Re: [Rd] Debugging "SETLENGTH() cannot be applied to an ALTVEC object."?

Tal, I don't have a debian machine at my fingertips, but I don't see that error when installing heatmaply into a clean library in R 3.5.0 (that takes a while...). I suspect you're hitting old installed versions of packages in that build on that machine, especially since the failure is not

Re: [Rd] download.file does not process gz files correctly (truncates them?)

Hey all, I don't have a strong opinion about whether the default should ultimately eventually change or not. Many people who use windows (a set which does not include me) seem to think it would be better. I will say that like Hugh, I'm strongly against making the argument mandatory as an interim

Re: [Rd] Proposed speedup of ifelse

Hugh, (Note I speak for myself only and not for R-core) Thanks for looking into this. I think it's great to have community members that are interested in contributing to R and helping it continue to get better. And I think, and my local experiments bear out, that using anyNA as a fastpass

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

Greg, I see what you mean, but on the other hand, that's not how we think about real numbers working either, and doubles have that behavior generally. It might be possible to put checks in (with a potentially non-trivial overhead cost) to disallow that kind of thing, but again R (and everyone

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

Emil et al., On Mon, Jun 11, 2018 at 1:08 AM, Emil Bode wrote: > I don't think there's much wrong with is.na(as_date(Inf, > origin='1970-01-01'))==FALSE, as there still is some "non-NA-ness" about > the value (as difftime shows), but that the output when printing is > confusing. The way cat is

Re: [Rd] mean(x) for ALTREP

Serguei, The R 3.5.0 release includes the fundamental ALTREP framework but does not include many 'hooks' within R's source code to make use of methods on the ALTREP custom vector classes. I have implemented a fair number, including for mean() to use the custom Sum method when available, in the

Re: [Rd] debugonce() functions are not considered as debugged

Gabor, Others can speak to the origins of this more directly, but from what I recall this has been true at least since I was working in this space on the debugcall stuff a couple years ago. I imagine the reasoning is what you would expect: a single bit of course can't tell R both that a function

Re: [Rd] length of `...`

As of 3.5.0 the ...length() function does exactly what you are asking for. Before that, I don't know of an easy way to get the length without evaluation via R code. There may be one I'm not thinking of though, I haven't needed to do this myself. Hope that helps. ~G On Thu, May 3, 2018 at 7:52

Re: [Rd] vctrs: a type system for the tidyverse

Hadley, Responses inline. On Wed, Aug 8, 2018 at 7:34 AM, Hadley Wickham wrote: > >>> Method dispatch for `vec_c()` is quite simple because associativity and > >>> commutativity mean that we can determine the output type only by > >>> considering a pair of inputs at a time. To this end, vctrs

Re: [Rd] vctrs: a type system for the tidyverse

Actually, I sent that too quickly, I should have let it stew a bit more. I've changed my mind about the resolution argument I Was trying to make. There is more information, technically speaking, in the factor with empty levels. I'm still not convinced that its the right behavior, personally. It

Re: [Rd] vctrs: a type system for the tidyverse

Hadley, Looks interesting and like a fun project from what you said in the email (I don't have time right now to dig deep into the readme) A few thoughts. First off, you are using the word "type" throughout this email; You seem to mean class (judging by your Date and factor examples, and the

Re: [Rd] conflicted: an alternative conflict resolution strategy

Hadley, Overall seems like a cool and potentially really idea. I do have some thoughts/feedback, which I've put in-line below On Thu, Aug 23, 2018 at 11:31 AM, Hadley Wickham wrote: > > > > conflicted applies a few heuristics to minimise false positives (at the > cost of introducing a few

Re: [Rd] Proposal: more accurate seq(from, to, length=n)

Suharto, My 2c inline. On Fri, Sep 7, 2018 at 2:34 PM, Suharto Anggono Suharto Anggono via R-devel wrote: > In R, > seq(0, 1, 0.1) > gives the same result as > (0:10)*0.1. > It is not the same as > c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1) , > as 0.1 is not represented exactly. I am

Re: [Rd] Testing for vectors

Hadley, > I was thinking primarily of completing the set of is.matrix() and > is.array(), or generally, how do you say: is `x` a 1d dimensional > thing? > Can you clarify what you mean by dimensionality sense and specifically 1d here? You can have a 1d array which is different from what your

Re: [Rd] Testing for vectors

Hadley, On Sat, Jul 7, 2018 at 1:32 PM, Hadley Wickham wrote: > On Sat, Jul 7, 2018 at 1:50 PM, Gabe Becker wrote: > > Hadley, > > > >> > >> I was thinking primarily of completing the set of is.matrix() and > >> is.array(), or generally, how do y

Re: [Rd] Part of fastpass in 'sort.list' can make sorting unstable

Thanks for catching this. This is easy to take out without touching the rest of the machinery. It also wouldn't be too hard to write a still-faster-but-not-quite-as-much-path which correctly reverses the sortedness of a sorted vector that includes ties. My suspicion, without being the one who will

Re: [Rd] Base R examples that write to current working directory

Martin et al, I have submitted a patch on bugzilla which fixes all of the examples I could easily find which were not already writing only to temporary files or switching to a temp directory before writing files to the working directory. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17403

Re: [Rd] Bug in tools::md5sum - does not work when filepath contains tilde (ie home directory)

Dean, I filed a patch for this in bugzilla yesterday so depending on reception this should be fixed in devel soon. Best, ~G On Fri, Jun 29, 2018, 3:58 AM Dean Attali wrote: > I've reproduced on ubuntu and winodws with R3.4.3 > > When the filepath contains a tilde, the result is NA. But if

Re: [Rd] methods(class = class()) - improve for |cl.| > 1 ?

Martin and Kevin, Perhaps a variant of methods which more directly addresses the use-case Kevin mentions might be in order? I am happy to prepare a patch which implements a methodsForObj function (name very much negotiable), or a third obj argument to methods which takes the actual object and

Re: [Rd] R_ext/Altrep.h should be more C++-friendly

Michael, Thanks for reaching out. This was brought up by Romaine Francois offline to me as well. What he does as a workaround is #define class klass extern "C" { #include } #undef class While we consider changing Altrep.h, the above should work for you in the immediate term. Let me know

Re: [Rd] Bias in R's random integers?

Hi all, On Thu, Sep 20, 2018 at 9:30 AM, Paul Gilbert wrote: > > > There are only two small problems that occur to me: > > 1/ Researchers that want to have reproducible results (all I hope) need to > be aware the change has happened. In theory they should have recorded the > RNG they were using,

[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

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

to SimpleIntegerList. On Sat, Mar 29, 2014 at 1:10 PM, Gabe Becker becker.g...@gene.com 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 than INT.MAX, that we want to convert

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,

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

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

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, One of the things that has come up from the recent Release/Devel

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

Re: [Bioc-devel] a S4 dispatching question

Mike On 08/06/2014 11:45 AM, Gabe Becker wrote: 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

Re: [Bioc-devel] writeVcf performance

/2014 09:34 AM, Gabe Becker wrote: 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

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 becke...@gene.com wrote

Re: [Bioc-devel] writeVcf performance

AM, Gabe Becker wrote: 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. I think Val is arriving at a (much) more efficient implementation, but... I

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] 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

Re: [Bioc-devel] writeVcf performance

2, 2014 at 1:33 PM, Martin Morgan mtmor...@fhcrc.org mailto:mtmor...@fhcrc.org wrote: On 08/27/2014 11:56 AM, Gabe Becker wrote: The profiling I attached in my previous email is for 24 geno fields, as I said, but our typical usecase involves

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)) mysyms

Re: [Bioc-devel] writeVcf performance

On 09/08/14 08:43, Gabe Becker wrote: Val, That is great. I'll check this out and test it on our end. ~G On Mon, Sep 8, 2014 at 8:38 AM, Valerie Obenchain voben...@fhcrc.org mailto:voben...@fhcrc.org wrote: The new writeVcf code is in 1.11.28. Using the illumina file you

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

Becker becker.g...@gene.com Cc: bioc-devel@r-project.org, Jim Fitzgerald fitzgerald.ja...@gene.com Sent: Thursday, October 30, 2014 10:23:58 AM Subject: Re: [Bioc-devel] R-devel update schedule/strategy for Bioc devel build machines - Original Message - From: Gabe

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

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

On Tue, Mar 24, 2015 at 7:28 AM, Wolfgang Huber whu...@embl.de 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

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 james.f.hes...@gmail.com wrote:

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 sandmann.tho...@gene.com wrote: Hi Karolis, These classes have

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] Short URLs for packages?

, 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 becker.g...@gene.com wrote: On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd

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

the right thing. ~G Best, --t ~G --t On Mar 23, 2015, at 8:38 AM, Gabe Becker becker.g...@gene.com wrote: 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

Re: [Bioc-devel] building R and bioconductor

. Using biocLite, you will get the specific package versions required for your R version. If you want more control, I think packrat [1,2] from RStudio or this paper [3] by Gabe Becker et al. might helpful. [1] https://rstudio.github.io/packrat/ [2] https://github.com/rstudio/packrat [3

Re: [Bioc-devel] building R and bioconductor

Martin, On Tue, Apr 28, 2015 at 10:52 AM, Martin Morgan mtmor...@fredhutch.org 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

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 lawrence.mich...@gene.com wrote: On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org wrote:

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 becker.g...@gene.com wrote: On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. tim.tri...@gmail.com wrote: how

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

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 becker.g...@gene.com wrote: Herve, This is probably a naive question, but what usecases are there for creating

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

, to keep genome, 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 becker.g...@gene.com wrote: Herve, This is probably a naive question

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

On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. tim.tri...@gmail.com 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

[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 http://www.r-pkg.org/services#api Basically, I would really like two things, in

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

, 2015 at 10:47 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Gabe Becker becker.g...@gene.com To: bioc-devel@r-project.org Cc: csardi gabor csardi.ga...@gmail.com Sent: Wednesday, May 27, 2015 10:31:43 AM Subject: [Bioc-devel] Meta-information about

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

Re: [Bioc-devel] remove history vignettes

ld vignettes 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 <becker.g...@gene.com> wrote: > >> Zuguang, >> >> From what I can

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,

[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

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

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

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

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

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 <

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

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

hlighted what I refer to > as the inspector below as an example: > > setClass("file", > contains="file_virtual", > validity=function(object){ > # Check that object is as expected > > } > ) >

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

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,

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] 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

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,

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

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

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" <becke...@gene.com> wrote: > So r packages don't really have a formal "corresponding author" concept, > though they do h

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

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.

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

for recent versions. On Thu, Oct 5, 2017 at 3:58 PM, Gabe Becker <becke...@gene.com> 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

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 <becke...@gene.com> wrote: > Correct. The actual order of checks is: > >1. did switchr already retrieve tha

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 <becke...@gene.com> 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. B

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

nifest(..., type = "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 &l

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

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] modify _R_CHECK_FORCE_SUGGESTS_ ?

<lawrence.mich...@gene.com > wrote: > Only if Rsubread is used unconditionally. > > On Fri, May 18, 2018 at 2:00 PM, Gabe Becker <becker.g...@gene.com> wrote: > > Vivek, > > > > Why (ie in what sense) is the package suggested? Is it used in your > tests, > > e

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

[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

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

ation 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'm trying to track down t

Re: [Bioc-devel] BiocManager now on CRAN

ers 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 vignette proper,

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

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

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 =

Re: [Bioc-devel] Missed deadline

; 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

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,

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