursday, March 3, 2016 1:20:46 AM > Subject:

Re: [Bioc-devel] License question for experimental data package

Thank you all for the useful suggestions and links. I like the idea of using a CC0 license. That's likely what I will go for. Best, davide On Fri, Mar 4, 2016 at 7:42 AM Tim Triche, Jr. wrote: > I was going to mention droit d'auteur under EU common law, but somehow >

Re: [Rd] vignette index

Within R these are determined by \VignetteIndexEntry{}. I think you are referring to the order on the CRAN landing page for your package https://cran.r-project.org/web/packages/bst/index.html, and then the question is for a CRAN member. In Rnw \documentclass{article} %

Re: [Rd] ALLOCATE in a FORTRAN subroutine

Hi, Until you get a more definitive answer, I will make an attempt to give some advice. When using an assumed sized array (i.e. REAL*8 array1(*)) you still need to allocate the memory prior to calling the Fortran subroutine, so you would still need to know its maximum length. Arrays created

Re: [Rd] vignette index

I think the online order of vignette files are not based on vignette title or filename alphabetically. I am just curious: by what order these vignette files were displayed online so I can make changes accordingly? Thanks, Zhu -Original Message- From: Duncan Murdoch

Re: [Bioc-devel] Package reference manuals in html

Using the integrated help system is nice, but isn't always ideal. Just for example: when I'm ssh'd into my work cluster I don't get a nice web page, I instead get the ascii-formatted version, which is considerably harder to read and doesn't include proper links. Running a second local instance

Re: [Rd] vignette index

On 04/03/2016 9:44 AM, Wang, Zhu wrote: Dear helpers, I have multiple vignette files for a package, and I would like to have the "right" order of these files when displayed online. For instance, see below: https://cran.r-project.org/web/packages/bst/index.html The order of vignette links on

Re: [Bioc-devel] spliceSites Vignette build error

I can reproduce the error quite consistently by running either R CMD build or by sourcing the Stangled vignette. Here is my sessionInfo after doing the latter. If you are running an older R devel please update it. > sessionInfo() R Under development (unstable) (2016-02-25 r70222) Platform:

Re: [Bioc-devel] Identify Bioc build machines

There are a number of variables defined. You could check to see if the variable BBS_HOME is defined (it does not matter what the value is in your case, just whether it is defined or not). Dan - Original Message - > From: "Thomas Dybdal Pedersen" > To:

Re: [Rd] vignette index

This probably belongs on r-package-de...@r-project.org as it is not about the development of R itself, but about package development. -- Brian On Fri, 2016-03-04 at 14:44 +, Wang, Zhu wrote: > Dear helpers, > > I have multiple vignette files for a package, and I would like to have the >

Re: [Bioc-devel] spliceSites Vignette build error

Are you using R-devel on your computer? - Original Message - > From: "Wolfgang Kaisers" > To: "bioc-devel" > Sent: Friday, March 4, 2016 12:41:30 AM > Subject: [Bioc-devel] spliceSites Vignette build error > Dear All, > >

[Rd] vignette index

Dear helpers, I have multiple vignette files for a package, and I would like to have the "right" order of these files when displayed online. For instance, see below: https://cran.r-project.org/web/packages/bst/index.html The order of vignette links on CRAN is different from what I hoped for:

Re: [Bioc-devel] License question for experimental data package

I am pretty sure in general "data" is not copyrightable per se ( http://www.lib.umich.edu/copyright/facts-and-data), so while I might contact the original authors as a courtesy, if the data has been released into any public database, then you should be free to do with it as you please. Providing

Re: [Bioc-devel] Package reference manuals in html

Hi, this is just to clarify the relation between the two github repos https://github.com/Bioconductor-mirror/BiocStyle and https://github.com/Bioconductor/BiocStyle mentioned by Martin: actually, these two are perfectly in sync right now. The "This branch is 3 commits ahead, 3 commits behind

Re: [Rd] as.vector in R-devel loaded 3/3/2016

> Morgan, Martin > on Fri, 4 Mar 2016 12:36:25 + writes: > I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to

Re: [Rd] as.vector in R-devel loaded 3/3/2016

Thanks. Indeed I was having a permission issue installing/updating packages and had put a version of Matrix in my personal library which must have been getting loaded ahead of the one in revel library. Sorry for the bother. On Friday, March 4, 2016, Morgan, Martin

Re: [Bioc-devel] Package reference manuals in html

One thing about accessing the html versions locally (e.g., via ? with options(help_type="html")] or help.start() or Rstudio) is that you get the version relevant to your R / Bioconductor, rather than whatever is at the top of google; I guess the same applies to the pdf versions, and the reason

Re: [Rd] R 3.2.4 rc issue

On 4 March 2016 at 09:11, peter dalgaard wrote: | Thanks for the info, Dirk. | | The tarball builds don't run make check (because of a policy decision that it is better to have the sources available on all platforms for testing than to have none if it breaks on a single platform). However the

Re: [Rd] as.vector in R-devel loaded 3/3/2016

I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to reproduce Jeff's error, though. > library(Matrix) > as.vector function (x, mode = "any")

Re: [Rd] ALLOCATE in a FORTRAN subroutine

On 04/03/2016 3:34 AM, MAURICE Jean - externe wrote: Hi, I am a FORTRAN developer and I am 'translating' R functions in FORTRAN subroutines. I am 'new' to R. It's my first question in this mailing-list and English is not my natural language. Very often, an R function gives an 'array' as

[Rd] ALLOCATE in a FORTRAN subroutine

Hi, I am a FORTRAN developer and I am 'translating' R functions in FORTRAN subroutines. I am 'new' to R. It's my first question in this mailing-list and English is not my natural language. Very often, an R function gives an 'array' as result and you don't have to bother with the dimension of

Re: [Rd] as.vector in R-devel loaded 3/3/2016

> peter dalgaard > on Fri, 4 Mar 2016 09:21:48 +0100 writes: > Er, until _what_ is fixed? > I see no anomalies with the version in R-pre: Indeed. The problem ... I also have stumbled over .. is that I'm sure Jeff is accidentally loading a different version

[Bioc-devel] Identify Bioc build machines

Hi Are there any environment variables set on the bloc build machines that unique identify them as such? The reason I ask is that I’m planning to create a testthat PR that adds a skip_on_bioc (similar to skip_on_cran) function. While I know you generally shouldn’t skip unit tests on build

Re: [Bioc-devel] SVN Commit - Problem with the Version Number

Dear all, Thanks a lot for your help. I managed to commit the new version of the package to the release branch. Many thanks again for your replies. Best, Sandro On 3 Mar 2016 16:28, "Dan Tenenbaum" wrote: > You can merge from devel into release (as long as it's only bug

Re: [Rd] as.vector in R-devel loaded 3/3/2016

Er, until _what_ is fixed? I see no anomalies with the version in R-pre: > library(Matrix) > as.vector standardGeneric for "as.vector" defined from package "base" function (x, mode = "any") standardGeneric("as.vector") Methods may be defined for arguments: x, mode Use