Re: [Bioc-devel] Gviz: implementing support for FaFiles from AnnotationHub

For what it's worth and from an earlier comment in this thread, one way to use git (for Johanne's benefit) within the context of svn (for Florian's benefit) is to svn co Gviz, then on top of svn create a new git repository branch and update at will, then merge changes to master and provide

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

Just to say that this is a great idea. If this starts as a github package (or in svn, we can create a location for you if you'd like) I and others would I am sure be happy to try to provide any guidance / insight. The main design principles are probably to reuse as much as possible from

Re: [Bioc-devel] citation() error for BiocParallel and S4Vectors

It is this commit r69509 | hornik | 2015-10-12 07:06:54 -0400 (Mon, 12 Oct 2015) | 1 line Fixes for PR #16240 and PR #16550. which is failing when

Re: [Bioc-devel] SV4Vectors installation problem

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Marcin Cieslik > Sent: Thursday, October 15, 2015 7:46 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] SV4Vectors installation problem > > Dear Bioconductors, > > Somewhere in

Re: [Bioc-devel] ideas for ScanBamParam filters

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Michael Lawrence > Sent: Friday, October 16, 2015 7:56 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] ideas for ScanBamParam filters > > Maybe I just missed these, but these are a

Re: [Bioc-devel] readGAlignmentPairs with discordant strand

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Michael Lawrence > Sent: Friday, October 16, 2015 7:41 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] readGAlignmentPairs with discordant strand > > Now that GAlignmentPairs

Re: [Bioc-devel] upgrading

Technically, prior to the release we were using R-3.2 for both release and devel. Only after the release did we 'support' R-devel, implying a new installation of BiocInstaller. I guess you were using R-devel prior to the release and had an unsupported installation of BiocInstaller.

Re: [Bioc-devel] A method for combining SummarizedExperiment objects

Hi Pete -- looks like a good idea. I think the generic could be adjusted to pass named (not x, y) args to methods, rather than trying (incorrectly) to combine them. I don't think the inefficiency of recursion is a particular concern, because it is not like hundreds (or even tens) of objects

Re: [Bioc-devel] readGAlignmentPairs with discordant strand

.com] Sent: Saturday, October 17, 2015 9:48 AM To: Hervé Pagès Cc: Michael Lawrence; Morgan, Martin; bioc-devel@r-project.org Subject: Re: [Bioc-devel] readGAlignmentPairs with discordant strand This might have been lost in this thread. If there is an easy way to coerce a GAlignmentsList where all

Re: [Bioc-devel] error in stable AnnotationHub

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Kasper Daniel Hansen > Sent: Saturday, October 10, 2015 11:04 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] error in stable AnnotationHub > > Using Bioconductor 3.1 and the

Re: [Bioc-devel] AnnotationHub: cleanup

Hi Kasper -- we'll try to act on these, but some comments / looking for clarification... > -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Kasper Daniel Hansen > Sent: Monday, September 14, 2015 10:45 PM > To: bioc-devel@r-project.org >

Re: [Bioc-devel] Shouldn't we distinguish between package-specific and dependency errors?]

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Michael Lawrence > Sent: Thursday, September 24, 2015 2:51 PM > To: Ludwig Geistlinger > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Shouldn't we distinguish between

Re: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase?

Oops, I forgot to mention that I implemented this in devel, version 2.31.1. It's in SVN now and all being well via biocLite() on Saturday afternoon Eastern time. From: Morgan, Martin Sent: Friday, December 04, 2015 9:22 AM To: Philipp Angerer; Bioc-devel

Re: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase?

Hi Phillip -- es$foo accesses phenoData(es)$foo, so I implemented .DollarNames.eSet for this. An ExpressionSet is rectangular and has two-dimensional subsettings, the core data is a matrix, and generally ExperessionSet behaves like a matrix. So rather than names() try colnames(). Thanks for

Re: [Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

>From the Bioconductor side of things, the general feeling is that this is a >step in the right direction and worth the broken packages. Martin Morgan From: R-devel [r-devel-boun...@r-project.org] on behalf of Martin Maechler [maech...@stat.math.ethz.ch]

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

At least for the R package side of things, I think the question of how to invoke R CMD in a Makefile is moot for AnalysisPageServer -- remove the Makefile, and the shared object is created automatically when the package is built with R CMD build AnalysisPageServer. But for the record the

Re: [Bioc-devel] bplapply Processes Sometimes Stall

Hi Dario -- the most likely explanation, without a reproducible example, is that the code used on workers sometimes puts R into a state that it cannot recover from. The first approach to debug this is to run the code serially, e.g., using SerialParam and perhaps register(SerialParam()) (to

[Bioc-devel] Updated package submission policies

Bioconductors -- we intend to change the way new packages are submitted and reviewed before being added to the Bioconductor repository. Please see additional detail on the support site at https://support.bioconductor.org/p/76472/. Best wishes, Martin This email message may contain legally

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

We switched to TwoBitFile with a recent ensembl release, thinking that it had better performance and other characteristics compared to the previous FaFile. The 'recipe' used to create the FaFiles did not explicitly trim the label; that appears to be something done by Rsamtools::indexFa and

[Bioc-devel] Bioconductor GSOC sponsorship?

Hi -- Bioconductor has sometimes participated in Google Summer of Code (https://developers.google.com/open-source/gsoc/timeline?hl=en , https://developers.google.com/open-source/gsoc/faq#how_does_a_mentoring_organization_apply). If there is interest in the community to sponsor participation

Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

Thanks Ludwig I'll have a look. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Wednesday, January 06, 2016 12:07 PM To: bioc-devel@r-project.org Subject: Re:

Re: [Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

Hi Sonali -- relistToClass was originally in IRanges Packages such as Biostrings that Depend: or Import: IRanges and then create a 'relistToClass' method created a methods table on INSTALLATION, noting that the generic is in IRanges. The 'relistToClass' generic was moved from IRanges to

Re: [Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

Great! Just re-installing the packages via biocLite() would have been sufficient. Martin From: Sonali B Arora [sar...@fredhutch.org] Sent: Monday, December 21, 2015 4:56 PM To: Morgan, Martin; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Rsamtools

Re: [Bioc-devel] Warning: no visible global function definition for ‘seqlevels<-’

Yes, that's right, either import(GenomeInfoDb) or importFrom(GenomeInfoDb, "seqlevels<-") Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Venkat Malladi [venkat.mall...@utsouthwestern.edu] Sent: Tuesday, December 22, 2015

Re: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

You are right that BiocGenerics creates and exports a generic Position. I think you are right that the warning is coming from DESeq2, which imports(BiocGenerics) and imports(ggplot2). The solution is for the DESeq2 author to do as you did, importFrom() selectively, or continue to declare

Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

Hi Ludwig -- It would be really great to see what you've put together; can you make your code available somewhere, maybe via github? I think the facilities already in Bioconductor include: - select() and the OrganismDb (e.g., Homo.sapiens) packages - (Recently introduced, in bioc-devel)

Re: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

-devel-boun...@r-project.org] on behalf of Morgan, Martin [martin.mor...@roswellpark.org] Sent: Saturday, December 19, 2015 2:02 PM To: Lo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? You are right that BiocGenerics

Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

Oops, those newly added functions in GenomicFeatures are GenomicFeatures::mapRangesToIds GenomicFeatures::mapIdsToRanges Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Morgan, Martin [martin.mor...@roswellpark.org] Sent: Friday

Re: [Bioc-devel] as.table not available for HitsList anymore?

Hi Nico -- Hervé is on vacation until early January. My minimal example 'works', so I wonder if this is a conflict with another package (does S4Vectors::as.table(ovl) work?) or a unique feature of your HitsList? traceback() output after the error might help. Martin > library(S4Vectors) >

Re: [Bioc-devel] Progress Message Order in bplapply

Hi Dario -- it was this commit r111519 | mtmor...@fhcrc.org | 2015-12-15 14:34:18 -0500 (Tue, 15 Dec 2015) | 2 lines port: r111463, bugfix: workers=1, tasks=0 assigns all X to one chunk

Re: [Bioc-devel] bplapply Processes Sometimes Stall

Hi Dario -- This didn't cause problems for me. One thing you might do is to re-use the MulticoreParam() like this param = bpstart(MulticoreParam(25)) lapply(1:20, function(variety) bplapply(1:100, function() {}, BPPARAM = param)) bpstop(param) Also there have been a number of

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

I would rather mapIds() continue to operate on a single column, return a named character vector, and by default provide a 1:1 relationship between input and output. multiVals=CharacterList does actually return a 1:many mapping in a way that retains parallel structure (I guess, maybe module

Re: [Bioc-devel] Bioc twitter bot is on repeat

I'm not saying that every one of us follow Bioc on twitter... ;) From: Robert M. Flight [rfligh...@gmail.com] Sent: Tuesday, November 24, 2015 6:51 PM To: Morgan, Martin; Jim Hester; Michael Love Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bioc

Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

tran -arch x86_64" \ > FC="gfortran -arch x86_64" \ > --with-system-zlib \ > --with-blas='-framework Accelerate' \ > --with-lapack \ > CPPFLAGS="-D__ACCELERATE__ \ > --enable-R-framework=no \ >

Re: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?

>From the head of > PANTHER.db:::.keys function (x, keytype) { t2t <- .type2table(x) t2c <- .type2col(x) I wonder if many of the columns / keytypes are mislabeled, e.g., > PANTHER.db:::.type2col(PANTHER.db) CLASS_IDCLASS_TERM COMPONENT_IDCOMPONENT_TERM

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

I think the answer to 1 should be yes, duplicate keys are allowed. For instance, a vector of ids and a factor that groups the ids somehow (e.g., by experiment), with ids unique in each group. So I'm for step #2. Martin From: Bioc-devel

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

Marcin -- I join with Herve in strongly discouraging you from this approach. Because you wish only to change upper versus lower case of your package name, and because some operating systems ignore case, your package will go through a release where it is not available under either upper- or

[Bioc-devel] R / Bioconductor job opportunity: Senior Programmer / Analyst

The Bioconductor team has an opening available for a Senior Progammer / Analyst, see https://www.roswellpark.org/careers/administrative/senior-programmeranalyst-4301 for details. Bioconductor is an exciting and reward work environment. Please contact me (martin.morgan at roswellpark.org)

Re: [Bioc-devel] Use of EnsDb in the AnnotationDbi framework

Thanks Johannes, this is a valuable contribution and I've added it to the 'official' vignette. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer Johannes [johannes.rai...@eurac.edu] Sent: Thursday, January 07, 2016 9:10 AM

Re: [Bioc-devel] IRanges - PartitioningByEnd not found when package method runs.

(TGAC) [ben.w...@tgac.ac.uk] Sent: Thursday, January 14, 2016 4:20 AM To: Hervé Pagès; Morgan, Martin; bioc-devel@r-project.org Subject: RE: [Bioc-devel] IRanges - PartitioningByEnd not found when package method runs. Hi, Herve, Martin, Thanks! I've changed the function to use IntegerList instead

Re: [Bioc-devel] topGO and cat() and print() statements in program code

I followed your lead and updated topGO in Bioc devel branch to version 2.23.3, replacing cat() with message() directly rather a wrapper .cat2message(). I did not change use of cat() in print() and show() methods, where output to stdout is appropriate. Generally, using message() simplified

Re: [Bioc-devel] TIMEOUTs on Morelia

I don't see an error, but on linux under valgrind and current R-devel / bioc packages and especially > packageVersion("S4Vectors") [1] '0.9.26' I see > rse[1:2,] # hangs ==23105== Invalid read of size 4 ==23105==at 0xD0B8D4D: int_bsearch (Rle_class.c:606) ==23105==by 0xD0B8C45:

Re: [Bioc-devel] topGO and cat() and print() statements in program code

Hi Witold -- if you'd like to submit a patch, I will apply this to the package and notify the maintainer. I suggest you either use svn to check out the 'devel' version of the package, make your changes, and forward to me (martin.morgan at roswellpark.org) the output of svn diff (basic

Re: [Bioc-devel] Vignette building fails

I tried to build your vignettes on my own computer, but they are taking too long. From http://bioconductor.org/developers/package-guidelines/#correctness the time limit for checking a package (which includes running the vignette code, though not building the vignette) is 5 minutes. Do your

[Bioc-devel] Course: Statistics and Computing in Genome Data Science, July 10-15, 2016

Registration is now open for the popular week-long R / Bioconductor course "Statistics and Computing in Genome Data Science", held annually in Bressanone - Brixen, Italy. Please see http://www.huber.embl.de/csama2016/ for more details. This email message may contain legally privileged and/or

[Bioc-devel] Deadline for new package submissions for this release

Bioc developers! This is a reminder that, according to the release schedule http://bioconductor.org/developers/release-schedule/ new packages need to be submitted by March 25 in order to be previewed and made available in the next release, scheduled for April 15. Package and submission

[Bioc-devel] bnlearn method / generic definition (was Re: R CMD check problems)

This reproduces the problem > loadNamespace('graph') > loadNamespace('bnlearn') Error: .onLoad failed in loadNamespace() for 'bnlearn', details: call: setMethod("nodes", cl, function(object) .nodes(object)) error: no existing definition for function 'nodes' and it's because of the way

[Bioc-devel] Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June

Bioconductors! Please plan to attend BioC2016: Where Software and Biology Connect, June 24 (Developer Day) - 26, Stanford University, Stanford, CA. See http://bioconductor.org/help/course-materials/2016/BioC2016/ for additional information. DEVELOPERS: Please consider offering a

Re: [Bioc-devel] bplapply Processes Sometimes Stall

The change I had my eye on was not ported to patched, so (a) it could have been a more general R issue or (b) you got lucky. It would be great to get something (easily) reproducible in 3.2.3. Martin From: Bioc-devel on

Re: [Bioc-devel] bplapply Processes Sometimes Stall

Please ensure that your Debian system is running R-devel and using the current BiocParallel by providing the output of sessionInfo(). From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Dario Strbenac [dstr7...@uni.sydney.edu.au] Sent:

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: [Bioc-devel] Imports, depends and warnings

I think the only unavoidable case is when the package you import 'does it wrong'. If that's not the case, then please provide an (easy-to-reproduce -- start with a simple package.skeleton() and add a couple of Imports: and import() statements, rather than providing your current package).

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

-02-27 r70232) -- "Unsuffered Consequences" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) From: Federico Marini <mari...@uni-mainz.de> Sent: Thursday, March 3, 2016 3:44 AM To: Morg

Re: [Bioc-devel] Custom build of packages

I guess asking on the devel mailing list rather than sending mail to a particular individual means that you get the benefit of whatever global wisdom is available. All packages are built nightly, in both release and devel, and across three architectures. The build system is more complicated

Re: [Bioc-devel] Why bioconductor?

I think pull requests on https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md would be welcome. Martin On 10/10/18 11:51 AM, Ludwig Geistlinger wrote: While this might be obvious to most of us, it seems to be less clear to others. In

Re: [Bioc-devel] Files in the 'vignettes' directory but no files in 'inst/doc'

Just to emphasize that the 'right' solution from the Bioc perspective is to make sure that the vignette is evaluated https://stackoverflow.com/a/44094582/547331 rather than to add a pdf to inst/doc -- no sense in providing the user with a 'picture of code' when there are no guarantees that

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

There is .BBSoptions, which can be placed in the root of your package, but this is insidious, as evidenced by your own use case -- gmapR doesn't support windows, so your package doesn't support windows, so any package that Depends: or Imports: your package doesn't support windows, so actually