Re: [Bioc-devel] on the subject of combine, cbind and rbind

Well, combine() has been extremely useful in my work and I would love to have a version for SummarizedExperiment's. I do appreciate that it might not be the job of cbind. merge did the work for me for DataFrame's. Best, Kasper On Tue, Jul 12, 2016 at 4:24 PM, Hervé Pagès

Re: [Bioc-devel] Rhtslib 1.5.3 fails on install

Hi Johannes, On 07/12/2016 09:06 AM, Johannes Helmuth wrote: Dear Bioconductor Developers, I use `Rhtslib` in two Bioconductor packages, namely `bamsignals` and `normr`. Apparently, the development version of `Rhtslib` (version 1.5.3) fails on install because automake is not available on the

Re: [Bioc-devel] on the subject of combine, cbind and rbind

Hi Kasper, On 07/12/2016 09:31 AM, Kasper Daniel Hansen wrote: combine() is the old style way of combining ExpressionSets and friends and is pretty powerful, for example dealing with pData objects with different columns (which is the case for almost all data). It seems to me that cbind() on

Re: [Bioc-devel] GenRank package build error 0.99.4

- Original Message - > From: "Chakravarthi Kanduri" > To: "bioc-devel" > Sent: Tuesday, July 12, 2016 12:37:29 PM > Subject: Re: [Bioc-devel] GenRank package build error 0.99.4 > Dear Bioconductor developers, > > The latest build of

Re: [Bioc-devel] GenRank package build error 0.99.4

Dear Bioconductor developers, The latest build of GenRank package (development version) shows error (http://bioconductor.org/checkResults/devel/bioc-LATEST/GenRank/). The package was built successfully on my local computer and on Travis, but fails on Bioconductor build system. When I checked

Re: [Bioc-devel] on the subject of combine, cbind and rbind

Seems like merge() might be the appropriate verb here. On Tue, Jul 12, 2016 at 9:31 AM, Kasper Daniel Hansen wrote: > combine() is the old style way of combining ExpressionSets and friends and > is pretty powerful, for example dealing with pData objects with

Re: [Bioc-devel] normr 0.99.5 Test Coverage "unknown"

obviously "cannot do the coverage report" On Tue, Jul 12, 2016 at 12:32 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > Without knowing the details it seems self-evident to me that the build > system can do the coverage report if the package doesn't build. > > Best, > Kasper >

Re: [Bioc-devel] normr 0.99.5 Test Coverage "unknown"

Without knowing the details it seems self-evident to me that the build system can do the coverage report if the package doesn't build. Best, Kasper On Tue, Jul 12, 2016 at 12:29 PM, Johannes Helmuth wrote: > Dear Bioconductor Developers, > > I recently contributed a

[Bioc-devel] on the subject of combine, cbind and rbind

combine() is the old style way of combining ExpressionSets and friends and is pretty powerful, for example dealing with pData objects with different columns (which is the case for almost all data). It seems to me that cbind() on SummarizedExperiments is much less powerful. Specifically rbind()

[Bioc-devel] normr 0.99.5 Test Coverage "unknown"

Dear Bioconductor Developers, I recently contributed a package `normR` for calling enrichment and differences in ChIP-seq data (http://bioconductor.org/packages/normr/). To test the functionality of the package, I used `testthat`. All the tests run well when using `testthat::test()`, `R CMD

[Bioc-devel] Rhtslib 1.5.3 fails on install

Dear Bioconductor Developers, I use `Rhtslib` in two Bioconductor packages, namely `bamsignals` and `normr`. Apparently, the development version of `Rhtslib` (version 1.5.3) fails on install because automake is not available on the Bioconductor build system (see

[Bioc-devel] 48-hour build cycle for devel packages

Developers, We're temporarily switching to a 48-hour (instead of 24-hour) build cycle for devel packages. The new schedule is as follow: 1) Builds will start on Saturdays, Mondays, and Wednesdays at 7:15 pm (Seattle time) every week. 2) Build reports will be generated about 32 hours