Re: [Bioc-devel] "convert" graphics error for new submission

Maybe an antivirus issue? On Thu, Apr 5, 2018 at 8:30 PM, Vincent Carey <st...@channing.harvard.edu> wrote: > No, I did not do anything for this. > > On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >>

Re: [Bioc-devel] "convert" graphics error for new submission

No, I did not do anything for this. On Thu, Apr 5, 2018 at 5:03 PM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > It seems like this has 'gone away', was that something you did, or...? > > > > On 04/02/2018 04:34 PM, Vincent Carey wrote: > >> for two h

[Bioc-devel] "convert" graphics error for new submission

for two host-types I am seeing an error that I do not know how to address Loading required package: ontologyIndex sh: line 1: 76907 Abort trap: 6 'convert' 'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim 'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null sh: line 1: 76914 Abort

Re: [Bioc-devel] Error: node stack overflow

I get the following on MacOSX, after library(rJava); library(GenomicRanges) -- take rJava out of the mix and there is no error. I ran into this originally as an interaction between rJava and Gviz, and have reported to Florian. That seemed to be MacOSX-specific. > gr1 <-

Re: [Bioc-devel] AnnotationHub (2)

can you pass along some of the magic kasper? what encode portal are you talking about? On Tue, Mar 27, 2018 at 5:16 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > What is the current state for AnnotationHub (2)? I have recently figured > out (read: pestered the people who

Re: [Bioc-devel] Thanks to Andrzej...

Strongly seconded. We will miss you Andrzej! On Wed, Feb 28, 2018 at 6:53 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > I want to extend a sincere thanks to Andrzej Oleś. Andrzej has been making > many visible and hidden contributions to the project over the last several > years.

[Bioc-devel] giggle and bioc

I just noticed the nature methods paper on giggle, which is "25x faster than bedtools". Has anyone tried to deploy or interface? https://github.com/ryanlayer/giggle has a link to biorxiv, paper in current nature methods [[alternative HTML version deleted]]

Re: [Bioc-devel] gwaswloc class broken

16,481] (imputed) N > MAPPED_TRAIT MAPPED_TRAIT_URI > > [1] post-traumatic stress disorder http://www.ebi.ac.uk/efo/EFO_0001358 > --- > seqinfo: 23 sequences from GRCh37 genome > > > cheers, > > robert

Re: [Bioc-devel] R version check in BiocChech

On Mon, Feb 19, 2018 at 11:27 AM, Alexey Sergushichev wrote: > Kevin, > > > It does not request users to make R-devel a _requirement_ of their > package. > > Sadly it does for new packages. New packages submitted to Bioconductor 3.7 > are _required_ to have R >= 3.5

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

It is important but not completely clear how to address. I think it has been written that bioc package checking should make minimal use of the internet, and most checking concerning manipulation of net-derived objects should use "mocks". One possible approach is to test with calls to the

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/24/2018 03:38 PM, Wolfgang Huber wrote: > >> GenomicFeatures_1.31.3 imports RMySQL. >> >> I'm having great trouble installing RMySQL from source on a recent MacOS >> (10.13.3) with homebrew. >> >> The

[Bioc-devel] project templating tools

Does anyone have experience with http://projecttemplate.net/index.html ? I am wondering if there may be a fruitful connection to approaches to workflow construction/authoring practices. [[alternative HTML version deleted]] ___

Re: [Bioc-devel] BiocParallel and AnnotationDbi: database disk image is malformed

good question some of the discussion on http://sqlite.1065341.n5.nabble.com/Parallel-access-to-read-only-in-memory-database-td91814.html seems relevant. converting the relatively small annotation package content to pure R read-only tables on the master before parallelizing might be very

[Bioc-devel] BiocParallel on macosx: socketConnection failures with MulticoreParam

from example(bplapply), after register(MulticoreParam(2, timeout=5)) bplppl> bplapply(1:10, fun) *Error in socketConnection(host, port, TRUE, TRUE, "a+b", timeout = timeout) : * * cannot open the connection* *In addition: Warning message:* *In socketConnection(host, port, TRUE, TRUE, "a+b",

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

As I plan to "fix a bug" in release version of BiocSklearn, I tried %vjcair> git checkout remotes/upstream/RELEASE_3_6 Here is the result; what would I do to make some changes, alter DESCRIPTION version to 1.0.1, commit and push so that the build system has 1.0.1? Note: checking out

Re: [Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

no answers yet? would it work to put your matrices as separate assays in a SummarizedExperiment? as long as they are conformant in dimensions and dimnames I think that would work. That SummarizedExperiment would then work well in an MAE. On Mon, Oct 23, 2017 at 1:00 PM, Francesco Napolitano

Re: [Bioc-devel] R6 class v.s. S4 class

I want to raise a question about this from the perspective of intersystems interfacing. You can use reticulate to import your python into R, once you have installed the python library for biothings_client library(reticulate) bt = import("biothings_client") mv = bt$get_client("variant") myv =

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron wrote: > Thanks for all your thoughts Joey, and I hope I didn't come across as > ... > > On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie > wrote: > > ... > > > - There actually *still isn't

Re: [Bioc-devel] GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs

You can get the information through the merged tables: > dbListTables(con) [1] "gds" "gds_subset""geoConvert" [4] "geodb_column_desc" "gpl" "gse" [7] "gse_gpl" "gse_gsm" "gsm" [10] "metaInfo" "sMatrix" > cdesc =

Re: [Bioc-devel] Failure to create PDF vignette with BiocStyle 2.4.1

I ran into this -- BiocStyle was modified by Andrzej to solve it. I am now at BiocStyle 2.5.39 and biocValid() does not complain. So try updating BiocStyle. On Tue, Oct 3, 2017 at 9:29 PM, Stefan Mutter wrote: > Hi, > > > I hope I am writing this to the right list. >

Re: [Bioc-devel] external dependencies

I'd also comment that if you make the package visible I would be willing to have a look at the issues involved in porting to windows. No guarantees but at least get some sense of context. On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan wrote: > I want to add,

Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

. {:start= and external css have been tried. On Tue, Sep 26, 2017 at 5:15 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > I am running into this limitation now, while writing a background document > for an edX course. > > I am going to try to make linux my prod

Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

>>>> > >>>> For the user encountering this problem I think a better solution is to > >>>> increase the number of DLLs allowed by R, for instance editing > >>>> .Renviron to contain the line > >>>> > >>>> R_M

Re: [Bioc-devel] [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

IMHO the pedagogic value of a unified document that treats a topic thoroughly is quite high. Building the whole workflow on an arbitrary user's system seems to me to be a lower priority. Thus using the environment variable in the build system to avoid this limit seems an appropriate solution.

[Bioc-devel] non-ASCII strings in data for a developing package

The Cell Line Ontology includes tokens like CSMaß1H cell which trigger warnings if included in .rda files in data folder. They can be masked using iconv but it seems unfortunate to do this. The offending .rda files can be kept elsewhere and loaded by function. Is that the appropriate

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

can you say a little more about what resource will be tapped and what it will look like? you can already use uniprot identifiers as keys into org.Hs.eg.db On Tue, Sep 12, 2017 at 9:05 AM, Aditya Bhagwat < adb2...@qatar-med.cornell.edu> wrote: > Hey guys, > > I love the org.Hs.eg.db package (and

Re: [Bioc-devel] Identical methods in two packages

For this particular problem, it may be worth noting that http://geneontology.org/page/ontology-structure describes CC, MF, BP as "sub-ontologies" of GO. AnnotationDbi might replace its Ontology() with subontology() to acquire those tokens. On Tue, Sep 12, 2017 at 4:28 PM, Michael Lawrence

[Bioc-devel] clarifying initialization for BiocCheck

"Consider clarifying how 6 object(s) are initialized" Suppose an object is initialized via data() ... how can I make this note go away? I don't understand how to clarify the situation. [[alternative HTML version deleted]] ___

[Bioc-devel] requesting more infrastructure on build/bot system

I have looked through the docs but cannot see where this is addressed. I would like to use the redland package from CRAN but it has SystemRequirements: Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>= 1.0.14) is there a particular procedure for requesting such

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

e that >> replaceSlots() saved some copying, but that's no longer really the >> case. The only potential benefit is that it can skip validity checks, >> but usually you want those. >> >> Michael >> >> On Wed, Sep 6, 2017 at 12:55 PM, Vincent Carey >> &

[Bioc-devel] role of replaceSlots in BiocGenerics

Is this the preferred way of adjusting content in a live object? It is not accessible except via ":::" [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] improving navigation within workflows

require some > more > > > work. > > > > > > Cheers, > > > Andrzej > > > > > > On Sun, Jul 16, 2017 at 9:36 PM, Aaron Lun <a...@wehi.edu.au > <mailto:a...@wehi.edu.au> > > > <mailto:a...@wehi.edu.a

Re: [Bioc-devel] Change in BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz

I can't reproduce this. Did you get 688,190,187 bytes in your tar.gz? Could it be an incomplete transfer? On Sat, Jul 22, 2017 at 5:47 PM, Janssen-10, R.R.E. < r.r.e.janssen...@umcutrecht.nl> wrote: > Hello, > > It seems that the tarball BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz has >

Re: [Bioc-devel] improving navigation within workflows

like this? http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html On Sun, Jul 16, 2017 at 11:53 AM, Aaron Lun wrote: > Hello all, > > I was wondering if there's any plans to improve the navigation for the > BioC workflows. I was

Re: [Bioc-devel] how to minimally serialize a FilterRules object

Interesting. I am finding that fr@listData$g is extremely slow and returns z in a peculiar format > fr@listData$g filter (fr = , g = c("function (x) ", "2 * x"), z = c("c(2.25030343990823, 0.0689130508451947, 0.898164844240903, -0.269136190861786, ", "0.286806384719545, -0.61182037109871,

Re: [Bioc-devel] What to do about std::cerr/cout warnings in external libraries?

Have you looked at the Bioconductor package Rhtslib? Is your package's source visible on github? If so please provide the URL. If not, please provide more details on the error messages observed. It would seem to me that the best way to proceed would be to link to Rhtslib. On Tue, Jun 20, 2017

Re: [Bioc-devel] getAnnMap: org.Hs.eg.db package not attached and load is FALSE

That was an early approach to identifier mapping (ca. 2005 book), but things have changed a lot since then. Assuming you are dealing with human genes, you could use > select(Homo.sapiens, keys="5966", keytype="ENTREZID", columns="SYMBOL") *'select()' returned 1:1 mapping between keys and

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Suppose you had a handler for SIGABRT in your code. Could CMD check check for that and, if found, refrain from warning? That is somewhat involved and goes beyond Bioc but it seems a principled way of dealing with operations in binary infrastructure whose behavior we cannot control. The problem

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

I am sure there are better responses to come, but here are a few initial comments. On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson wrote: > Dear all, > > SummarizedExperiment and matrixStats both contain a method/function called > rowRanges one operates on a

Re: [Bioc-devel] masking functions

in the NAMESPACE file import(gplots) import(plotrix, except=plotCI) can help avoid the warning you mention. If this is not a solution for you you will have to provide more details. On Fri, Mar 31, 2017 at 1:07 AM, Zimmermann, Michael T., Ph.D. < zimmermann.mich...@mayo.edu> wrote: > Dear

Re: [Bioc-devel] Update devel branch

see http://bioconductor.org/developers/how-to/source-control/ from which I infer svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BaalChIP will give you a clean checkout of current devel source you make changes in there then in the BaalChIP folder, do svn commit you should

Re: [Bioc-devel] any interest in a BiocMatrix core package?

a in the backend in C++ it will be > extremely backend dependent what is fast and how to do it. That doesn't > mean we shouldn't do it though. > > Best, > Kasper > > > > On Fri, Mar 3, 2017 at 6:47 AM, Vincent Carey <st...@channing.harvard.edu> >

Re: [Bioc-devel] any interest in a BiocMatrix core package?

Kylie, thanks for reminding us of matter -- I saw you speak about this at the first Bioconductor Boston Meetup, but it went like lightning. For developers contemplating an approach to representing high-volume rectangular data, where there is no dominant legacy format, it is natural to wonder

Re: [Bioc-devel] any interest in a BiocMatrix core package?

What is the data type for an expression value? Is it assumed that double precision will be needed? On Fri, Feb 24, 2017 at 4:50 PM, Aaron Lun wrote: > It's a good place to start, though it would be very handy to have a C(++) > API that can be linked against. I'm not sure how

Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

might there have been an object that references the obsolete class around? On Wed, Feb 22, 2017 at 1:25 PM, Levi Waldron wrote: > Thank you, Martin. I did that and went through the long tree re-installing > from source the re-starting R and trying my example again.

[Bioc-devel] sort(RangedSummarizedExperiment) fails

after example(RangedSummarizedExperiment) > rse1 class: RangedSummarizedExperiment dim: 200 6 metadata(0): assays(1): counts rownames: NULL rowData names(1): feature_id colnames(6): A B ... E F colData names(1): Treatment > sort(rse1) Error in get(name, envir = asNamespace(pkg),

Re: [Bioc-devel] Registering native routines with Rcpp

some more news on registration https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html On Mon, Feb 6, 2017 at 12:08 PM, Kevin Ushey wrote: > For what it's worth, the Rcpp team is aware that CRAN will soon be emitting > NOTEs for packages not registering native

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

i did not mean to implicate biocLite ... i am being too terse. i mention it because, after so many years of biocLite being spectacularly reliable ... persistence of a problem with its performance implies a serious upstream problem that would be very nice to eradicate ... On Wed, Feb 1, 2017 at

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/30/2017 09:52 AM, Levi Waldron wrote: > >> On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan >> wrote: >> >>> It seems like this is a local cache of the rstudio file that

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

For what it is worth I ran into the same situation with a new employee about two weeks ago. We got around it by doing manual installs of required packages but did not obtain a systematic solution. We did not have time to trace the situation sufficiently for a report. On Mon, Jan 30, 2017 at 9:52

Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

On Thu, Jan 5, 2017 at 9:33 PM, Anand MT wrote: > Hi, > > > I recently pushed few bug fixes and removed some dependency packages which > were no longer required. I did this a week ago and updated version to 1.0.4 > from 1.0.30. > > Build reports are OK for updated version.

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

sessionInfo()? I just did biocLite("MWASTools") with a devel version of R/BiocInstaller, and it seems to work well. On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea < andrea.rodriguez-martine...@imperial.ac.uk> wrote: > Hi, > > > I'm trying to install my MWASTools package (devel

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

pace Wolfgang Huber ... Peter I don't mean to be rude. Your comments deserve more study. But it was fun to remember GPos, which I had forgotten. On Wed, Nov 23, 2016 at 6:34 PM, Vincent Carey <st...@channing.harvard.edu> wrote: > library(GenomicRanges) > class?GPos > > On

Re: [Bioc-devel] makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)

*(forgot to carbon list)* *Did you not see a message like:* *Import genomic features from the file as a GRanges object ... OK* *Prepare the 'metadata' data frame ... OK* *Make the TxDb object ... OK* *Warning message:* *In makeTxDbFromGRanges(gr, metadata = metadata) :* * The following

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

sessionInfo()? On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante wrote: > Hello, > > Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') > stopped working with the error: > > > Error in file(file, "rt") : cannot open the connection > > From the

Re: [Bioc-devel] compiler package

search for ByteCompile at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file On Sun, Oct 30, 2016 at 4:12 PM, Ioannis Vardaxis < ioannis.varda...@math.ntnu.no> wrote: > Hi, > > Is it acceptable to use the compiler R-package to compile some functions > which use a

[Bioc-devel] Fwd: Question about a package submission

nges()) -- Forwarded message -- From: Ioannis Vardaxis <ioannis.varda...@math.ntnu.no> Date: Thu, Oct 27, 2016 at 7:27 AM Subject: Re: [Bioc-devel] Question about a package submission To: Vincent Carey <st...@channing.harvard.edu> R Under development (unstable) (2016-10-20

Re: [Bioc-devel] Question about a package submission

Please send a reproducible example with value of sessionInfo() at time of error. On Thu, Oct 27, 2016 at 7:06 AM, Ioannis Vardaxis < ioannis.varda...@math.ntnu.no> wrote: > Hi, > > I am using the R-devel version for writing an R package. I tried to use > the c(Granges,Granges) command to merge

[Bioc-devel] odd svn event

%master> svn up p11-kit: invalid config filename, will be ignored in the future: /etc/pkcs11/modules/gnome-keyring-module svn: Unable to parse URL '/bioconductor/!svn/bc/117512/trunk/madman/Rpacks/ggcyto/vignettes/Top features of ggcyto.Rmd' any hint on how to solve? thanks

Re: [Bioc-devel] VCF Intersection Using readVcf Remarkably Slow

Dario's computer is faster than mine > system.time(commonMutations <- readVcf(anotherFile, "hg19", rowRanges(aSet))) user system elapsed 426.271 57.296 483.766 The disk infrastructure is a determinant of throughput. Most VCF queries are decomposable and can be parallelized. After

Re: [Bioc-devel] Why sleuth is not in Bioconductor?

http://pachterlab.github.io/sleuth/download On Wed, Sep 14, 2016 at 6:20 AM, Ted Wong wrote: > Dear all, > > I thought Sleuth (https://github.com/pachterlab/sleuth) is part of the > Bioconductor. But I'm not able to find it anywhere. > > What's the status of the package?

Re: [Bioc-devel] problem in building package GSAR

you have to do "svn add" for any new source files to be archived On Mon, Aug 8, 2016 at 9:35 AM, Rahmatallah, Yasir wrote: > Dear Wolfgang, > > I believe I did upload the source code (.R) of the new functions as well > as their manual pages (.Rd). > First I checked out a

Re: [Bioc-devel] Listing package-specific methods

1) is the package connection key, or is it the 'directness' of the method in connection with the class of interest? (sorry to be so vague, there must be a more scientific term...) 2) it seems useful to get the signature too. this uses string operations to get at something that the class

Re: [Bioc-devel] poor performance of snpsByOverlaps()

I think you can get relevant information rapidly from the dbsnp vcf. You would acquire ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz.tbi and wrap in a TabixFile > tf class: TabixFile

Re: [Bioc-devel] GEOquery for Bioc devel

Hmm. Very important piece of software so we should try to remedy this. I had assigned some GEOquery problems in the edX class and there were some people who could not get getGEO to work, but the problem seemed intermittent. There was a workaround posted on the support site which involved

Re: [Bioc-devel] how to declare vignette processing properly

on a system with pandoc-citeproc, this error is avoided. good call dan! On Fri, May 6, 2016 at 1:15 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > Is pandoc-citeproc installed? > > > - Original Message - > > From: "Vincent Carey" <st...@channi

[Bioc-devel] how to declare vignette processing properly

this is for the current svn version of yriMulti, from 00check.log * checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", : It seems you should call rmarkdown::render()

Re: [Bioc-devel] Error on genes-method,OrganismDbi

Try 1.13.9 of OrganismDbi -- I ran into this and Val answered yesterday. You need to get 1.13.9 from svn source. On Tue, May 3, 2016 at 5:57 AM, Hector Corrada Bravo wrote: > Hello all, > > I just ran into this error. Any help appreciated: > > >library(Mus.musculus) > > gr

Re: [Bioc-devel] select(Homo.sapiens,...) failing

it from svn. > Let me know if you still have problems after updating. > > Val > > > On 05/02/2016 11:53 AM, Vincent Carey wrote: > > biocValid() says all is well ... > > > >> select(Homo.sapiens, keys="1001", keytype="ENTREZID", colu

[Bioc-devel] select(Homo.sapiens,...) failing

biocValid() says all is well ... > select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL") *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : * * object '.testSelectArgs' not found* > sessionInfo() R version 3.3.0 beta (2016-04-01 r70412) Platform:

Re: [Bioc-devel] Bioc-devel Digest, Vol 145, Issue 60

be helpful (and feasible) to have a generic that addresses this, but there is variation in the number of resources to be consulted to annotate a given platform, and no natural choice of resource for various types of feature. So programming and documentation at the user level seem inevitable for an

Re: [Bioc-devel] Bioc-devel Digest, Vol 145, Issue 60

I am in favor of simplifying the binding of useful metadata to our genome-wide objects. Before we automate this I think we should define a widely applicable procedure for this task ... and see how it works in examples from the ExperimentData library and ExperimentHub. Using fData for

Re: [Bioc-devel] OpenMP on OS X

other packages use #ifdef _OPENMP #include #endif have you tried that? On Fri, Apr 15, 2016 at 11:21 AM, Aaron Taudt wrote: > Hi, > > I am using openmp support in my C++ code and it builds just fine on Windows > and Linux. The morelia build output for OS X however

Re: [Bioc-devel] Feedback on OrganismDb development

On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr. wrote: > Great! This is an awesome opportunity to move to ENSEMBL as a default ;-) > (only half kidding, by the way) > > 1) BSGenome/2bit would be great -- I use this sometimes to generate fusion > transcripts with defined

Re: [Bioc-devel] Feedback on OrganismDb development

On Thu, Apr 7, 2016 at 10:34 AM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > BioC developers, > > After the release we plan to continue development the OrganismDb class > and packages. This email outlines some ideas for future direction. We're > interested in feedback on

Re: [Bioc-devel] File Layout

of this sort. Sincerely, Vincent Carey On Tue, Feb 9, 2016 at 10:28 PM, Val Krem via Bioc-devel < bioc-devel@r-project.org> wrote: > Hi all, > > I am trying to use the LDHeatmap die analysis of LD. > Genodata ID followed by the snps > > ID 1 2 2 1 2 2 1 .1 > > ID

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

On Mon, Jan 11, 2016 at 9:29 AM, Robert Castelo wrote: > hi, > > if i'm interpreting this correctly, the news archive of the UCSC Genome > Browser accessible here: > > http://genome.ucsc.edu/goldenPath/newsarch.html > > announced on June 29th, 2015, that they are

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

for these annotation selections? On Mon, Jan 11, 2016 at 1:40 PM, Robert Castelo <robert.cast...@upf.edu> wrote: > hi, > > On 01/11/2016 04:07 PM, Vincent Carey wrote: > [...] > >> Is it true that there is an asymmetry between Entrez gene ID and Ensembl >> gene ID for queryi

Re: [Bioc-devel] what is SummarizedExperiment a Vector of?

t it's a whole > other thing for a SummarizedExperiment to be a Vector. It could be > made to work, but I sort of doubt there is much consistency right now. > Perhaps I'm wrong. > > On Tue, Dec 15, 2015 at 11:15 AM, Vincent Carey > <st...@channing.harvard.edu> wrote: > &g

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

On Mon, Nov 23, 2015 at 1:11 PM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: > 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

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

In our discussions of the multiassay object/analysis problem, https://github.com/vjcitn/biocMultiAssay Kasper Hansen has suggested elaborations of the Hits API (see for example sec. 4 of http://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf

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

It also seems worth mentioning that the graph package ( http://bioconductor.org/packages/release/bioc/html/graph.html) has reasonable numbers of dependers and importers and could undoubtedly play a role in feature-feature management. On Sun, Nov 8, 2015 at 8:49 AM, Vincent Carey <

[Bioc-devel] svn woes

svn: OPTIONS of ' https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLBase': SSL handshake failed: Secure connection truncated (https://hedgehog.fhcrc.org) i got through once today after removing content of .subversion this strategy does not work now anyone else encountering this,

Re: [Bioc-devel] svn woes

On Wed, Oct 28, 2015 at 10:58 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > - Original Message ----- > > From: "Vincent Carey" <st...@channing.harvard.edu> > > To: "bioc-devel" <bioc-devel@r-project.org> > > Sent: Wed

Re: [Bioc-devel] SummarizedExperiment with alternate back end

> > around with linkedExperiments where those mappings are enforced; it's > > > becoming more of an issue with the TARGET pediatric AML study, where > > there > > > are numerous diagnosis-remission-relapse trios whose identity I wish to > > > verify periodically. The

[Bioc-devel] SummarizedExperiment with alternate back end

i am dealing with ~700 450k arrays they are derived from one study, so it makes sense to think of them holistically. both the load time and the memory consumption are not satisfactory. has anyone worked on an object type that implements the rangedSE API but has the assay data out of memory?

Re: [Bioc-devel] SummarizedExperiment with alternate back end

e >> are numerous diagnosis-remission-relapse trios whose identity I wish to >> verify periodically. The SNPs on the 450k array are great for this >> purpose, but minfi doesn't really have a slot for them per se, so live in >> metadata(). >> >> >> --t >>

Re: [Bioc-devel] AnnotationHub: cleanup

I followed part of this interchange with interest. I would love to see very wide adoption and appreciation of AnnotationHub and what I will describe does not seem to constitute important obstacles to this, but I have to confess that aspects of the model and grammar are confusing to me. I use

[Bioc-devel] svn cleanup failing on macosx

%vjcair> svn cleanup svn: E02: Can't open file '/Users/stvjc/Bioconductor/Devel/.svn/pristine/a3/a3c49be77e25c550a14eb1a4a8891736d970ebda.svn-base': No such file or directory %vjcair> touch /Users/stvjc/Bioconductor/Devel/.svn/pristine/a3/a3c49be77e25c550a14eb1a4a8891736d970ebda.svn-base

Re: [Bioc-devel] help with imports for new package and other questions

On Fri, Aug 14, 2015 at 10:03 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Indeed, you need to use importFrom to selectively import. In this process you'll realize how great it would be to have a function called importEverythingFromExcept( PACKAGE, NOT_THESE_FUNCTIONS)

[Bioc-devel] annoSet?

It seems to me we may need a class to manage related annotation structures. For example, the chromImpute segmentations of the genome defined for various cell types. I would like to be able to take a region of the genome (say a SNP) and ask how the state varies across cell types. AnnotationHub

Re: [Bioc-devel] annoSet?

PM, Martin Morgan mtmor...@fredhutch.org wrote: On 08/12/2015 02:01 PM, Vincent Carey wrote: It seems to me we may need a class to manage related annotation structures. For example, the chromImpute segmentations of the genome defined for various cell types. I would like to be able to take

Re: [Bioc-devel] Short URLs for packages?

OK, got it. On Wed, Aug 5, 2015 at 9:43 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Vincent Carey st...@channing.harvard.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: Tim Triche, Jr. ttri...@usc.edu, bioc-devel@r-project.org, Gabe Becker

Re: [Bioc-devel] vignettes with different builders in one package?

Thanks for all input. Henrik's comments deserve to be in WRE or developer doc for bioc, IMHO. On Tue, Aug 4, 2015 at 3:02 AM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: You can mix any type and number of vignette formats in a package. What vignette engine is used is solely specified by

Re: [Bioc-devel] Request for comment metagenomeFeatures package

very interesting development, we have several folks who will take a look. FYI %vjcair R CMD INSTALL greeng*b Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help Loading required package: digest Loading required package: tools Loading required package: utils Loading required

Re: [Bioc-devel] Request for comment metagenomeFeatures package

On Tue, Aug 4, 2015 at 3:00 PM, Martin Morgan mtmor...@fredhutch.org wrote: On 08/04/2015 06:43 AM, Nathan Olson wrote: We are starting to work on an infrastructure for annotation of 16S metagenomic sequencing datasets and would like your comments and/or contributions. Below are links to

[Bioc-devel] vignettes with different builders in one package?

Am I correct that this is not allowed? I have an old Sweave vignette and a newer Rmd vignette in gwascat but do not see how to build so that both vignettes are properly situated in the installed doc folder. The WRE manual doesn't address multiple builders. So I am planning to translate the older

Re: [Bioc-devel] Short URLs for packages?

Has there been a solution to the short URL question? On Tue, Mar 24, 2015 at 7:14 AM, Martin Morgan mtmor...@fredhutch.org wrote: On 03/24/2015 02:31 AM, Wolfgang Huber wrote: Before we start a religious war, can we make progress on the pragmatic goal of making it possible to provide such

Re: [Bioc-devel] Short URLs for packages?

OK, thanks. Should we add a little bit to each package landing page indicating how to link? On Tue, Jul 7, 2015 at 3:52 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Vincent Carey st...@channing.harvard.edu To: Martin Morgan mtmor...@fredhutch.org

Re: [Bioc-devel] Multiple colData in SummarizedExperiment

yes, if a formal extension is warranted. the metadata slot could also be used. On Thu, Jun 18, 2015 at 2:59 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: I think the more clean solution for Davide (if he inists on having separate objects; I decided against it in minfi) is to

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