Re: [Bioc-devel] BiocParallel

2012-11-14 Thread Martin Morgan
, Nov 14, 2012 at 12:23 PM, Martin Morgan mtmor...@fhcrc.org wrote: Interested developers -- I added the start of a BiocParallel package to the Bioconductor subversion repository and build system. The package is mirrored on github to allow for social coding; I encourage people to contribute via

Re: [Bioc-devel] BiocParallel

2012-11-15 Thread Martin Morgan
Kasper On Wed, Nov 14, 2012 at 7:14 PM, Ryan C. Thompson r...@thompsonclan.org wrote: I just submitted a pull request. I'll add tests shortly if I can figure out how to write them. On Wed 14 Nov 2012 03:50:36 PM PST, Martin Morgan wrote: On 11/14/2012 03:43 PM, Ryan C. Thompson wrote: Here

[Bioc-devel] BiocParallel -- update

2012-12-03 Thread Martin Morgan
Bioc Developers -- BiocParallel generated quite a bit of discussion, so I'm providing a brief update. Version 0.0.5 is available to R-devel users via biocLite; it's in svn https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel and github

Re: [Bioc-devel] Reading FASTQ/BAM from open file handle?

2012-12-04 Thread Martin Morgan
On 12/04/2012 01:27 PM, Ryan C. Thompson wrote: Hi all, I'm currently experimenting with using quip (https://github.com/dcjones/quip#readme) to save disk space when storing FASTQ and BAM files. One thing that would be nice is to read quip-compressed FASTQ or BAM files directly into R. Obviously

Re: [Bioc-devel] Rsamtools segfault

2012-12-21 Thread Martin Morgan
On 12/21/2012 10:56 AM, Michael Lawrence wrote: I can segfault R by doing this: coverage(BamFile(character())) This was with Rsamtools_1.11.12. Thanks should be caught in 1.11.14. Martin Michael [[alternative HTML version deleted]] ___

Re: [Bioc-devel] Add OrgDb class to slot, warning during build

2012-12-22 Thread Martin Morgan
Hi Jesper -- On 12/22/2012 05:09 PM, Jesper Gådin wrote: Hello all, #I have been attempting to create a slot in my own class foo that is supposed to contain an OrgDb object from the AnnotationDbi-package. Actually it works, but during my build I get this warning: ** R ** inst ** preparing

Re: [Bioc-devel] Add OrgDb class to slot, warning during build

2012-12-23 Thread Martin Morgan
] rtracklayer_1.16.3stats4_2.15.1 tools_2.15.1 [19] XML_3.95-0.1 zlibbioc_1.2.0 On Sun, Dec 23, 2012 at 8:06 AM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: Hi Jesper -- On 12/22/2012 05:09 PM, Jesper Gådin wrote: Hello all, #I have been

Re: [Bioc-devel] subsetByOverlaps export missing from NAMESPACE in GenomicRanges

2012-12-23 Thread Martin Morgan
On 12/23/2012 05:19 PM, Jesper Gådin wrote: Yes thanks that is probably the reason why it is missing from GenomicRanges. Noticed that it was in IRanges and had already put it in the import, but forgot to also put in my export... After I put it in exports it works as intended. actually,

Re: [Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

2013-02-03 Thread Martin Morgan
On 02/03/2013 03:35 AM, Wolfgang Huber wrote: Hi, In LaTeX, I like to use the tilde in connection with equation or section references, e.g. Equation~(\ref{eq:bla}) or Section~\ref{sec:blo}, to make sure they are not separated by a line break. This has worked well for two decades and still

Re: [Bioc-devel] ShortRead: optional custom labeling of samples in QA report

2013-02-12 Thread Martin Morgan
On 02/12/2013 06:29 AM, Julian Gehring wrote: Hi, Since the attached file didn't make it all the way through to the mailing list, you can find it at http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/0001-Example-patch-for-naming-samples-in-BAMQA.patch. Thanks Julian the request seems

Re: [Bioc-devel] Webpage spring cleaning - Package submission

2013-02-22 Thread Martin Morgan
On 02/22/2013 07:08 AM, Wolfgang Huber wrote: I would like to suggest clarification of the information in the Package Guidelines [1] and the Package Submission [2] pages. 1. Information that is actually of type guideline is (only) stated on the submission page, which is confusing. Shouldn't

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Martin Morgan
On 03/13/2013 04:02 AM, Joern Toedling wrote: Hello, I have encountered a strange issue with the plotting function in my package girafe that I need some help with. I haven't changed anything in the plot methods or the NAMESPACE of the package recently, and it worked before, yet I observe the

[Bioc-devel] BioC2013, July 18-19 (Developer Day July 17), Seattle: Registration Open

2013-03-15 Thread Martin Morgan
for the analysis and comprehension of high-throughput genomic data. Proposals for lab sessions are also being accepted, see https://secure.bioconductor.org/BioC2013/lab_submit.php Check back regularly for updates to the schedule! Looking forward to seeing you in Seattle. Martin Morgan, on behalf

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-18 Thread Martin Morgan
PM, Martin Morgan wrote: On 03/13/2013 04:02 AM, Joern Toedling wrote: Hello, I have encountered a strange issue with the plotting function in my package girafe that I need some help with. I haven't changed anything in the plot methods or the NAMESPACE of the package recently, and it worked

Re: [Bioc-devel] C++ code performance issues

2013-03-21 Thread Martin Morgan
On 03/21/2013 11:30 AM, Peter Glaus wrote: Hi, I am working on BitSeq package, which has both command line C++ version and Bioconductor version in which R calls the same C++ code with .C function. While testing the development version of package on R 3.0.0 I noticed that the R version runs much

Re: [Bioc-devel] C++ code performance issues

2013-03-22 Thread Martin Morgan
at http://bioconductor.org/checkResults/devel/bioc-LATEST/ by clicking on the different machine names, george2, moscato2, petty Martin Peter. On 21/03/13 19:36, Martin Morgan wrote: On 03/21/2013 11:30 AM, Peter Glaus wrote: Hi, I am working on BitSeq package, which has both command

Re: [Bioc-devel] graphite build error on George2

2013-03-28 Thread Martin Morgan
On 03/28/2013 03:20 AM, Enrica wrote: Dear Bioconductor, I'm one of the authors of the graphite package. I've noticed that the build host george2 seems to have a problem building the package. In particular, it seems there is a segmentation fault caused by the function sp_moralize(). This

Re: [Bioc-devel] Bioconductor coding standards

2013-04-02 Thread Martin Morgan
On 04/02/2013 09:04 AM, Alejandra Gonzalez-Beltran wrote: Hi Ulrich, While not for Bioconductor, this Google's R style guide might be useful: http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Bioc doesn't dictate coding style. The use of '.' in any kind of symbol is

Re: [Bioc-devel] RFC: IntervalTrees for GRanges objects

2013-04-03 Thread Martin Morgan
On 04/03/2013 10:28 AM, Kasper Daniel Hansen wrote: Making IntervalTree chromosome would also be a great addition for organisms with many sequences, like bee (due to an incomplete genome; 10,000s of sequences). It does not matter for humans, but findOverlaps is excruciatingly slow for bee's. I

Re: [Bioc-devel] pointer and big matrix in R

2013-04-12 Thread Martin Morgan
On 04/12/2013 10:02 AM, Servant Nicolas wrote: Dear all, I have a S4 object (HTCexp from HITC package), composed of one big matrix, and two genomicRanges objects, A and B which describe the matrix raws and columns. I thinking about a way to decrease the memory size of this object. I also have

Re: [Bioc-devel] pointer and big matrix in R

2013-04-13 Thread Martin Morgan
to the Bioconductor web site http://bioconductor.org/developers/ so if there are comments, corrections, etc., please don't hesitate to let me know. Martin nicolas Le 12 avr. 2013 à 19:44, Martin Morgan mtmor...@fhcrc.org a écrit : On 04/12/2013 10:02 AM, Servant Nicolas wrote: Dear all, I have a S4 object

Re: [Bioc-devel] Federation of sub-packages acceptable for Bioconductor?

2013-04-16 Thread Martin Morgan
On 04/16/2013 05:59 AM, Ulrich Bodenhofer wrote: Hi, Some students of mine are currently working on a unified R interface to multiple C/C++ algorithms of a kind (too early to mention details). The special challenges are that some of these algorithm have special requirements, that not

[Bioc-devel] Course: Intermediate R / Bioconductor for High-Throughput Sequence Analysis, 28-29 May, Seattle

2013-05-01 Thread Martin Morgan
Bioconductors! Please join us for an intermediate course on use of R / Bioconductor for high-throughput sequence analysis, a brief outline of which is below. More Information: https://secure.bioconductor.org/Seattle-May-2013/ Intermediate R / Bioconductor for High-Throughput Sequence Analysis

Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4 methods for union class

2013-05-07 Thread Martin Morgan
On 05/07/2013 04:04 AM, Renaud Gaujoux wrote: Hi, I am getting an error when calling an S4 method, which is defined for a union class that includes ExpressionSet, on a LumiBatch object: The error prototype is as follows: - 'A' is Union of 'B' and 'C' - 'D' extends 'C' - a method myfun()

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

2013-05-18 Thread Martin Morgan
On 05/18/2013 05:18 PM, Michael Lawrence wrote: Hi guys, Just wondering about the rationale of deprecating keepSeqlevels and renameSeqlevels. Sure, it's possible to do those things with seqlevels, somehow, but those functions make the high-level operation fairly obvious. They're very well

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

2013-05-18 Thread Martin Morgan
On 05/18/2013 05:42 PM, Martin Morgan wrote: Some of the most common operations are straight-forward, e.g., gr = GRanges(paste0(chr, c(1:22, X, Y)), IRanges(1, 100)) seqlevels(gr) = sub(chr, ch, seqlevels(gr)) To get a more comprehensive example I should have followed my own

Re: [Bioc-devel] \VignetteIndexEntry

2013-05-20 Thread Martin Morgan
On 05/20/2013 02:00 PM, Wolfgang Huber wrote: I am puzzled by the interpretation of the %\VignetteIndexEntry directive by the build system. On http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html of the four vignettes for this package, two are listed with titles 1. empy title

Re: [Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

2013-05-20 Thread Martin Morgan
, where keepSeqlevels(gr1, gr2), would have worked for two GRanges objects. Martin Michael On Sat, May 18, 2013 at 6:00 PM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: On 05/18/2013 05:42 PM, Martin Morgan wrote: Some of the most common operations

[Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

2013-05-21 Thread Martin Morgan
Pulling this over to Bioc-devel. It's tempting to strip this from the DESCRIPTION files of the ~500 packages that include it. It's not useful in the context of the Bioconductor release schedule, and makes a forward promise that cannot be guaranteed. Is this something that has come up before?

Re: [Bioc-devel] OpenMP error when using ShortRead::FastqStreamer with parallel::parLapply

2013-05-27 Thread Martin Morgan
On 05/26/2013 11:57 PM, Michael Stadler wrote: Dear bioc core developers, We have recently (a few months back?) started to get error messages of the type: libgomp: Thread creation failed: Resource temporarily unavailable when using ShortRead::FastqStreamer in combination with

[Bioc-devel] biomaRt::getBM column names

2013-06-07 Thread Martin Morgan
Hi Steffen -- getBM now returns the 'description' rather than 'name' of biomaRt columns, e.g., mart - useMart(ensembl) datasets - listDatasets(mart) mart-useDataset(hsapiens_gene_ensembl,mart) df - getBM(attributes=c(affy_hg_u95av2, hgnc_symbol,

Re: [Bioc-devel] biocLite should warn when called from a non-current R version

2013-06-19 Thread Martin Morgan
On 06/19/2013 03:01 PM, Simon Anders wrote: Hi On 19/06/13 23:44, Martin Morgan wrote: As a message (not warning or error), how about New features are available in Bioconductor version 2.12, R version 3.0.1. See http://bioconductor.org/install and if the instructions / dire

Re: [Bioc-devel] biocLite should warn when called from a non-current R version

2013-06-19 Thread Martin Morgan
On 06/19/2013 09:15 PM, Hervé Pagès wrote: Hi Martin, On 06/19/2013 05:21 PM, Martin Morgan wrote: On 06/19/2013 03:01 PM, Simon Anders wrote: Hi On 19/06/13 23:44, Martin Morgan wrote: As a message (not warning or error), how about New features are available in Bioconductor version

Re: [Bioc-devel] biocLite should warn when called from a non-current R version

2013-06-20 Thread Martin Morgan
requirements, etc... ;-) H. On 06/19/2013 10:50 PM, Martin Morgan wrote: On 06/19/2013 09:15 PM, Hervé Pagès wrote: Hi Martin, On 06/19/2013 05:21 PM, Martin Morgan wrote: On 06/19/2013 03:01 PM, Simon Anders wrote: Hi On 19/06/13 23:44, Martin Morgan wrote: As a message (not warning or error), how

Re: [Bioc-devel] svn and package version numbers

2013-06-30 Thread Martin Morgan
On 06/30/2013 03:32 PM, Dan Tenenbaum wrote: On Jun 30, 2013 12:43 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Also, as far as I understand, the package does not get build using the new commit, if it has already been build with that version number before. The package is

[Bioc-devel] BioC 2013, July 17 (Developer Day) 18-19: 'Early' registration deadline July 1

2013-06-30 Thread Martin Morgan
public data repositories with Bioconductor • Annotations in Bioconductor • RGalaxy / AnnotationHub See you in Seattle! Martin -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

[Bioc-devel] Reminder: new features in devel only

2013-07-02 Thread Martin Morgan
A friendly reminder that new features or major changes should be introduced into the 'devel' branch only; only bug fixes should be introduced to the release branch. This is so that users of the 'release' branch gain a stable user experience. I clarified this (and the importance of version

Re: [Bioc-devel] finding specific (outdated!) bioc package archives?

2013-07-08 Thread Martin Morgan
It's actually ambiguous. The best that can be done is to bisect the svn log for the commit that is consistent with the date stamp in packageDescription(edgeR). This would be from the command line and in the branch for the appropriate release svn log -v

Re: [Bioc-devel] GenomicRanges::assays

2013-07-09 Thread Martin Morgan
The problem is that the dimnames are stored in only one location, and this is not on the assays. When you ask for the assays, the dimnames are added, triggering a full copy of the data. If the dimnames are not of interest, then assays(BS, withDimnames=FALSE) This is not really ideal, so I'll

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Martin Morgan
- Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence lawrence.mich...@gene.com wrote: If it's an informational message, like one you might log, use

Re: [Bioc-devel] appending 2 GappedAlignments using c takes long

2013-07-10 Thread Martin Morgan
- Nicolas Delhomme delho...@embl.de wrote: Hej Bioc Core! There was some discussion last year about implementing a BamStreamer (à la FastqStreamer), but I haven't seen anything like it in the current devel. I've implemented the following function that should do the job for me - I

Re: [Bioc-devel] BiocStyle for styling Sweave (and other?) vignettes

2013-07-16 Thread Martin Morgan
is not as convenient as cut-and-paste. Thanks for the feedback. Martin cheers, robert. On 07/14/2013 05:23 PM, Martin Morgan wrote: Developers -- Sweave-style vignettes often include copy-pasted versions of basic LaTeX macros and other commands. We've created the BiocStyle package to make

Re: [Bioc-devel] [devteam-bioc] BiocStyle and knitr: option clash for package color

2013-07-22 Thread Martin Morgan
On 07/22/2013 01:56 PM, Maintainer wrote: Dear BiocStyle-Maintainer, I try to use BiocStyle (0.0.13) in a knitr vignette. It seems both knitr and BiocStyle include the color package with different options (knitr: without any option; BiocStyle with usenames,dvipsnames). That's why R CMD build

Re: [Bioc-devel] BiocStyle for styling Sweave (and other?) vignettes

2013-07-22 Thread Martin Morgan
Thanks Renaud for your comments. On 07/21/2013 11:52 PM, Renaud wrote: Hi, this package is a nice idea indeed. For what is worth, I developed a similar feature within the pkgmaker package (on CRAN), especially to enable easy CRAN/Bioc package referencing/linking, with the inclusion of an extra

Re: [Bioc-devel] BiocStyle for styling Sweave (and other?) vignettes

2013-07-22 Thread Martin Morgan
copy and paste code from other sources. yes, for instance knitr puts everything in figure/. This has been updated. Thanks for the comments Kasper. Best, Kasper On Sun, Jul 14, 2013 at 11:23 AM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: Developers -- Sweave

Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-08-02 Thread Martin Morgan
On Fri, Aug 2, 2013 at 4:24 AM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: On 07/31/2013 04:05 PM, Hervé Pagès wrote: Hi Dario, Thanks for providing the file. The file has 55780092 records in it and yes it only contains primary

Re: [Bioc-devel] R CMD check and par(mfrow=…) in vignettes

2013-08-07 Thread Martin Morgan
On 08/06/2013 05:25 AM, Wolfgang Huber wrote: Hi one of my packages [1] has several places in its vignette where multi-panel figures are generated via the likes of par(mfrow=c(4,2)) within fig=TRUE code chunks. The package builds fine with 'R CMD build', and the vignette builds fine when

Re: [Bioc-devel] Rsamtools Unable to Compile on FreeBSD 9.1

2013-08-18 Thread Martin Morgan
On 08/18/2013 07:18 PM, Aric Gregson wrote: Hello, I am trying to install Rsamtools but am having difficulty on R version 3.0.1 Patched (2013-05-26 r62815) Platform: amd64-portbld-freebsd9.1 (64-bit) I receive the following error when installing from within R. I suspect it is a PATH issue, it

[Bioc-devel] Bioconductor Job Opportunities

2013-08-20 Thread Martin Morgan
robust and performant R and C / C++ code for efficiently organizing and processing large volumes of sequence data. Please do not hesitate to contact me with any questions. Best wishes, Martin Morgan -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024

Re: [Bioc-devel] Error installing GenomicRanges

2013-08-23 Thread Martin Morgan
On 08/23/2013 04:48 PM, James Diggans wrote: All - trying to install GenomicRanges on a RHEL 5.7 machine today and ran into the following error from line 78 in SummarizedExperiment-rowData-methods.R: R biocLite(GenomicRanges) BioC_mirror: http://bioconductor.org Using Bioconductor version

Re: [Bioc-devel] More than 4Mb

2013-08-25 Thread Martin Morgan
On 08/25/2013 12:55 PM, Hernandez Ferrer, Carles wrote: Dear All, I have developed a package that uses 3 binary files (Affymetrix Power Tools). I thought to include them into the package but the executables size is more than the 4Mb allow by Biocondutor. Mus I create some type of experimental

Re: [Bioc-devel] org-mode vignettes

2013-08-28 Thread Martin Morgan
!). The parenthetical comment came from passing some festive commentary through a civility filter -- option three is don't do it!. Martin Best wishes, Wolfgang On 28 Aug 2013, at 14:28, Martin Morgan mtmor...@fhcrc.org wrote: On 08/28/2013 02:50 AM, Wolfgang Huber wrote: Hi

Re: [Bioc-devel] BiocParallel status

2013-09-03 Thread Martin Morgan
On 09/03/2013 05:25 AM, Hahne, Florian wrote: Hi List, Martin, I just wanted to quickly ask about the status of the BiocParallel package and the cluster support in particular. Is this project finished? And are there plans to having BiocParallel as a proper package again, or will it remain a GIT

Re: [Bioc-devel] [BioC] readGappedAlignments and param argument

2013-09-10 Thread Martin Morgan
On 09/10/2013 03:40 AM, Elena Grassi wrote: You can use summarizeOverlaps with a 'BamFileList' created by something like myFiles = dir(/some/dir, pattern=bam$) bfl = BamFileList(myFiles, yieldSize=100) olaps = summarizeOverlaps(features, bfl) see the example on the help page

Re: [Bioc-devel] R-version

2013-09-16 Thread Martin Morgan
On 09/15/2013 07:12 AM, Wolfgang Huber wrote: Dear Julian thanks. Since this has come up here and elsewhere, and since the next Bioc release is coming up, let's remind ourselves that we should make development against 3.0.1 Patched (2013-09-03 r63824) -- Good Sport. Martin - should this be

[Bioc-devel] R and Bioconductor versions for the forthcoming release

2013-09-16 Thread Martin Morgan
’ of Bioconductor for its packages has been changed to the upcoming 2.13, but this can be set by the environment variable R_BIOC_VERSION, e.g. in file Renviron.site. Martin Morgan, Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024

Re: [Bioc-devel] memory not mapped error when installing Bioc 2.13 packages on R 3.0.2

2013-09-28 Thread Martin Morgan
On 09/28/2013 05:19 AM, Nicolas Delhomme wrote: Hej all! When trying to install the following packages c(GO.db,org.Hs.eg.db,PFAM.db,AnnotationForge,Category,DESeq2,ReportingTools,rtracklayer,GenomicFeatures,biovizBase,QuasR,VariantAnnotation,gmapR,VariantTools) from Bioc 2.13 on R3.0.2, I'm

Re: [Bioc-devel] Proof-of-concept parallel preloading FastqStreamer

2013-10-02 Thread Martin Morgan
On 10/02/2013 11:58 AM, Gregoire Pau wrote: Hello Ryan, You may be interested in the function sclapply(...) located in the HTSeqGenie package. sclapply is a multicore dispatcher that accepts 3 main arguments (inext, fun, max.parallel.jobs). The data produced by the function inext, executed in

Re: [Bioc-devel] Problem with GRanges

2013-10-15 Thread Martin Morgan
On 10/15/2013 05:04 AM, Michael Lawrence wrote: You need a new version of GenomicRanges, because IRanges changed. Unfortunately there is no way to force a package update when a dependency changes. Sorry. BiocInstaller::biocLite() can help (diagnose) these problems. Martin On Tue, Oct 15,

Re: [Bioc-devel] Problem with GRanges

2013-10-15 Thread Martin Morgan
On 10/15/2013 05:06 AM, Martin Morgan wrote: On 10/15/2013 05:04 AM, Michael Lawrence wrote: You need a new version of GenomicRanges, because IRanges changed. Unfortunately there is no way to force a package update when a dependency changes. Sorry. BiocInstaller::biocLite() can help (diagnose

[Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

2013-10-18 Thread Martin Morgan
Bioconductor developers, Thank you for your contributions to our last release, with a total of 749 packages! This is a great resource for the bioninformatics community. No good deed goes unpunished. The 'devel' version of R no longer builds vignettes in the inst/doc directory. Vignette

Re: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

2013-10-21 Thread Martin Morgan
=English_Australia.1252 attached base packages: [1] parallel stats graphics grDevices utils [6] datasets methods base other attached packages: [1] Biobase_2.23.1 BiocGenerics_0.9.0 Date: Fri, 18 Oct 2013 14:58:52 -0700 From: Martin Morgan mtmor...@fhcrc.org To: bioc-devel@r

Re: [Bioc-devel] upgrade instructions at http://bioconductor.org/install/

2013-10-25 Thread Martin Morgan
On 10/24/2013 06:51 AM, Levi Waldron wrote: I just noticed that there is no mention on http://bioconductor.org/install/of how to upgrade from the previous Bioconductor. I think it would be helpful to advise that it can be done with biocLite(BiocUpgrade). Thanks Levi, the instructions have

[Bioc-devel] Using integrated contains in Bioconductor packages

2013-11-05 Thread Martin Morgan
Hi package developers -- I found this article pretty intersting reading http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html?WT.ec_id=NBT-201310 especially of course the comments of Robert Gentleman and the reasons for success of R (external packages written by domain experts) and

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

2013-11-06 Thread Martin Morgan
On 11/04/2013 11:34 AM, Michael Lawrence wrote: The dynamic nature of R limits the extent of these checks. But as Ryan has noted, a simple sanity check goes a long way. If what he has done could be extended to the rest of the search path (people always forget to attach packages), I think we've

Re: [Bioc-devel] tab completion for library()

2013-11-13 Thread Martin Morgan
On 11/13/2013 09:17 AM, Tim Triche, Jr. wrote: This seems like what I'm looking for, but it doesn't do what I'd expect: R rc.options(ipck=TRUE) R rc.options()$ipck [1] TRUE R require(Biostr\t # nothing happens Should I be using one of the intermediate/undocumented functions to grab a list of

Re: [Bioc-devel] Minimal update of relevant packages only

2013-11-13 Thread Martin Morgan
On 11/13/2013 01:29 PM, Luo Weijun wrote: I noticed that under R 3.0, I frequently get prompt to update other packages after package installation like: invoking biocLite with biocLite(suppressUpdates=TRUE) gives you a quieter version. Using Bioconductor version 2.13 (BiocInstaller 1.12.0),

Re: [Bioc-devel] Trying to reduce the memory overhead when using mclapply

2013-11-14 Thread Martin Morgan
On 11/14/2013 12:13 AM, Leonardo Collado Torres wrote: Dear BioC developers, I am trying to understand how to use mclapply() without blowing up the memory usage and need some help. My use case is splitting a large IRanges::DataFrame() into chunks, and feeding these chunks to mclapply(). Let

Re: [Bioc-devel] [BioC] GTF file error when using easyRNAseq

2013-11-15 Thread Martin Morgan
On 11/15/2013 10:22 AM, Michael Lawrence wrote: Doesn't look like genomeIntervals has any C code (?), so a performance comparison would be interesting. rtracklayer jumps through all sorts of hoops to handle obscure things like URL encoding in GFF3. The code in genomeIntervals seems more

Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric

2013-12-03 Thread Martin Morgan
On 12/03/2013 02:29 AM, Julian Gehring wrote: Hi, Some of the chromosomes out in the world are fairly large (e.g. wheat chr 3B with 995 Mbp [1]). Currently, the 'seqlengths' of the reference sequence are stored as 'integers' which do not allow to store lengths of this size. Are there any

Re: [Bioc-devel] Conflict between BiocStyle and the verbatim package

2013-12-03 Thread Martin Morgan
On 12/03/2013 12:30 PM, Nicolas Delhomme wrote: Hej Martin! I’d like to have multi-line comments in my vignette and the easiest way I know is to use the “comment” environment from the verbatim package - i.e. \begin{comment}…\end{comment}. However, when I do this, i.e. load the verbatim

Re: [Bioc-devel] Rsamtools BAM SAM?

2013-12-05 Thread Martin Morgan
On 12/04/2013 11:17 PM, Taku Tokuyasu wrote: Hello, We are trying to support NGS pipelines with SAM input to htseq-count, w/o requiring a samtools install. Has Rsamtools implemented / planned any support for BAM to SAM conversion? I notice this has been requested before (e.g. May 2012,

Re: [Bioc-devel] Rsamtools BAM SAM?

2013-12-05 Thread Martin Morgan
mailto:lawrence.mich...@gene.com wrote: It would be appreciated to know where the current counting methods fall short; i.e., why htseq-count is necessary. Thanks, Michael On Thu, Dec 5, 2013 at 12:30 AM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: On 12

Re: [Bioc-devel] Conflict between BiocStyle and the verbatim package

2013-12-11 Thread Martin Morgan
On 12/03/2013 12:50 PM, Martin Morgan wrote: On 12/03/2013 12:30 PM, Nicolas Delhomme wrote: Hej Martin! I’d like to have multi-line comments in my vignette and the easiest way I know is to use the “comment” environment from the verbatim package - i.e. \begin{comment}…\end{comment}. However

[Bioc-devel] New Seattle Bioconductor group members

2013-12-16 Thread Martin Morgan
Bioconductors, Two new members, Sonali Arora and Nate Hayden, have joined the Bioconductor group here in Seattle. Look for their increasing participation in this list as they engage with the project, and say hi when you have a chance! Martin -- Computational Biology / Fred Hutchinson Cancer

Re: [Bioc-devel] edgeR crashes when xlsxjars is loaded

2013-12-16 Thread Martin Morgan
Crashes for me in locfit's C code but in a pretty weird way -- the variable 'd' is not accessible. (gdb) p d Cannot access memory at address 0x7fef3b30 but d has been allocated on the stack. backtrace below. valgrind reports many invalid writes associated with Java, but I think this is

Re: [Bioc-devel] edgeR crashes when xlsxjars is loaded

2013-12-16 Thread Martin Morgan
On 12/16/2013 02:34 PM, Ryan C. Thompson wrote: Indeed, loading rJava and calling .jinit() also triggers the bug. I have updated my script (same URL as before) to demonstrate this. I run the bad code before and after calling .jinit(), and it only crashes the second time. The following

Re: [Bioc-devel] codetoolsBioC does not suggest methods from packages not defining generic

2013-12-19 Thread Martin Morgan
Thanks Michael for this fix; codetoolsBioC is in need of some work (maybe not a lot) but I don't think anyone in the Seattle group will be taking this up in the near future. If you or someone in the broader community (this kind of facility is useful in R generally) is interested in taking over

Re: [Bioc-devel] Bulky installation and loading triggered by function import

2013-12-19 Thread Martin Morgan
On 12/19/2013 10:00 AM, Luo Weijun wrote: My gage package imports a single function from pathview package. I just noticed that to install gage from scratch, users need to install pathview and all its dependencies, i.e. packages specified as both Imports and Depends in the pathview DESCRIPTION

Re: [Bioc-devel] how to use footnote in BiocStyle

2013-12-19 Thread Martin Morgan
On 12/19/2013 01:44 PM, Ou, Jianhong wrote: Hi All, I tried to add \footnote in \author tag like %\VignetteIndexEntry{MyPackage Vignette} %\VignetteDepends{MyPackage} %\VignetteKeywords{hello} %\VignettePackage{MyPackage} \documentclass[12pt]{article} style, echo=FALSE, results=tex=

Re: [Bioc-devel] Byte compiling of packages

2014-01-08 Thread Martin Morgan
On 01/08/2014 07:43 AM, Julian Gehring wrote: Hi, R-2.13 introduced the byte code compiler package 'compiler' [1], which can be used to precompile the R code of a package at installation time (using the ByteCompile field in the Description file or '--byte-compile' with R CMD INSTALL). I have

Re: [Bioc-devel] [devteam-bioc] problem w/ exprs- method and LumiBatch objects

2014-01-10 Thread Martin Morgan
On 01/10/2014 12:07 AM, Maintainer wrote: dear maintainers of Biobase and lumi, this is a question raised from a different thread a few days ago here: https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005129.html the matrix of genes by samples expression values in an 'ExpressionSet'

Re: [Bioc-devel] S3 method best practices

2014-01-11 Thread Martin Morgan
] 2 3 2 [2] 1 2 2 base::c(a=IRanges(1, 2), IRanges(2, 3)) IRanges of length 2 start end width [1] 2 3 2 [2] 1 2 2 Martin Morgan Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org

[Bioc-devel] Seattle Short Course, Feb 27-28: Introduction to Bioconductor for Sequence Analysis

2014-02-04 Thread Martin Morgan
, and visualization. The course involves a combination of presentations and hands-on exercises; participants should come prepared with a modern laptop with wireless internet access. See you in Seattle! Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview

Re: [Bioc-devel] Memory use and coverage from BamFile

2014-02-12 Thread Martin Morgan
On 02/12/2014 05:04 AM, Sean Davis wrote: On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence lawrence.mich...@gene.com wrote: This is a nice suggestion. What about integration with BiocParallel? Yep, makes good sense. Since there is IO involved, one needs to be a bit careful about

Re: [Bioc-devel] Subsetting eSet-like objects with duplicated indices

2014-02-12 Thread Martin Morgan
On 02/11/2014 05:03 PM, Benilton Carvalho wrote: Hi, I'm trying to understand why FeatureSet objects behave slightly different than eSet objects. There's a combination of things going on, some of which are unfortunate / unintended. The basic problem is that, with regard to row names,

Re: [Bioc-devel] Include indel counts in applyPileups

2014-02-13 Thread Martin Morgan
On 02/13/2014 08:09 AM, Sean Davis wrote: Hi, Martin. How difficult would it be to include insertions/deletions in seq and qual in the applyPileups method for PileupFiles? The use case is to look at the context around variants for increases mismatch rates. Indels will have a small impact on

Re: [Bioc-devel] BatchJobs and BiocParallel

2014-02-14 Thread Martin Morgan
On 02/14/2014 09:20 AM, Laurent Gatto wrote: Dear all, Looking back in my (sparse) notes from the last European Bioc meeting, I saw two points that were mentioned during the BatchJobs and BiocParallel talk that are of particular interest to me. - BatchJobs: is there support, or are there any

Re: [Bioc-devel] Help in designing class based on SummarizedExperiment

2014-02-14 Thread Martin Morgan
Hi Peter -- I'm not really sure that I can provide good advice here; it feels a bit like a 'round peg square hole' fit with SummarizedExperiment, since your 'pos' is not characterized by genomic ranges, and columns of 'assay' does not correspond to separate samples. One possibility is to

Re: [Bioc-devel] cigarToRleList fails

2014-02-20 Thread Martin Morgan
On 02/20/2014 02:32 PM, Hervé Pagès wrote: Hi Jesper, On 02/20/2014 02:13 PM, Jesper Gådin wrote: Very true that it is quite difficult to find the documentation when one is not aware of its existence :P Yeah, this has been a source of frustration for many people. And always a source of

Re: [Bioc-devel] Error in .doLoadActions(where, attach) :

2014-02-20 Thread Martin Morgan
On 02/20/2014 03:05 PM, Jesper Gådin wrote: Hi all, Tried to R CMD build and check the AllelicImbalance package, but got a strange NOTE during R CMD check (see below). Have checked previous versions of AllelicImbalance to try to find when the NOTE/Error got introduced, but the R CMD check on

Re: [Bioc-devel] Error in .doLoadActions(where, attach) :

2014-02-20 Thread Martin Morgan
LibPath AllelicImbalance 1.1.13 /home/user/bin/R-devel/r-devel/library downgrade with biocLite(AllelicImbalance) Error: 1 package(s) too new Did the rdev CMD check again, but same error as before. /Jesper On Fri, Feb 21, 2014 at 12:24 AM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor

[Bioc-devel] subversion unavailable 9am - 2pm Sunday, 23 February

2014-02-22 Thread Martin Morgan
Developers, The Bioconductor subversion repository will not be available 9am - 2pm Sunday, 23 February PST. This may affect the Sunday build report, as well as any git-svn bridge activity. Apologies for the last-minute notification. Martin -- Computational Biology / Fred Hutchinson Cancer

Re: [Bioc-devel] BiocStyle and fonts

2014-03-11 Thread Martin Morgan
On 03/11/2014 10:38 AM, Laurent Gatto wrote: Dear all, Compiling the following with Sweave \documentclass{article} style, eval=TRUE, echo=FALSE, results=tex= BiocStyle::latex() @ \bioctitle{Hello world} \begin{document} \maketitle \section{Section} Some text pxdata= print(Hello world) @

Re: [Bioc-devel] BiocStyle and fonts

2014-03-12 Thread Martin Morgan
On 03/12/2014 08:18 AM, Laurent Gatto wrote: Should we then just drop \RequirePackage{helvet} from BiocStyle? That seems a reasonable solution to me. yep! Martin Laurent Cheers, Andrzej -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box

Re: [Bioc-devel] 'droplevels' argument in `[` method for SummarizedExperiment?

2014-03-12 Thread Martin Morgan
On 03/12/2014 03:02 PM, Wolfgang Huber wrote: Hi Martin, Mike a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’ object (the class inherits from ‘SummarizedExperiment’) by samples, he often ends up with unused factor levels in the colData. (Esp. since the

Re: [Bioc-devel] fatal error when installing BioC devel on R devel

2014-03-13 Thread Martin Morgan
Because R is on a yearly release cycle, and Bioconductor is on a six-month release cycle, both the Bioconductor 'release' and 'devel' branches after our April release will use R version 3.1.*. R-devel will not be used again until after our October release. Instructions on the developer

Re: [Bioc-devel] restrictToSNV for VCF

2014-03-21 Thread Martin Morgan
On 03/20/2014 05:20 PM, Hervé Pagès wrote: Hi, On 03/19/2014 01:10 PM, Michael Lawrence wrote: You can apparently use 1D extraction for VCF, which is a little surprising; I learned it from restrictToSNV. This is inherited from SummarizedExperiment: example(SummarizedExperiment) se1

Re: [Bioc-devel] SummarizedExperiment

2014-03-24 Thread Martin Morgan
On 03/20/2014 06:29 PM, Kasper Daniel Hansen wrote: It used to be the case that when a SummarizedExperiment was constructed, dim names was removed from the matrices in assay. One could then either use (1) assay(, withDimnames = TRUE) which ensured dim names in the return value, but implied

Re: [Bioc-devel] A question on IRanges package

2014-04-03 Thread Martin Morgan
On 04/03/2014 04:42 PM, Michael Lawrence wrote: I'll look at the code. As far as tracking line numbers, no, because the code is bundled into a package -- there are no files anymore. In principle, that could be improved, but as far as I know, it hasn't been. If you're I think there's an option,

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