Re: [R-pkg-devel] Checking for C++11

On 16 November 2015 at 16:45, Marvin Wright wrote: | Thanks, that helped. However, a user with gcc < 4.7 will still get cryptic | errors. | | I had another idea: I created a file src/AAA_check_cpp11.cpp, checking the | preprocessor directive “__cplusplus”, see

[Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

I have published `RTCGA.rnaseq` R package that provides datasets from TCGA project containig RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like `RTCGA.RNAseq` and if that's possible, how should I do that and to whom should I

Re: [R-pkg-devel] Checking for C++11

Thanks, that helped. However, a user with gcc < 4.7 will still get cryptic errors. I had another idea: I created a file src/AAA_check_cpp11.cpp, checking the preprocessor directive “__cplusplus”, see

Re: [R-pkg-devel] Checking for C++11

On 16 November 2015 at 13:07, Marvin Wright wrote: | I would like to check for C++11 support in a package. The package requires gcc >= 4.7 or clang >= 3.0. Windows is handled differently in Makevars.win. I tried two approaches in Makevars so far, but both give warnings in CRAN checks. | |

Re: [Bioc-devel] Unexpected behaviour with Assays and Vector classes

Hi Aaron, On 11/15/2015 12:37 PM, Aaron Lun wrote: Hi Herve, I would have expected GRanges behaviour, where the metadata is affected by the replacement. For example, with GRanges objects, I often use the metadata to store statistics or descriptors relevant to each genomic interval, e.g., peak

Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

Hi Marcin, It's technically possible to change the name. In order to try to keep this the less disruptive, we would only do this in devel and we would need to create a new package there by cloning the current package and changing its name. Then we would add a deprecation/redirection message in

Re: [Rd] Best way to implement optional functions?

On 16/11/2015 4:00 AM, Richard Cotton wrote: On 22 October 2015 at 22:55, Duncan Murdoch wrote: I'm planning on adding some new WebGL functionality to the rgl package, but it will pull in a very large number of dependencies. Since many people won't need it, I'd like

Re: [Rd] Best way to implement optional functions?

Roxygen2 documents imported and re-exported functions. See http://www.r-bloggers.com/roxygen2-5-0-0/ Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance

Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

Hello, How does your package differ to importing GSE62944 into R with AnnotationHub http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It seems like unnecessary duplication. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW

Re: [Bioc-devel] Base class for interaction data - expressions of interest

While I'm on this point, there's another, more subtle issue with using sparseMatrix(). Specifically, there's a distinction between zeros and missing values when considering a ContactMatrix. For example, in Hi-C data, a zero in the matrix means there aren't any read pairs mapping between the

[Rd] Small request of a feature improvement in the next version of R

Hi Everyone, Sorry to bother the list with this small request, but I've run into this issue and was wondering if it could be fixed in the next version of R. Sorry if it was raised in a previous thread: So when I try the following I get an error: > m <- list() >

Re: [Rd] Best way to implement optional functions?

On 22 October 2015 at 22:55, Duncan Murdoch wrote: > I'm planning on adding some new WebGL functionality to the rgl package, but > it will pull in a very large number of dependencies. Since many people won't > need it, I'd like to make the new parts optional. > Can

Re: [Bioc-devel] Base class for interaction data - expressions of interest

Hello all, I thought I might give an update on the state of affairs for the InteractionSet package. Currently, there's three classes: - the GInteractions class, inheriting from Vector and intended to represent pairwise interactions between genomic regions (based on suggestions from Malcolm

Re: [Bioc-devel] Unexpected behaviour with Assays and Vector classes

Hi Aaron, On 11/16/2015 09:39 AM, Hervé Pagès wrote: Hi Aaron, On 11/15/2015 12:37 PM, Aaron Lun wrote: Hi Herve, I would have expected GRanges behaviour, where the metadata is affected by the replacement. For example, with GRanges objects, I often use the metadata to store statistics or