Re: [Bioc-devel] Question about BiocGeneric::order

On 05/11/2017 06:44 PM, Hervé Pagès wrote: Hi Michael, On 05/11/2017 03:27 PM, Michael Lawrence wrote: There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a

Re: [Bioc-devel] Question about BiocGeneric::order

Hi Michael, On 05/11/2017 03:27 PM, Michael Lawrence wrote: There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a default for the 'method' argument that

Re: [Bioc-devel] Question about BiocGeneric::order

There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a default for the 'method' argument that differs from that of the generic. Since R 3.3, base::order() is smart

Re: [Bioc-devel] Question about BiocGeneric::order

Thank you Hervé, I got that. Good to know that BioC 3.6 require R 3.4.0. Yours Sincerely, Jianhong Ou TEL: 508-856-5379 LRB 608 Bioinformatician of Bioinformatics core at Department of Molecular, Cell and Cancer Biology UMASS Medical School 364 Plantation Street Worcester, MA 01605

Re: [Bioc-devel] Question about BiocGeneric::order

Hi Jianhong, I can't reproduce this but I'm using R 3.4.0. You seem to be using Bioc devel (aka BioC 3.6) with R devel. This is not supported. Both, BioC 3.5 (current release) and BioC 3.6 require R 3.4.0. Cheers, H. On 05/11/2017 01:11 PM, Ou, Jianhong wrote: I got error when I try order

[Bioc-devel] Question about BiocGeneric::order

I got error when I try order for Rle object by following codes: library("BiocGenerics") library(XVector) order(Rle(1)) ## Error in match.arg(method) : 'arg' must be of length 1 > sessionInfo() R Under development (unstable) (2017-05-10 r72667) Platform: x86_64-apple-darwin16.5.0 (64-bit) Running

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On Thu, 2017-05-11 at 12:23 +, Martyn Plummer wrote: > On Thu, 2017-05-11 at 06:37 -0500, Dirk Eddelbuettel wrote: > > On 11 May 2017 at 10:17, Erwan Le Pennec wrote: > > >  Dear all, > > > > > >  I've stumbled a similar issue with the package cluster when  > > > compiling the 3.4.0

Re: [Rd] R-3.3.3/R-3.4.0 change in sys.call(sys.parent())

Here is a case where the current scheme fails: > with(datasets::mtcars, xyplot(mpg~wt|gear)$call) xyplot(substitute(expr), data, enclos = parent.frame()) Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, May 11, 2017 at 1:09 AM, Deepayan Sarkar wrote: > On

[Bioc-devel] unable to push local changes to bioconductor svn repository

Hi, I got a new Linux computer, cloned my package from github, made some changes. I am able to update the changes to github, but can not push it to Bioconductor svn repository. Can someone help me to solve the problem. The following is what I did: git svn clone

Re: [R-pkg-devel] Re-creating vignettes after update of data or different mechanism to create reports?

> On 11 May 2017, at 15:49, Duncan Murdoch wrote: > > On 11/05/2017 8:31 AM, Rainer Krug wrote: >> Hi >> >> I am building two packages: >> >> - a data package which contains the data and function to extract it (several >> datasets, linked, like an sql database) and

Re: [R-pkg-devel] Guidance on importind multiple text files for @example

Hi, I am creating a function ftsc(x) where x is given by: x<-cname <- file.path("C:/Users/anand/Desktop/Internship", "dataftc") In the dataftc folder I have stored all the text files to be clustered by my function. So, while creating the package I have to include an example and that is my problem.

Re: [R-pkg-devel] Guidance on importind multiple text files for @example

On 11/05/2017 6:42 AM, ujjwal anand wrote: Hello Sir/Ma'am, I am trying to build a package on R. But my function, which takes a folder full of text files as an argument. So, could you please share some ideas on how to import a folder (which contains multiple text files) for "@example". Not

Re: [R-pkg-devel] Fwd: Re-creating vignettes after update of data or different mechanism to create reports?

> On 11 May 2017, at 14:59, Holger Hoefling wrote: > > Hi Rainer, > > thanks for the explanation. No problem. > You probably already considered this - but you could version-bump the > analysis package with every data package update (and make the latest data > package

Re: [R-pkg-devel] Fwd: Re-creating vignettes after update of data or different mechanism to create reports?

Hi Rainer, thanks for the explanation. You probably already considered this - but you could version-bump the analysis package with every data package update (and make the latest data package the minimum requirement). Given how large the data package is - the overhead of an analysis package

[R-pkg-devel] Fwd: Re-creating vignettes after update of data or different mechanism to create reports?

Sorry - forgot to cc the list > Begin forwarded message: > > From: Rainer Krug > Subject: Re: [R-pkg-devel] Re-creating vignettes after update of data or > different mechanism to create reports? > Date: 11 May 2017 at 14:41:03 GMT+2 > To: Holger Hoefling >

[R-pkg-devel] Re-creating vignettes after update of data or different mechanism to create reports?

Hi I am building two packages: - a data package which contains the data and function to extract it (several datasets, linked, like an sql database) and - an analysis package which contains functions to analyse the data in the data package and depends on the data package. The data package is

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On Thu, 2017-05-11 at 06:37 -0500, Dirk Eddelbuettel wrote: > On 11 May 2017 at 10:17, Erwan Le Pennec wrote: > >  Dear all, > > > >  I've stumbled a similar issue with the package cluster when  > > compiling the 3.4.0 version with the settings of Fedora RPM specs.  > > Compiling R with

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On 11 May 2017 at 10:17, Erwan Le Pennec wrote: | Dear all, | | I've stumbled a similar issue with the package cluster when | compiling the 3.4.0 version with the settings of Fedora RPM specs. | Compiling R with the default setting of configure yields a version that | works for

[R-pkg-devel] Guidance on importind multiple text files for @example

Hello Sir/Ma'am, I am trying to build a package on R. But my function, which takes a folder full of text files as an argument. So, could you please share some ideas on how to import a folder (which contains multiple text files) for "@example". Thanks, Ujjwal Anand [[alternative HTML

Re: [Rd] xrealloc namespace conflict

On 11 May 2017 at 12:16, Patrick Perry wrote: | I've done a bit more investigation into this issue. Here is my current | understanding of the situation: | | 1. I have a package on CRAN (corpus-0.3.1) that passes tests on all | platforms except for Linux. | 2. My package defines a C function,

Re: [Rd] xrealloc namespace conflict

I've done a bit more investigation into this issue. Here is my current understanding of the situation: 1. I have a package on CRAN (corpus-0.3.1) that passes tests on all platforms except for Linux. 2. My package defines a C function, "xrealloc", for internal use. 3. The libreadline library

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

Dear all, I've stumbled a similar issue with the package cluster when compiling the 3.4.0 version with the settings of Fedora RPM specs. Compiling R with the default setting of configure yields a version that works for cluster... and nlme. I did not find the exact option that

Re: [Rd] R-3.3.3/R-3.4.0 change in sys.call(sys.parent())

On Wed, May 10, 2017 at 2:36 AM, William Dunlap via R-devel wrote: > Some formula methods for S3 generic functions use the idiom > returnValue$call <- sys.call(sys.parent()) > to show how to recreate the returned object or to use as a label on a > plot. It is often