Re: [Bioc-devel] BiocManager now on CRAN

-devel/ > users have R 3.5.0 or greater going forward. > > > Regards, > Marcel > > > On 07/16/2018 11:51 AM, Gabe Becker wrote: > > Marcel et al, > > > > My genbankr package is one of the ones that mentions biocLite (in > > README.md, actually, not the vigne

Re: [Bioc-devel] BiocManager now on CRAN

Marcel et al, My genbankr package is one of the ones that mentions biocLite (in README.md, actually, not the vignette proper, but still...). Historically this was just because I had missed your email and hadn't updated it, but when I sat down to do it I ran into an issue: BiocManager, while a hug

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

: > Only if Rsubread is used unconditionally. > > On Fri, May 18, 2018 at 2:00 PM, Gabe Becker wrote: > > Vivek, > > > > Why (ie in what sense) is the package suggested? Is it used in your > tests, > > examples, or vignette? > > > > If so, those woul

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

Vivek, Why (ie in what sense) is the package suggested? Is it used in your tests, examples, or vignette? If so, those would also fail during R CMD check if the package is not available even if that environment variable is were false, wouldn't they? ~G On Fri, May 18, 2018 at 1:55 PM, Bhardwaj,

Re: [Bioc-devel] Missed deadline

t; 6 - write paper (decide which journal) >> 7 - have submission of paper + package ready for October deadline. >> >> Regarding the sequence of events - do other authors usually release on >> bioconductor before submission of a paper or at the same time? >> What would yo

Re: [Bioc-devel] Missed deadline

Indeed, and to be a bit more explicit about Levi's point, you *can* publish your package to bioconductor any time after the deadline, it will simply go to the development repo for ~6 months, which, as he points out, may not be a bad thing if it's not ready yet. On Tue, Apr 3, 2018 at 8:06 AM, Levi

Re: [Bioc-devel] [R-pkg-devel] DESCRIPTION file building problem

Dario, Does this ever happen if you build in the parent directory? I don't think building within the package directory is best practice and I'm not sure it's (officially) supported at all. The error message seems to support that. ~G On Wed, Mar 21, 2018 at 9:40 AM, Dario Righelli wrote: > Hi,

Re: [Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]

Paul, I don't think these are necessarily in conflict. If myigv represents the IGV session/state, then add_track(myigv, vcfobj) could call down to add_track(myigv,VariantTrack(vcf)) so you'd get the default behaviors. you could also support add_track(myigv, vcf, title = "bla", homVarColor = "whate

Re: [Bioc-devel] IGV - a new package in preparation

Paul, Sounds cool! My one note after a quick first pass is that here: On Wed, Mar 7, 2018 at 2:15 PM, Paul Shannon wrote: > > Note that though igv.js typically gets its track data from CORS/indexed > webservers, the IGV package will also support locally created R data.frames > describing either

Re: [Bioc-devel] as.list fails on IRanges inside of lapply(, blah)

t; be restored (with a deprecation warning) once all the packages that > need a fix get one (only 7 packages left on my list). I should be done > with them in the next couple of days. > > H. > > > On 02/20/2018 09:41 AM, Gabe Becker wrote: > >> All, >> >> I&

[Bioc-devel] as.list fails on IRanges inside of lapply(, blah)

All, I'm trying to track down the new failure in my genbankr package and it appears to come down to the fact that i'm trying to lapply over an IRanges, which fails in the IRanges to list (or List?) conversion. The particular case that fails in my example is an IRanges of length 1 but that does no

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

IT seems like you could also force a copy of the reference object via $copy() and then force a refresh of the conn slot by assigning a new db connection into it. I'm having trouble confirming that this would work, however, because I actually can't reproduce the error. The naive way works for me on

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

Arman, Not on the Bioc team per se, but I would say only have a checkout of the release branch when you need it, ie a bug is reported, you have fixed it in devel, and you are ready to push the very narrow bugfix to release. I only keep "master" checkouts of my packages on a permanent basis. You g

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

FYI, that seems to be a locale issue, as the locale defines the sort order. The first one is sorting alphabetically in a case-insensitive manner, eg aAbBcC etc, the second is sorting in a case sensitive manner, where capital letters all come before lower-case letters, e.g. ABC...YZabc... You can

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On Thu, Oct 5, 2017 at 10:03 PM, Gabe Becker wrote: > Oh, and the svn/git walking knows about release branches so it will find > hot-patch versions correctly, as well. > In the Bioc case, I mean, not generally. And with that flurry of emails I'm off to bed. Best, ~G > >

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Oh, and the svn/git walking knows about release branches so it will find hot-patch versions correctly, as well. ~G On Thu, Oct 5, 2017 at 10:01 PM, Gabe Becker wrote: > Correct. The actual order of checks is: > >1. did switchr already retrieve that exact version for something else

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

ot;bioc") it'll search (i) the CRAN archives, (ii) the Bioconductor repos(es), and then (iii) the Bioconductor Git repos - is that a correct observation? (I installed from https://github.com/gmbecker/switchr) /Henrik On Thu, Oct 5, 2017 at 4:15 PM, Gabe Becker wrote: > In point

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

k for recent versions. On Thu, Oct 5, 2017 at 3:58 PM, Gabe Becker wrote: > Henrik et al., > > My switchr package (on CRAN, github at: http://github.com/gmbecker/switchr, > preprint of the paper here: https://arxiv.org/abs/1501.02284 > <https://arxiv.org/abs/1501.02284>

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Henrik et al., My switchr package (on CRAN, github at: http://github.com/gmbecker/switchr, preprint of the paper here: https://arxiv.org/abs/1501.02284 ) can do this. In fact, installing (cohorts of) old versions of packages is one of it's primary purposes. Speci

Re: [Bioc-devel] Can copy right holder and correspondence be two differentindividuals?

7;t do any implementation then it gets murkier. Anyway that's how I treat authorship for r packages. Hope that helps, ~G On May 20, 2017 10:29 AM, "Gabe Becker" wrote: > So r packages don't really have a formal "corresponding author" concept, > though they do have a n

Re: [Bioc-devel] Can copy right holder and correspondence be two differentindividuals?

So r packages don't really have a formal "corresponding author" concept, though they do have a number of related concepts that may do what you need: Authors/creators/contributors go in the authors (@R) field in the description. These are the people who created the package. Copyright holder is a f

Re: [Bioc-devel] R6 and Bioconductor

On May 12, 2017 4:23 PM, "Garth Ilsley" wrote: Thank you. > One place where one might think of using R6 is in the implementation of a mutable data model underlying a GUI like a Shiny app. > If mutable semantics are required, consider using S4 reference classes, as they offer more features than R

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

On Fri, Apr 7, 2017 at 12:46 PM, wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > > On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: >> >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> >>> > On 04/06/2017 03:29 AM, Michael Lawrence wrote: >>> > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morg

Re: [Bioc-devel] Citation of an accompanying paper

Alina, Typically in cases like the one you describe, people want users to use the paper citation when citing use of the package. Whether this is what they "should" want is somewhat debatable, but at least it seems reasonable, as by using the package users are, assumedly, applying the method your p

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

On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun wrote: > Hi everyone, > > > I was thinking of something that you could supply any supported matrix > representation to a registered function via .Call; the C++ constructor > would recognise the type of matrix during class instantiation; and > operations

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

Hey all, I just wanted to chime in on this as it relates to some work I'm doing with Luke Tierney and Tomas Kalibera. There's another approach to this that will be available in the near future (we hope). Alternative internal representations of atomic vectors, including compact representations, ar

Re: [Bioc-devel] GitHub and svn

Mani, Related to what Kasper said, one thing you can do is commit directly to the canonical repo for your package (which again is not on github once the package is accepted) from rstudio. It supports svn. ~G On Oct 15, 2016 11:38 AM, "Kasper Daniel Hansen" < kasperdanielhan...@gmail.com> wrote:

Re: [Bioc-devel] S4 overwrite inspector of virtual class

maybe validator is the proper term in R? i've highlighted what I refer to > as the inspector below as an example: > > setClass("file", > contains="file_virtual", > validity=function(object){ > # Check that object is

Re: [Bioc-devel] S4 overwrite inspector of virtual class

Zach, Is an inspector a method you define on your classes? I'm not quite following what you mean by your question. AFAIK inspectors are not generally a thing in R (at least that go by that name). ~G On Mon, Aug 15, 2016 at 9:42 AM, Zach Skidmore wrote: > Hi All, > > I'm currently transforming

Re: [Bioc-devel] memory inefficiency problem of building MSPC packages

Jurat, Have you tried posting on the bioconductor support site ( support.bioconductor.org)? That is the appropriate venue for usage questions such as yours, and I suspect you may get a better response there. The bioc-devel mailinglist is intended for a different type of question. Best, ~G On Mo

Re: [Bioc-devel] Imports version that's only available on github?

Alex (et al), Yihui is currently working towards a CRAN release for a modern version of DT, so sometime "soon" (I have no insight into what definition of soon is in use here) things should work in your particular case. ~G On Fri, Aug 5, 2016 at 11:02 AM, Martin Morgan < martin.mor...@roswellpark

Re: [Bioc-devel] [devteam-bioc] Segfault in Rsamtools when R built with static libz

Martin and Michael, It looks like I have been conflating two issues when trying to deal with these things. The problem of grabbing the system libz seems to have gone away in the Rsamtools case earlier than in the libR.so case during my process. wwI will check back in if something raises it's head

[Bioc-devel] Segfault in Rsamtools when R built with static libz

Hi all, I build the R installations on our research cluster. Unfortunately we are running an older OS so the system versions of various libraries (libz, bz2, pcre and libcurl, specifically) are not modern enough to build R with. For protection from ABI incompatability when R is interacting with o

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

I wonder if raw only means "raw after line return munging"? can you attach the file that gets downloaded via email? (off list is fine) On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres wrote: > Hi, > > I'm trying to figure out what is going wrong with an error that pops > up on Windows o

Re: [Bioc-devel] DT CRAN vs github versions

Laurent, I'd argue quite strongly against this from a systems perspective. Your package wouldn't be installable via biocLite. That function can see github repos, but only when told to and not as dependencies AFAIK. A package passing but being uninstsllable would be a Very Bad Thing (tm) IMHO. You

Re: [Bioc-devel] Identify Bioc build machines

On Fri, Mar 4, 2016 at 7:33 AM, Dan Tenenbaum wrote: > There are a number of variables defined. You could check to see if the > variable BBS_HOME is defined (it does not matter what the value is in your > case, just whether it is defined or not). > > Dan > > > - Original Message - > > Fro

Re: [Bioc-devel] C library or C package API for regular expressions

Jirka, Do you mean with millions of different patterns (motifs)? If not, the R-level regular expression functions are vectorized, and so the looping will already happen for you in C. Also, have you confirmed that the R evaluation overhead will actually dominate the pattern matching here if you ju

[Bioc-devel] A bioconductor package archive?

Hi all, Unless I'm missing something, there is no archive of prior source packages for Bioconductor, in the vein of CRAN's Web Archive. It has generally been accepted, I think, that if you need a version of a package - e.g., for precise reproducibility - you can go to the still-existing release r

Re: [Bioc-devel] remove history vignettes

s are still > there. They even exist in the release branch: > http://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html > > > On Tue, Nov 17, 2015 at 3:44 PM, Gabe Becker wrote: > >> Zuguang, >> >> From what I can see, you have not updated the

Re: [Bioc-devel] remove history vignettes

Zuguang, >From what I can see, you have not updated the version number of your package, so I suspect you'll find that none of your changes have propogated at all, though I can't entirely swear to that. I believe Bioc packages only update in the repo (which I assume is also when the splash-pages a

Re: [Bioc-devel] is.unsorted method for GRanges objects

Pete, What does sorted mean for granges? If the starts are sorted but the ends aren't does that count? What if only the ends are but the ranges are on the negative strand? Do we consider seqlevels to be ordinal in the order the levels are returned from seqlevels ()? That usually makes sense, but

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

I agree with Michael. External dependencies are not avoidable in our field, but they do put the user in a bad situation with respect to trusting their software (and performing reproducible analyses). If I have KEGGREST version x,y,z installed, and it was passing all it's tests when it was deployed

Re: [Bioc-devel] version increments for unchanged packages

Stephanie, As far as I know, it is so that package versions are unique to specific releases of bioconductor. This has the benefits of 1. providing assurances that that particular version of a package is tested and confirmed to work within that release, and 2. enforces that the source cod

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

or fixSeqinfo is clearer after all > > Statistics is the grammar of science. > Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> > > On Fri, Jun 5, 2015 at 1:41 PM, Gabe Becker wrote: > >> >> >> On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr.

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. wrote: > how about just > > gr <- addSeqinfo(gr, "hg19") > Add sounds like it's, well, adding rather than replacing (Which it sometimes would do. gr <- fixSeqInfo(gr, "hg19") instead? ~G -- Gabriel Becker, Ph.D Computational Biologist Genente

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

except > > one. This is a usecase where genome(GR) is not constant. I suggest, > partly > > for compatibility, to keep genome, but perhaps do something like > > standardizeGenome() > > or something like this. > > > > I would indeed love, love, love a funct

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

me, but perhaps do something > like > standardizeGenome() > or something like this. > > I would indeed love, love, love a function which just cleans it up. > > Kasper > > On Fri, Jun 5, 2015 at 2:51 PM, Gabe Becker wrote: > >> Herve, >> >> This is prob

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Herve, This is probably a naive question, but what usecases are there for creating an object with the wrong seqinfo for its genome? ~G On Fri, Jun 5, 2015 at 11:43 AM, Michael Lawrence wrote: > On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès wrote: > > I also think that we're heading towards som

Re: [Bioc-devel] Meta-information about bioc and bioc-package releases

, 2015 at 10:47 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Gabe Becker" > > To: bioc-devel@r-project.org > > Cc: "csardi gabor" > > Sent: Wednesday, May 27, 2015 10:31:43 AM > > Subject: [Bioc-devel] Meta-inf

[Bioc-devel] Meta-information about bioc and bioc-package releases

Hey all, I've been wondering if bioc could offer a way to query information about itself similar - though not necessarily identical - to what Gabor Csardi's (cc'ed) crandb offers http://www.r-pkg.org/services#api Basically, I would really like two things, in i

Re: [Bioc-devel] jupyter notebooks as vignettes?

Martin, I have a package on Github (DynDocModel) that was part of my thesis which will happily process jupyter notebooks (they were called IPython Notebooks at the time). It (IIRC) supports tangling, weaving, restructuring, etc. I can look at productionizing it if that is something Bioc thinks i

Re: [Bioc-devel] building R and bioconductor

Martin, On Tue, Apr 28, 2015 at 10:52 AM, Martin Morgan wrote: > > Downloading a specific version of Bioconductor packages retrospectively is > challenging, unless the version is the final version in a release cycle. > This is because the Bioc repository only contains one version of a package >

Re: [Bioc-devel] building R and bioconductor

. > > > > I am wondering if there is an automated way, or a repository, to > > recursively retrieve all the package versions required in a certain > > version of R. > > Using biocLite, you will get the specific package versions required for > your R version. If yo

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

On Tue, Mar 24, 2015 at 7:28 AM, Wolfgang Huber wrote: > > 5. At the end of the day I find myself casting my lot for landing pages > with the form > > http://bioconductor.org/release/BiocGenerics/ > > which leads to a little less typing but not the dynamic resolution that > started this (version

Re: [Bioc-devel] doi (was Re: Short URLs for packages?)

Martin, On Mon, Mar 23, 2015 at 11:28 AM, Martin Morgan wrote: > On 03/23/2015 09:55 AM, Gabe Becker wrote:>> >Thus it is more likely that > a person will do the right thing if it happens > >> >to be the most convenient thing IMHO. Anything to advance this strate

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

ier and more rigorous. We could have a biocCite or figure out how to get citation to do the right thing. ~G > > Best, > > --t > > > ~G > > >> >> --t >> >> > On Mar 23, 2015, at 8:38 AM, Gabe Becker wrote: >> > >> > On Mon,

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

at sentence. That's not an attack on you, I know that the above reflects the current state of affairs, I'm simply saying that perhaps Bioconductor, as a project, can help/encourage people to do better. ~G > > --t > > > On Mar 23, 2015, at 8:38 AM, Gabe Becker wrote: &g

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

On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd < b.fisc...@dkfz-heidelberg.de> wrote: > > During the production process of the paper we want to link to the > accompanying > BioC package that is in devel, but not yet in release. Before the first > release, the > link (e.g. www.bioconductor.org/) s

Re: [Bioc-devel] development vs release version

Eric, (inline) On Sun, Mar 22, 2015 at 10:44 AM, Eric Frichot wrote: > Hi everyone, > > Does it mean that I have to wait the next bioconductor release ? > > If it is the case, imagine that I add new features for my package, do I > have to wait the next release (every 6 month) for these features

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

Jim et al., Why have two accessors (rowRanges, rowData), each of which are less flexible than the underlying structure and thus will fail (return NULL? or GRanges()/DataFrame() ?) in some proportion of valid objects? ~G On Tue, Mar 3, 2015 at 2:37 PM, Jim Hester wrote: > Motivated by the discu

Re: [Bioc-devel] CRAN package with Bioconductor dependencies

Even if it is allowed, what is the reasoning behind not simply putting the package in Bioconductor? It seems like a fair bit of pain for very little benefit. ~G On Mon, Mar 2, 2015 at 3:22 PM, Ryan C. Thompson wrote: > I thought CRAN packages weren't allowed to depend on Bioconductor packages >

Re: [Bioc-devel] Importing classes into NAMESPACE

~G > > Regards, > Karolis > > On Wed, Feb 25, 2015 at 3:31 PM, Gabe Becker wrote: > >> Karolis, >> >> Do you really not need any of the methods for GRanges and ExpressionSet >> objects? import(GenomicRanges) might be better, even though the package

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

Why does splitting a VRanges give a GRangesList with VRanges objects as elements? Seems like it should return a VRangesList. > spl = split(vr, sampleNames(vr)) > class(spl) [1] "GRangesList" attr(,"package") [1] "GenomicRanges" > class(spl[[1]]) [1] "VRanges" attr(,"package") [1] "VariantAnnotatio

Re: [Bioc-devel] BamTallyParam argument 'which'

I think we need to be a little careful of trying to know the users intentions better than they do here. Reduce is a (very) easy operation to do on a GRanges, so if the user didn't, are we really safe assuming they "meant to" when passing the GRanges as a which? I would argue for "the samtools way

Re: [Bioc-devel] Importing classes into NAMESPACE

Karolis, Do you really not need any of the methods for GRanges and ExpressionSet objects? import(GenomicRanges) might be better, even though the package isn't exactly small. ~G On Wed, Feb 25, 2015 at 6:27 AM, Thomas Sandmann wrote: > Hi Karolis, > > These classes have constructor functions of

Re: [Bioc-devel] A quick questions on writing R functions

Dongmei, This isn't really the right list for this type of question. That said, I can give you a few pointers. The actual section of the manual you quoted is about documenting your function, not the code of the function itself. That said, "eval" is not a good name for your function. It doesn't t

Re: [Bioc-devel] recalling methods

Hey guys, Surgically removed from promptClass: classInSig <- function(g, where, cl) { cl %in% unique(unlist(findMethods(g, where)@signatures)) } genWithClass <- function(cl, where) { allgen <- getGenerics(where = where) ok <- as.logical(unlist(lapply(allgen, clas

Re: [Bioc-devel] bioc pkgs depending on packages that are only in github?

ackages from > other > >>> sources. > >>> > >>> with increased utility of devtools/install_github perhaps we can relax > >>> this? > >>> > >>> is it a can of worms we don't want to open? > >>> > >>>

Re: [Bioc-devel] R-devel update schedule/strategy for Bioc devel build machines

Dan, Thanks for the quick and thorough response. This info will be instrumental as we try to mach your build systems locally. ~G On Fri, Oct 31, 2014 at 1:28 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Dan Tenenbaum" > > To: &quo

[Bioc-devel] R-devel update schedule/strategy for Bioc devel build machines

Bioc admins, We have an automatic build/test mechanism for our internal packages which we'd like to match the Bioc build machines as closely as possible. AFAIU, the exact commit-specific version of R-devel used on your devel build server changes occasionally within Bioc releases, and we'd like to

Re: [Bioc-devel] writeVcf performance

files with > > 1e5 records. Right now the choice of # records per chunk is simple, based > on total records only. We are still experimenting with this. You can > override default chunking with 'nchunk'. Examples on the man page. > > Valerie > > > On 09/08/14 08:43,

Re: [Bioc-devel] Warning "Register native routines" during BiocCheck

Does the DLL that gets created have a symbol called coxmat? On unixalikes nm [file] will show the symbols in the library. If coxmat (by itself) is not a symbol you may be running afoul of CPP name mangling.  Try using extern 'C' { } around the function declaration if that is the case. ~G On S

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

, 2014 at 12:19 PM, Sean Davis wrote: > > > On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker wrote: > >> Hey all, >> >> We are in the (very) early stages of experimenting with something that >> seems relevant here: classed identifiers. We are using them for &g

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

Hey all, We are in the (very) early stages of experimenting with something that seems relevant here: classed identifiers. We are using them for database/mart queries, but the same concept could be useful for the cases you're describing I think. E.g. > mysyms = GeneSymbol(c("BRAF", "BRCA1")) > my

Re: [Bioc-devel] writeVcf performance

f() in release is ~ 90%. > > Valerie > > > > > On 09/04/14 15:28, Valerie Obenchain wrote: > >> Thanks Gabe. I should have something for you on Monday. >> >> Val >> >> >> On 09/04/2014 01:56 PM, Gabe Becker wrote: >> >>> Val an

Re: [Bioc-devel] Please bump version number when committing changes

Michael, Tags could work. Another approach would be to update the repository and then look in the log to see if the version number was changed in the most recent commit. In a sense this is the converse of what our GRANBase package does when locating historical package versions within the Bioc SVN

Re: [Bioc-devel] Please bump version number when committing changes

Dan, If that is is a hard BioC policy I'll endeavor to follow it (I do already in the vast majority of cases), but I must say it makes the Bioc repository much less useful from a development standpoint. There are lots of reason to commit code that doesn't work and shouldn't yet be deployed, from

Re: [Bioc-devel] writeVcf performance

has been > experimenting with a chunk-wise + parallel algorithm. Unfortunately there > is some frustrating overhead with the parallelism. But I'm glad Val is > arriving at something quicker. > > Michael > > > On Tue, Sep 2, 2014 at 1:33 PM, Martin Morgan wrote: > >

Re: [Bioc-devel] writeVcf performance

The profiling I attached in my previous email is for 24 geno fields, as I said, but our typical usecase involves only ~4-6 fields, and is faster but still on the order of dozens of minutes. Sorry for the confusion. ~G On Wed, Aug 27, 2014 at 11:45 AM, Gabe Becker wrote: > Martin and

Re: [Bioc-devel] writeVcf performance

>>>> https://stat.ethz.ch/pipermail/bioc-devel/2014-August/006082.html >>>> >>>> It sounded like Michael was ok with working with/around heap >>>> initialization. >>>> >>>> Michael, is that right or should we still consider t

Re: [Bioc-devel] writeVcf performance

Val, Has there been any movement on this? This remains a substantial bottleneck for us when writing very large VCF files (e.g. variants+genotypes for whole genome NGS samples). I was able to see a ~25% speedup with 4 cores and an "optimal" speedup of ~2x with 10-12 cores for a VCF with 500k rows

Re: [Bioc-devel] biocLite message "R package not available" is confusing

Josef, The problems with reviewers you are describing sound very frustrating (for the author and the reviewer) but I suspect you think that biocLite is doing somethign that it is not (reimplementing the actual package installation machinery in R). Responses inline. On Tue, Aug 19, 2014 at 4:40 P

Re: [Bioc-devel] a S4 dispatching question

aFrame", i="ANY" > x="container", i="ANY" > x="eSet", i="ANY" > x="filterResultList", i="ANY" > x="filterSet", i="character" > > x="flowFrame", i="ANY" > ... > >

Re: [Bioc-devel] a S4 dispatching question

Mike, This can be done. I would argue that the convenience your users get from this is far outweighed by the damage this does to the ability to read and easily understand the code they are writing. Users, maintainers, etc now need to know the object class, what columns it has and what variables ar

Re: [Bioc-devel] A new way to manage side-by-side BioC release and Devel installs

ifficulty of switching between BioC release > and devel is that between October and April it also requires to switch > between R release and devel. How is that handled in switchr? > > Thanks, > H. > > > > On 07/24/2014 08:42 AM, Gabe Becker wrote: > >> Hey all,

[Bioc-devel] A new way to manage side-by-side BioC release and Devel installs

Hey all, One of the things that has come up from the recent Release/Devel distinction thread on this list is that people don't consider there to be an easy way of handling both at the same time. I'd like to offer an alternative based on the switchr https://github.com/gmbecker/switchr package I'm

Re: [Bioc-devel] Distinction between release and devel package websites

Andrzej, If you have the an important enough bugfix the correct procedure is to commit it to the release branch. Then users would simply update the package via biocLite. Note that this should be fixes ONLY. No new features. Regardless of how much the users want them, those belong in dev. ~G On

Re: [Bioc-devel] R CMD CHECK options

Siddharta, The development process I use, which as far as I know is the canonical "Right Way" (tm) is: (Build with no vignettes -this is often skipped) Install and test code or use devtools (repeat many times) Final install Build Check So basically, you should have already successfully installed

[Bioc-devel] error in summary method for KEGGHyperGResult

Hey all, Apologies if I missed something. I am trying to fix a bug a user identified in ReportingTools, so the original code is not my own. It seems that the summary() method for class KEGGHyperGResult has an error in it: > class(keggResults) [1] "KEGGHyperGResult" attr(,"package") [1] "Category

Re: [Bioc-devel] Packaging a medium/large project

The general rule of thumb is that R copies data only when it needs to (a piece of data is being modified while another variable/symbol is using it). So even though R has "pass by value" semantics, data is not being copied when being passed into functions (though if the local version of the data is

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

If you want to step into the environments where the errors are happening you want options(error=recover) not traceback. In that case, you can step into each of the frames. The .local is actually the body of the method being called though, nothing to do with an environment. ~G On Thu, Apr 3, 20

Re: [Bioc-devel] Overflow in as(rlelist, "IntegerList"

On Sat, Mar 29, 2014 at 1:10 PM, Gabe Becker wrote: > >> Hi all, >> >> Apologies if this gets duplicated. I was not subscribed when I originally >> sent it. >> >> We have a very large RleList, such that the sum of the lengths is larger >> th

[Bioc-devel] Overflow in as(rlelist, "IntegerList"

Hi all, Apologies if this gets duplicated. I was not subscribed when I originally sent it. We have a very large RleList, such that the sum of the lengths is larger than INT.MAX, that we want to convert to an also very large IntegerList (whole genome coverages by chromosome I believe, though I'm n