[Bioc-devel] Problems with converting GPos to GRanges.

Hello, I am trying to make the CAGEr package (1.27.2) pass its regression tests, and I am still struggling with the refactoring of GPos to UnstitchedGPos and StitchedGPos in the devel branch of Bioconductor... Currently, my problem is with the following command: promoters(GRanges(CTSScoordinat

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

Thanks Nitesh, The only reason DMRcatedata isn't passing BiocCheck is because of package numbering and the fact that the old version already exists - which this new version is supposed to overwrite (http://bioconductor.org/spb_reports/DMRcatedata_buildreport_20190912205035.html)

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

On 9/12/19 15:13, Pages, Herve wrote: > Hi Paul, > > On 9/12/19 11:47, Paul Shannon wrote: >> My package igvR requires a web browser. Unit tests, examples, vignette all >> will all fail if one is not available. >> >> Since the bioc build system, for good reason, does not provide a web >> browse

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

Thanks, Herve. How can I determine if a web browser is indeed installed? Sys.getenv("R_BROWSER”) returns: macOS: “/usr/bin/open” ubuntu: “xdc-open” I don’t think either of these actually reveals an actual and functioning installation. Other ideas? - Paul > On Sep 12, 2019, at 3:13 PM,

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

Hi Paul, On 9/12/19 11:47, Paul Shannon wrote: > My package igvR requires a web browser. Unit tests, examples, vignette all > will all fail if one is not available. > > Since the bioc build system, for good reason, does not provide a web browser, > I’d like to condition all browser-related cod

[Bioc-devel] R environment variable which indicates "running in the bioc build system"?

My package igvR requires a web browser. Unit tests, examples, vignette all will all fail if one is not available. Since the bioc build system, for good reason, does not provide a web browser, I’d like to condition all browser-related code on “not executing in the bioc build system”. Is there

Re: [Bioc-devel] Change package name

We don't encourage renaming of packages but there is a process for it. We will email you off list to provide further details. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 _

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

On this topic, one way of staying abreast of conflicts as you introduce them during the evolution of a project through use of the `conflicted` library toward the top of your project, usage modelled as follows: ``` ## Force use of package prefixes for ALL conflicting function names ## lacking reg

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

You don’t have to list it in your Namespace so long as it’s in your description file. This should fix the problem. On Thu, Sep 12, 2019 at 2:07 AM wrote: > Dear all, > > I am developing a Bioconductor package and have a problem with two > methods which have the same name. I am using the reduce()

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

In order to remove the warning message, you can do the following to import both packages, @rawNamespace import(GenomicRanges, except=�reduce�) @importFrom purrr reduce Then the NAMESPACE of direct "reduce" call will be reserved only to the package of "purrr". Which means that when you do "reduc

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

Thanks Tim. The assigned reviewer will review your package and provide suggestions as needed. Best, Nitesh > On Sep 12, 2019, at 3:15 AM, Tim Peters wrote: > > Hi Nitesh, > > Thanks, I have transformed DMRcatedata into an ExperimentHub package and > started an issue here > https://github.co

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

Third option: use Reduce() from base instead of purr::reduce(). On Thu, Sep 12, 2019 at 2:54 AM O'CALLAGHAN Alan wrote: > > Hi, > > Two options. > > First option: import either purrr::reduce or GenomicRanges::reduce, and > call the other with [pkg]::reduce. > > Second option: remove the import fo

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Thankyou Bernat! -Original Message- From: Bernat Gel Moreno Sent: Donnerstag, 12. September 2019 11:26 To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)? I have updated karyoploteR and it's now (from version 1.11.9

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Thankyou Bernat, Saw your email just now - since I have the "digest" option. Good that you brought the chromosomes parameter under my attention, I must be able to use that! Aditya -Original Message- From: Bernat Gel Moreno Sent: Donnerstag, 12. September 2019 08:47 To: bioc-devel@r

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

Hi, Two options. First option: import either purrr::reduce or GenomicRanges::reduce, and call the other with [pkg]::reduce. Second option: remove the import for both of these. Use purrr::reduce and GenomicRanges::reduce to call both functions. I think the second option leads to clearer code and

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

I have updated karyoploteR and it's now (from version 1.11.9 in devel) possible to use a BSgenome object or a seqinfo object as genome definitions in plotKaryotype. In both cases, if possible, it will by default automatically filter the chromosomes to the canonical ones (if defined) and retriev

[Bioc-devel] Duplicated method names in purrr and GenomicRanges

Dear all, I am developing a Bioconductor package and have a problem with two methods which have the same name. I am using the reduce() function from the R packages GenomicRanges and purrr. All methods from other packages are imported with @importFrom in all of my functions. During devtools:

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Thanks Michael and Herve, Will do that then. I extract from this discussion that exporting a function in a core BioC package is reserved for functions (1) whose name unambiguously communicates what they do (2) has the potential to be broadly used And that as(BSgenome, 'GRanges') is being fel

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Oh, and Aditya, take into account taht if you give karyoploteR a custom genome as you are planning to do, it will not paint the cytobands by default, you'll have to get them yourself and give them to plotKaryotype. If possible, I would recommend giving the genome by name ("hg19") and selecting

Re: [Bioc-devel] Troubles with Windows build

Hi Hervé, Thanks a lot for your very helpful and insightful reply! [...] I think this looks indeed like a leftover/stale .o file but I think the file is in the source tarball produced by the BUILD stage (msa_1.17.0.tar.gz). If you look at your cleanup.win script, it doesn't remove the stuff in s

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

Hi Nitesh, Thanks, I have transformed DMRcatedata into an ExperimentHub package and started an issue here https://github.com/Bioconductor/Contributions/issues/1247. Cheers, Tim On 23/8/19 3:46 am, Turaga, Nitesh wrote: Hi Tim, Based on what your have mentioned, it seems that DMRcatedata shou