Re: [Bioc-devel] rGADEM crash

___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr

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

the current Bioconductor release? The page at http://bioconductor.org/install/ does _not_ mention this important fact! Could somebody please fix this? Simon -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona

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

to simultaneously look to the .Rnw and .R files. cheers, robert. On 07/16/2013 04:59 PM, Martin Morgan wrote: On 07/16/2013 06:43 AM, Robert Castelo wrote: hi Martin, i have tried it out by simply adding the code snippet you specify below to the preamble of one of the vignettes of 'qpgraph

Re: [Bioc-devel] VcfFile and VcfFileList

=TabixFile, genome=character, param=missing file=TabixFile, genome=character, param=RangedData file=TabixFile, genome=character, param=RangesList file=TabixFile, genome=character, param=ScanVcfParam Does this fit your need/use case? Valerie On 07/17/2013 03:22 AM, Robert Castelo wrote: hi, i'm

[Bioc-devel] feature request: pmax for columns of DataFrame objects

hi, i would like to do the following: library(IRanges) do.call(pmax, data.frame(x=1:10, y=2:11)) [1] 2 3 4 5 6 7 8 9 10 11 with 'DataFrame' objects: do.call(pmax, DataFrame(x=1:10, y=2:11)) Error in do.call(pmax, DataFrame(x = 1:10, y = 2:11)) : second argument must be a list

Re: [Bioc-devel] very slow to use intronsByTranscript in GenomicFeatures

___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003

Re: [Bioc-devel] GSVA and LumiBatch objects

://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550

[Bioc-devel] problem w/ exprs- method and LumiBatch objects

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' object can be accessed and replaced with the

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

/bioc-devel https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax

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

hi Kasper, you're right. i should have done this upfront, this was too much S4 magic to be true :) cheers, robert. On 1/10/14 5:14 PM, Kasper Daniel Hansen wrote: Robert: The alternative to using exprs- is to instantiate a new object, just copying the old phenodata. Kasper On Fri, Jan

Re: [Bioc-devel] GSVA and LumiBatch objects

/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550

[Bioc-devel] bioconductor AMI shiny app

hi, i'm trying to use a shiny app through AWS and the bioconductor AMI, but i cannot make it work. i have created a security group in AWS that has open the 8787 and 6219 ports, the former for RStudio and the latter to access the shiny app. this is the command-line output from my desktop

[Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2

hi, this is just a warning to developers who may have C code in their packages. today i fixed a problem in the C code of the package VariantFiltering which can be reproduced with the following toy example. ===test.c #include stdio.h #include ctype.h int main(void) { char msg[]

Re: [Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2

hi Dan, On 06/12/2014 04:28 PM, Dan Tenenbaum wrote: [...] Thanks for figuring this out and sharing it. Note that on the build machines, the compiler used on Mavericks is not gcc but clang. More info here: http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/morelia-NodeInfo.html

Re: [Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2

development. Thanks for bringing it up! Nate On Mon 16 Jun 2014 07:42:36 AM PDT, Robert Castelo wrote: hi Nathaniel, On 06/14/2014 01:01 AM, Nathaniel Hayden wrote: Hi, Robert. You're welcome. It sounds like something isn't happening, but you think it should. Could you be more precise about what

Re: [Bioc-devel] mapping vector of gene ids to gene symbols

-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514

Re: [Bioc-devel] mapping vector of gene ids to gene symbols

deleted]] _ Bioc-devel@r-project.org mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo

[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

hi, after updating to the last devel version of all packages I cannot load one of the packages I develop, VariantFiltering, in MacOS (Snow Leopard) while the same version loads smoothly in LInux. This is the error I get: library(VariantFiltering) No methods found in IRanges for requests:

Re: [Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

] VariantAnnotation_1.11.16 XML_3.98-1.1 [41] xtable_1.7-3 XVector_0.5.7 [43] zlibbioc_1.11.1 Maybe try with a fresh install of R? Or try reinstalling everything that's outdated with biocLite()? Dan - Original Message - From: Robert Castelo robert.cast...@upf.edu

[Bioc-devel] NAMESPACE question

hi, i have the following warning message when installing the devel version (0.99.5) of my package 'qpgraph': ** testing if installed package can be loaded Warning: replacing previous import by 'IRanges::as.vector' when loading 'qpgraph' * DONE (qpgraph) after investigating the issue i think

Re: [Bioc-devel] NAMESPACE question

RSQLite_0.11.4 rtracklayer_1.25.17 sendmailR_1.2-1 [37] stringr_0.6.2tools_3.1.0 XML_3.98-1.1 xtable_1.7-4 [41] XVector_0.5.8zlibbioc_1.11.1 cheers, robert. On 10/07/2014 05:54 PM, Martin Morgan wrote: On 10/07/2014 08:15 AM, Robert Castelo wrote

[Bioc-devel] How to update annotation packages

Hi, i submitted one release ago the following annotation packages: MafDb.ALL.wgs.phase1.release.v3.20101123 MafDb.ESP6500SI.V2.SSA137.dbSNP138 phastCons100way.UCSC.hg19 for which i'm also the maintainer. while the functionality to access their annotation resides in another software

Re: [Bioc-devel] 'BiocInstaller' package not in repository error during nightly build

Error : ''BiocInstaller' package not in repository' while trying http://bioconductor.org/packages/3.1/bioc Execution halted -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr

[Bioc-devel] VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem

hi there, in my package VariantFiltering i have an example VCF file from a Hapmap CEU trio including three chromosomes only to illustrate its vignette. i've come across a problem with the function readVcf() in VariantAnnotation that may be specific of the situation of a VCF file not having

Re: [Bioc-devel] VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem

...@fhcrc.org wrote: This is a good question. I'm not sure we want seqlevelsStyle() to also alter the genome value. I think it's a reasonable request but I'd like to open it up to discussion. I've cc'd a few others for input. Valerie On 10/24/14 09:05, Robert Castelo

Re: [Bioc-devel] VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem

dropping chrM. I was proposing that this could be done with something like: genome(vcf, rectifySeqlevels=TRUE) - genome(txdb) For convenience, we might want that argument to be TRUE by default, but that would change current behavior. On Fri, Oct 24, 2014 at 3:41 PM, Robert Castelo

Re: [Bioc-devel] MacOS-specific error in VariantAnnotation::locateVariants() in devel

PM, Dan Tenenbaum wrote: Hi Robert, - Original Message - From: Robert Castelo robert.cast...@upf.edu To: bioc-devel@r-project.org Sent: Friday, November 21, 2014 8:40:07 AM Subject: [Bioc-devel] MacOS-specific error in VariantAnnotation::locateVariants() in devel hi, I have

[Bioc-devel] cryptic error in VariantAnnotation::locateVariants()

hi Valerie, i'm afraid i have hit another cryptic error in locateVariants() related to some recent update of the devel version of the package, could you take a look at it? (code below..) thanks!! robert. == library(VariantAnnotation)

Re: [Bioc-devel] VRanges with multiple samples

hi Michael, thanks for sharing your opinion, comments below, On 01/28/2015 06:22 PM, Michael Lawrence wrote: [...] Is your concern here scalability, ease of use, or what? If scalability, we should probably start thinking about a more efficient representation for repeated vectors, kind of like

[Bioc-devel] VRanges with multiple samples

hi, currently, the VariantFiltering package works with GRanges objects obtained from locateVariants() and predictCoding() to hold annotated variants and add further annotations. However, I'd like to use 'VRanges' objects which are, as far as i understand them, developed for exactly the

Re: [Bioc-devel] VariantAnnotation::isDelins() ??

addition. I'll put it on the TODO. If you need this immediately I'd be happy to accept a patch (with unit tests). Valerie On 02/10/2015 06:29 AM, Robert Castelo wrote: hi, in the VariantAnnotation package, the help of the functions for identifying variant types such as SNVs, insertions, deletions

[Bioc-devel] zero-width ranges representing insertions

dear devel people, specially Val and Michael, Hervé has recently added an annotation package that includes non-SNVs variants from dbSNP, it is called: library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38) if you execute the corresponding example you'll see the kind of information stored in the

Re: [Bioc-devel] zero-width ranges representing insertions

, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: dear devel people, specially Val and Michael, Hervé has recently added an annotation package that includes non-SNVs variants from dbSNP, it is called: library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38) if you

[Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

in my message below, the line that it says: head(loc_all$CDSID) it should say head(coding2$CDSID) cheers, robert. == hi, there is a little tiny bug in the current devel version of VariantAnnotation::predictCoding(), and more concretely within

Re: [Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

) To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] little tiny bug in CDSID annotations from predictCoding() Hi Robert, Thanks for reporting the typo and bug. Now fixed in 1.13.41. Valerie On 03/17/2015 10:58 AM, Robert Castelo wrote: in my message below, the line that it says

[Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

hi, there is a little tiny bug in the current devel version of VariantAnnotation::predictCoding(), and more concretely within VariantAnnotation:::.localCoordinates(), that precludes the correct annotation of the CDSID column: library(VariantAnnotation)

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

[[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona

Re: [Bioc-devel] show method for CompressedVRangesList-class

On Tue, Feb 24, 2015 at 2:36 PM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: so, yes, but IMO rather than inheriting the show method from a GRangesList, i think that the show method for CompressedVRangesList objects should be inherited from a VRangesList

Re: [Bioc-devel] show method for CompressedVRangesList-class

Lawrence wrote: If you're storing data on a relatively small number of individuals (say, hundreds), you should use SimpleVRangesList, not CompressedVRangesList. On Wed, Feb 25, 2015 at 7:10 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: i see you point

[Bioc-devel] show method for CompressedVRangesList-class

hi, i'm using the CompressedVRangesList class in VariantFiltering to hold variants and their annotations across multiple samples and found that there was no show method for this class (unless i'm missing the right import here) so i made one within VariantFiltering by copyingpasting from

Re: [Bioc-devel] show method for CompressedVRangesList-class

are in the accessing of the elements. But this seems like too much longer, so I will look into it. On Wed, Feb 25, 2015 at 8:12 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: my current reason to prefer

Re: [Bioc-devel] show method for CompressedVRangesList-class

inherit the method for GRangesList. On Tue, Feb 24, 2015 at 9:53 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: hi, i'm using the CompressedVRangesList class in VariantFiltering to hold variants and their annotations across multiple samples

[Bioc-devel] MafDb.ExAC.r0.3.sites missing from build

hi, i have just noticed that VariantFiltering breaks in the last build: http://www.bioconductor.org/checkResults/3.1/bioc-LATEST/VariantFiltering/zin2-buildsrc.html and the reason is that the devel annotation package

Re: [Bioc-devel] MafDb.ExAC.r0.3.sites missing from build

oops, how embarrassing :*} thanks Dan, just did it. On 4/10/15 11:35 PM, Dan Tenenbaum wrote: Robert, you just need to put MafDb.ExAC.r0.3.sites in Depends, Suggests, or Imports. Dan - Original Message - From: Robert Castelo robert.cast...@upf.edu To: bioc-devel@r-project.org Sent

[Bioc-devel] GSEABase::getOBOCollection() missing children

hi, importing an OBO file with GSEABase::getOBOCollection() I have observed missing children in the imported ontology. Here is an example with the Sequence Ontology: library(GSEABase) oboSOXP - getOBOCollection(http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo;) Warning message:

Re: [Bioc-devel] GSEABase::getOBOCollection() missing children

hi Martin, thanks for the quick fix!!! best regards, robert. On 06/05/2015 08:05 PM, Martin Morgan wrote: On 06/05/2015 08:51 AM, Robert Castelo wrote: hi, importing an OBO file with GSEABase::getOBOCollection() I have observed missing children in the imported ontology. Here is an example

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

/2015 09:49 PM, Michael Lawrence wrote: This changed recently. VariantAnnotation in devel no longer enforces a strand on VRanges, or at least it allows the * case. On Fri, May 22, 2015 at 11:33 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: Hi, I have

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

-- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550 ___ Bioc-devel@r

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

for negative strand variants? On Wed, Jun 10, 2015 at 5:54 AM, Robert Castelo robert.cast...@upf.edu wrote: Michael, regarding our email exchange three weeks ago, I found a couple of places in VariantAnnotation that IMO need to be updated to avoid enforcing strand on VRanges. these places occur when

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

strand for at least 2 reasons: (1) to be less error prone [of course this runs completely counter to flexibility] and (2) simplicity [we don't have to worry about what - means for ref/alt, overlap, etc]. On Thu, Jun 11, 2015 at 6:05 AM, Robert Castelo robert.cast...@upf.edu wrote: one option for me

Re: [Bioc-devel] strandless introns with VariantAnnotation::locateVariants()

and strand is set to '*' if different strands are found in the same list element. The fix has been checked into release and devel. Valerie On 06/11/2015 03:26 AM, Robert Castelo wrote: hi Valerie, thanks for the fix, it seems that it required a more complex update than i initially thought looking

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

() output with its input. The one for VRanges might do something like the above. Michael On Thu, Jun 11, 2015 at 9:14 AM, Robert Castelo robert.cast...@upf.edu wrote: Of course, the inclusion of strand would imply an interpretation of the variant and its strand (e.g., -) with respect

[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

hi, one of the recent changes in the devel IRanges has been to defunct the 'ifelse' method for 'Rle' objects. This was warned during the previous devel cycle and so it does with current release. One of the affected functions is the VRanges object constructor, 'VRanges()'. Since I use this

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

bring these methods back if there is a way to preserve the semantic of base::ifelse() (which relies on delayed evaluation of the 'yes' and 'no' arguments). H. The goal with Rle was to make it behave as conveniently

Re: [Bioc-devel] upgrading

Try in a fresh run: remove.packages("BiocInstaller") source("http://bioconductor.org/biocLite.R;) cheers, robert. Original message From: Kasper Daniel Hansen Date:20/10/2015 16:55 (GMT+01:00) To: bioc-devel@r-project.org Subject:

[Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

hi, I have encountered a problem when using the bpvec() function from the BiocParallel package with DNAStringSet objects and the "SerialParam" backend: library(Biostrings) library(BiocParallel) ## all correct when using the multicore backend bpvec(X=DNAStringSet(c("AC", "GT")),

Re: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

). Valerie - Forwarded Message - From: "Robert Castelo" <robert.cast...@upf.edu> To: bioc-devel@r-project.org Sent: Wednesday, September 2, 2015 8:12:33 AM Subject: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem hi, I have encountered a problem when

Re: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

rote: Hi Robert, Thanks for reporting the bug. The problem was with how 'X' was split before dispatching to bplapply() and affected both SerialParam and SnowParam. Now fixed in release (1.2.21) and devel (1.3.52). Valerie - Forwarded Message - From: "Robert Castelo"<robert.cast...@up

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

ranscripts mapped to Entrez Gene IDs. I'll work on this and will also investigate makeTxDbFromGRanges's failure on AnnotationHub's GFF files from GENCODE. H. On 01/11/2016 06:29 AM, Robert Castelo wrote: hi, if i'm interpreting this correctly, the news archive of the UCSC

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

9"))) ) user system elapsed 0.237 0.055 16.476 faster than a speeding snplocs? but perhaps there is information loss or other diminished functionality On Fri, Jun 17, 2016 at 12:53 PM, Robert Castelo <robert.cast...@upf.edu <mailto:robert.cast...@upf.edu>> wrote:

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

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 discontinuing the generation of UCSC Known Genes annotations for human, and provide the Gencode

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

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 querying org.Hs.eg.db (I tend to prefer Homo.sapiens as a symbol mapping resource)? Both ENTREZID and ENSEMBL are listed as keytypes. My question is

Re: [Bioc-devel] Classes to be supported by ggraph

hi, i use the part of the functionality of the graph package within my packages qpgraph and VariantFiltering. I mostly use the 'graphBAM' class that provides a memory-efficient representation of the graph and the possiblity to store data associated with nodes and edges via the 'nodeData()'

Re: [Bioc-devel] seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles

, it sounds like the user should be able to do seqlevelsStyle(x) <- "Ensembl" independently of whether this will result in seqlevels that are the same as if s/he had done seqlevelsStyle(x) <- "NCBI". Cheers, H. On 01/25/2016 02:39 AM, Robert Castelo wrote: hi, i would l

Re: [Bioc-devel] Support site unavailable

immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health

[Bioc-devel] vignette metadata dissapeared in Sweave/PDF vignettes

hi, I have noticed that in the recent release of BioC the vignettes produced as Sweave/PDF documents do not show anymore the metadata written using %\VignetteIndexEntry{}, while this seems to work fine with the HTML vignettes. compare for instance the vignette metadata in the landing pages

[Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

hi, there's a warning issued by GenomeInfoDb::keepStandardChromosomes() because of multiple compatible sequence styles, that i guess it should be corrected. this warning can be reproduced minimally as follows; library(GenomicRanges) library(GenomeInfoDb) gr <- GRanges(seqnames="1",

Re: [Bioc-devel] TabixFileList() constructor broken in devel

ist function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize = NA_integer_) { index <- as.character(index) .RsamtoolsFileList(file, index, ..., yieldSize = yieldSize, class = "TabixFile") } On Thu, Dec 29, 2016 at 11:5

Re: [Bioc-devel] TabixFileList() constructor broken in devel

tistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > -------- > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Robert Castelo <robert.cast...@upf.edu> &

[Bioc-devel] TabixFileList() constructor broken in devel

hi, the 'TabixFileList()' constructor in Rsamtools seems to be broken in devel: library(Rsamtools) example(TabixFileList) ## which actually does not construct any 'TabixFileList' TabixFileList(tbx) Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type

Re: [Bioc-devel] build on different version

/checkResults/devel/bioc-LATEST/ For now I would not worry about the error on toluca2. Valerie On 04/14/2017 02:42 AM, Robert Castelo wrote: hi, on tuesday april 11th i checked in changes for VariantFiltering version 1.11.10 and i've seen that today the build for tuesday gives errors on version

[Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

hi, it seems that recent changes to S4Vectors are breaking the coercion from the '*VCF' class to the 'VRanges' class. the traceback points to the private function 'recycleVector() from the 'S4Vectors' package, please find below the minimal example that reproduces the problem with the session

[Bioc-devel] build on different version

hi, on tuesday april 11th i checked in changes for VariantFiltering version 1.11.10 and i've seen that today the build for tuesday gives errors on version 1.11.9 with snapshot date from april 7th. i do my devel changes in the github repo rcastelo/VariantFiltering and check them into SVN,

Re: [Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

BiocInstaller_1.25.3 [22] GenomicFeatures_1.27.14 XML_3.98-1.5 On Wed, Apr 19, 2017 at 7:06 AM, Robert Castelo <robert.cast...@upf.edu> wrote: hi, it seems that recent changes to S4Vectors are breaking the coercion from the '*VCF' class to the 'VRanges' class. the traceback points to the private fu

[Bioc-devel] strand<- method for 'GPos' doesn't work

hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1) <- "-" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GPos" traceback() 10: methods::slot(object, name) 9: getElement(x,

Re: [Bioc-devel] strand<- method for 'GPos' doesn't work

great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1

Re: [Bioc-devel] strand<- method for 'GPos' doesn't work

now if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method

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

dear developers, in the framework of a package i maintain, VariantFiltering, i'm using the 'FilterRules' class defined in the S4Vector package and i'm interested in serializing (e.g., saving to disk via 'saveRDS()') 'FilterRules' objects where some rules may defined using functions. my

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

On 05/07/2017 20:39, Martin Morgan wrote: On 07/05/2017 12:59 PM, Robert Castelo wrote: dear developers, in the framework of a package i maintain, VariantFiltering, i'm using the 'FilterRules' class defined in the S4Vector package and i'm interested in serializing (e.g., saving to disk via

[Bioc-devel] GenomicRanges::cbind() problem

base other attached packages: [1] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 IRanges_2.10.3 [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 XVector_0.16.0 [4] GenomeInfoDbData_0.99.0 RCurl_1.95-4.8

Re: [Bioc-devel] GenomicRanges::cbind() problem

12, 2017 at 12:06 AM, Robert Castelo <robert.cast...@upf.edu> wrote: dear GenomicRanges developers, my package qpgraph is breaking in devel due to the following behavior of GenomicRanges: library(GenomicRanges) gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))

[Bioc-devel] how to verify upstream git changes

hi, i've had a smooth transition from SVN to git for all the software packages i maintain (thanks for the great documentation!!) and i have the following question. i keep a local git repository for each of my software packages, hanging from my github account and this means that i have to

Re: [Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

(in version 1.15.18) so now you should be able to install it again. Sorry for the inconvenience, H. On 12/19/2017 12:31 AM, Robert Castelo wrote: hi, multiple packages, among them, Gviz or VariantFiltering, currently break in the build machines with the following error: Error : object

[Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

hi, multiple packages, among them, Gviz or VariantFiltering, currently break in the build machines with the following error: Error : object ‘path’ is not exported by 'namespace:Rsamtools' see, for instance:

Re: [Bioc-devel] S4Vectors::DataFrame, S4Vectors::cbind() and non-elementwise metadata

on Annotated derivatives (e.g. shift()) propagate the object-wise metadata, even though it's not clear that this information will still be relevant for the transformed object. Cheers, H. On 10/25/2017 07:39 AM, Robert Castelo wrote: hi, i've the following question on how 'S4Vectors::cbind

[Bioc-devel] S4Vectors::DataFrame, S4Vectors::cbind() and non-elementwise metadata

hi, i've the following question on how 'S4Vectors::cbind()' works on 'DataFrame' objects. let's say i have the following two toy 'DataFrame' objects, each of them including some elementwise and non-elementwise metadata (i hope i'm using the right terminology!): library(S4Vectors) dtf1 <-

Re: [Bioc-devel] limma Suggests:statmod vs Imports:statmod

of limma that never use duplicateCorrelation or other functions that require statmod will never need to install it. For more info, see this old post about the same problem: https://support.bioconductor.org/p/16932/ Regards, Ryan On Thu, May 10, 2018 at 11:58 PM Robert Castelo <

[Bioc-devel] limma Suggests:statmod vs Imports:statmod

hi, this is a question for limma developers. at every new fresh installation of BioC and limma i get this message when i use 'duplicateCorrelation()': "statmod package required but is not installed" i just install 'statmod' and problem solved. this, however, triggers questions from some of

[Bioc-devel] gwaswloc class broken

hi, the 'gwasloc' class from the gwascat package seems to be broken in devel, i suspect due to recent changes in the 'GRanges' class or some other class upstream, because the definition of the 'gwasloc' class in gwascat/R/classes.R is: setClass("gwaswloc",

Re: [Bioc-devel] gwaswloc class broken

  traveling but will tackle asap    if u can coerce to granges it may help as the only purpose of gwaswloc is to have a concise show method    but the coercion might fail too On Tue, Feb 20, 2018 at 6:43 AM Robert Castelo <robert.cast...@upf.edu <mailto:robert.cast...@upf.edu>> w

[Bioc-devel] VariantAnnotation: streaming over a genomic range

hi, when i use the function 'readVcf()' from the 'VariantAnnotation' package through a 'TabixFile' object, i can stream over it even if i do not specify the argument 'yieldSize', although in that case the streaming is trivial because is reading the whole file into main memory: CEUvcf <-

Re: [Bioc-devel] RareVariantVis failed

nges, ...) :   assuming query ranges genome build is the one of the GScores object (Genome Reference Consortium GRCh37). Error in match.names(clabs, nmi) : names do not match previous names Calls: chromosomeVis ... eval -> eval -> eval -> rbind -> rbind -> match.names I will be than

Re: [Bioc-devel] Warnings in build for BioCor

Lluis, something you can do in you NAMESPACE to follow the advice below from Matthias if you are importing the functionality of a whole package is: import(pkgyouneed, except=functionmethodyoudefine) in this way, you're importing everything except that particular function or method that you

Re: [Bioc-devel] Dependency to PEER

hi, it seems that the PEER repository hasn't been updated in the last 7 years and that the package is distributed under a GPL-2 license. if i'm interpreting this correctly, you could copy that code into your package redistributing it under the GPL-2 license and asking the users of PEER to

Re: [Bioc-devel] proposal for additional seqlevelsStyle

I second this, and would suggest to name the style as 'GRC' for "Genome Reference Consortium". thanks Vince for bringing this up, being able to easily switch between genome styles is great. if 'paste0()' in R is one of the most influential contributions to statistical computing

Re: [Bioc-devel] proposal for additional seqlevelsStyle

g and some significant refactoring. It wouldn't be just a matter of adding a column to genomeStyles()$Homo_sapiens. H. On 12/10/19 14:19, Robert Castelo wrote: I second this, and would suggest to name the style as 'GRC' for "Genome Reference Consortium". thanks Vince for bringing

Re: [Bioc-devel] progress with BiocParallel::bpiterate

of the iteration is known... is bpiterate() providing functionality (REDUCE, maybe? that bplapply() does not? Martin On 11/27/19, 1:11 PM, "Bioc-devel on behalf of Robert Castelo" wrote: hi, the 'BiocParallel::bpiterate()' method shows progress through the foll

[Bioc-devel] progress with BiocParallel::bpiterate

hi, the 'BiocParallel::bpiterate()' method shows progress through the following call: setMethod("bpiterate", c("ANY", "ANY", "SerialParam"),     function(ITER, FUN, ..., REDUCE, init, reduce.in.order = FALSE,     BPPARAM=bpparam()) { [...]     progress <-

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

em. Probably also worth mentioning the itdepends package ( https://github.com/r-lib/itdepends), which I think tries primarily to determine the relationship between package dependencies and lines of code, which seems like complementary information. Martin On 2/6/20, 12:29 PM, "Robert Castelo&

[Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

hi, when i load the package 'GenomicScores' in a clean session i see thorugh the 'sessionInfo()' that the package 'Matrix' is listed under "loaded via a namespace (and not attached)". i'd like to know what is the dependency that 'GenomicsScores' has that ends up requiring the package

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