[Bioc-devel] igvR and igvShiny - anyone interested in taking ownership?

ges/release/bioc/html/RCyjs.html>: bioc rank 1268, also built on BrowserViz, but little used. igvShiny <https://github.com/paul-shannon/igvShiny>: not yet in bioc, but a worth candidate, useful to more than a few Please let me know if you are interested. - Paul [[al

Re: [Bioc-devel] BrowserViz build test times out, checks for web browser availability, apparently needs update

Thanks, Vince. You can find the package here: https://github.com/paul-shannon/BrowserViz - Paul > On Aug 25, 2021, at 12:41 PM, Vincent Carey > wrote: > > Sorry for delay in responding Paul. I had a look at BrowserViz and ran into > > > PORT_RANGE <- 12111

Re: [Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

; > I don't really have any great insight to offer here; superficially it sounds > like the server is sometimes rejecting connections, and these have happened > to line up with OS. > > Martin Morgan > > On 7/12/21, 8:46 PM, "Bioc-devel on behalf of Paul Shannon&

[Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

The problem is described in full here, with 4 lines of code to reproduce. https://support.bioconductor.org/p/9138262/ James MacDonald pointed out that my initial analysis is wrong. (Thank you, Jim!) I claimed this works on macOS, fails on linu

[Bioc-devel] BrowserViz build test times out, checks for web browser availability, apparently needs update

The BrowserViz package - currently timing out on malbec1 and nebbiolo1, supports json messaging over websockets between R and most web browsers. The unit tests for BrowserViz only run if a web browser is available. In recent years, a (presumably headless) web browser was offered on the Linux

[Bioc-devel] latest devel version of igvR - apparently not picked up by the build system

This is probably my error or misunderstanding. That admitted, I cannot figure out why version 1.11.2 of the igvR package has not been picked up in the daily devel builds. I *think* my commits were done properly, as this fresh clone from bioc master shows: cd /tmp git clone g...@git.bioco

[Bioc-devel] "there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'"

My package trena fails on all platforms with this error: there is no package called ‘BSgenome.Athaliana.TAIR.TAIR9’ Is Arabidopsis no longer supported by bioc? I remember some discussion related to this over the summer. - Paul ___ Bioc-devel@r-pr

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

er Center > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bioc-devel on behalf of Paul Shannon > > Sent: Friday, June 5, 2020 1:12 PM > To: Nystrom, Spencer > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-deve

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Thanks, Spencer. Sorry I missed the support posting - there’s no automatic forwarding from there to maintainers. I’ll take a look at this later today, then post back to the support list, and we will get a fix in. Thank you for pointing out the problem! - Paul > On Jun 5, 2020, at 9:46 AM, N

[Bioc-devel] core dump in MotifDb build

Dear Bioc, I have added the lasted HOCOMOCO motifs to MotifDb but changed no code. The package 1.29.6 dumps core during in the bioc devel linux build, and fails perhaps similarly on windows. http://bioconductor.org/checkResults/devel/bioc-LATEST/MotifDb/malbec2-buildsrc.html Any suggesti

Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11

Hi Lori, Is there a replacement for the athaliana package, org.At.tair.db? We sometimes use this in our work. - Paul > On Nov 18, 2019, at 6:24 AM, Shepherd, Lori > wrote: > > The Bioconductor Team is continuing to identify packages that will be > deprecated in the next release to allow f

[Bioc-devel] which web browser on the linux build machines? was Re: R environment variable which indicates "running in the bioc build system"?

On Sep 12, 2019, at 3:13 PM, Pages, Herve wrote: > > AFAIK the build machines have web browsers. Hi Herve, I’d like to do my local linux testing of igvR using the same web browser you have on the bioc linux build machines.I’d be grateful if you could tell me which one is installed. Thank

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

On Sep 12, 2019, at 4:28 PM, Pages, Herve wrote: > > However things seem to work as expected on the Linux builders: > > library(igvR) > igv <- igvR() > # attempting to open websocket connection on port 15000 > # BrowserViz websocket ready after 1.20 seconds > ping(igv) > # [1] "pon

Re: [Bioc-devel] R environment variable which indicates "running in the bioc build system"?

Thanks, Herve. How can I determine if a web browser is indeed installed? Sys.getenv("R_BROWSER”) returns: macOS: “/usr/bin/open” ubuntu: “xdc-open” I don’t think either of these actually reveals an actual and functioning installation. Other ideas? - Paul > On Sep 12, 2019, at 3:13 PM,

[Bioc-devel] R environment variable which indicates "running in the bioc build system"?

My package igvR requires a web browser. Unit tests, examples, vignette all will all fail if one is not available. Since the bioc build system, for good reason, does not provide a web browser, I’d like to condition all browser-related code on “not executing in the bioc build system”. Is there

[Bioc-devel] BSgenome.UCSC.hg38 seems to be deleted again on the build system

https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html Warning in .seqlengths_TwoBitFile(x) : mustOpen: Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory _

Re: [Bioc-devel] No such file or directory: BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit

Sorry for the inconvenience this has caused so far. > > H. > > On 6/24/19 12:31, Paul Shannon wrote: >> Warning in .seqlengths_TwoBitFile(x) : mustOpen: >>Can't open >> /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequen

[Bioc-devel] No such file or directory: BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit

Warning in .seqlengths_TwoBitFile(x) : mustOpen: Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory Timing stopped at: 0.176 0 0.175 Error in .seqlengths_TwoBitFile(x) : UCSC library operation

[Bioc-devel] Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

I see this error today in the macOS release build : ERROR in test_getFootprintsInRegionWithVariants: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed On June 8th, in release: ERROR in

[Bioc-devel] daily build failures for the trena package, related to BSgenome.Hsapiens.UCSC.hg38 2bit file

I get daily R CMD check failures visible at https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/malbec2-checksrc.html The recurring failure, which I cannot replicate on my own systems, is due to this error: test_.getScoredMotifs Warning in .seqlengths_TwoBitFile(x) : mustOpen:

Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

failed" problem on the build machines. > > Finally, another intriguing thing is that, according to the lastest 3.8 > build result, trena's unit tests also seemed to have a problem accessing > a file that belongs to another package: > > https://bioconductor.

Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

piens.UCSC.hg38 gets reinstalled every night on the builders > and that this happens at the time the build system is running 'R CMD > check' on trena. > > Package vignettes, examples, and unit tests should avoid re-installing > packages. > > H. > > On 4/

[Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

I cannot reproduce daily build failures found in the trena package by the build system. The build report shows: trena RUnit Tests - 86 test functions, 7 errors, 0 failures ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ERROR in test_bugInStartEndOf

Re: [Bioc-devel] use bioc docker images to reproduce linux build error?

= host, dbname = dbname) > > I see a .BBSoptions in trena for exclusion on Windows. The reason it's > not being respected is because it's malformed and needs a space after > the comma between the platforms. Just curious, what was the reason for > excluding this on Windows?

[Bioc-devel] use bioc docker images to reproduce linux build error?

Our package “trena” has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are they similar enough to the build system to give me good odds on reproduci

Re: [Bioc-devel] choosing R version dependency for existing packages

bug fixes only in the > point releases. So a dependency like R >= 3.5.0 would seem appropriate. > > I'm not sure whether these comments are helpful or not... __ > > Martin > > On 11/2/18, 3:19 PM, "Bioc-devel on behalf of Paul Shannon" > paul.thur

[Bioc-devel] choosing R version dependency for existing packages

A user of MotifDb requests - sensibly, I think - that I loosen the requirement Depends: R (>= 3.5.1) which I added before the release. This seems sensible and supported by, for example, R (>= 2.10) in GenomicRanges. Is this, then, the heuristic? - new packages should depend on the lastes

Re: [Bioc-devel] installed, system.file(package="RCyjs") is "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs"

That did it. Thank you! - Paul > On Jun 29, 2018, at 4:11 PM, Martin Morgan > wrote: > > > > On 06/29/2018 06:44 PM, Paul Shannon wrote: >> My package RCyjs reads an html/js/css file when the constructor is called, >> then sends that file to the user’s

[Bioc-devel] installed, system.file(package="RCyjs") is "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs"

My package RCyjs reads an html/js/css file when the constructor is called, then sends that file to the user’s browser. The actual path to that file is calculated at global scope in RCyjs-class.R: cyjsBrowserFile <- system.file(package="RCyjs", "browserCode", "dist", "rcyjs.html”) That file

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

if > there are initialize() methods around. You should be able to avoid this just > by defining your own initialize() method that just calls the next method. > Ideally though Gviz would just drop its one. > > Michael > > On Mon, May 7, 2018 at 11:14 AM, Paul Shannon >

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

ned by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz&#x

[Bioc-devel] class name collision in cache: igvR and Gviz

I just discovered a class name collision - AnnotationTrack, in Gviz and my new package igvR. wish to get wise counsel before proceeding with a fix. Here’s the error message: Found more than one class "AnnotationTrack" in cache; using the first, from namespace ‘igvR' Also defined by ‘Gv

Re: [Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

>dbListTables, >dbGetQuery, >dbListConnections, >dbDisconnect) > > BTW have you considered using RMariaDB instead of RMySQL? > > https://cran.r-project.org/web/packages/RMariaDB/ > > Cheers, > H. > > On 04/23/2018 11:12 AM, Paul Shannon

[Bioc-devel] dbApply name collision, RMySQL and RPostgreSQL, no direct call to either

Warning: replacing previous import ‘RMySQL::dbApply’ by ‘RPostgreSQL::dbApply’ when loading ‘trena’ We do not call dbApply directly anywhere in the package. I imagine it is called routinely by functions that we do call. Any suggestions on how to clear this warning? Thanks. - Paul _

Re: [Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

location - > > This is an issue on our end and if it occurs you should notify a Bioconductor > team member. > > > > Lori Shepherd > Bioconductor Core Team > Roswell Park Cancer Institute > Department of Biostatistics & Bioinformatics > Elm & Carlton St

[Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

I am trying to build IGV (a new submission) on windows (tokay2) after linux and macOS build clean. IGV needs its base class package, BrowserViz, at version >= 2.0, whose build report is OK for install, build, and build bin. BrowserViz 2.0.11 fails check, probably because now web browser is av

Re: [Bioc-devel] single-package build, from git trigger: new linux build report missing

27; > the event with 'X-GitHub-event: push'). > > Thanks for the heads-up > > Martin > > On 04/10/2018 06:09 PM, Paul Shannon wrote: >> Maybe this is already known. Maybe it’s my error. >> As recently as April 4th, a single-package build, initiated fr

[Bioc-devel] single-package build, from git trigger: new linux build report missing

Maybe this is already known. Maybe it’s my error. As recently as April 4th, a single-package build, initiated from a git push trigger, produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since then, and still today, I only get reports from tokay

[Bioc-devel] single-package build, from git trigger: new linux build report missing

Maybe this is already known. As recently as April 4th, a single-package build initiated from a git push trigger produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since then, and still today, I only get reports from tokay2 and merida2. The lin

Re: [Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

thoritative remarks on this. > > I don't know whether the methods sketched in > > https://stackoverflow.com/questions/15509231/unit-testing-node-js-and-websockets-socket-io > > could be used in this task, to go beyond checking the basic > R manipulations. > >

Re: [Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

Hi Vince, My dumb mistake, sorry. Now fixed, version 0.99.9, https://github.com/paul-shannon/IGV I’m looking forward to hearing your suggestions. - Paul > On Apr 9, 2018, at 4:49 PM, Vincent Carey wrote: > > Hi Paul -- I am trying to build your vignette but it has > >

[Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

> "Once your package builds and checks without errors or (avoidable) warnings, > a Bioconductor team member will provide a technical review of your package. > Other Bioconductor developers and users with domain expertise are encouraged > to provide additional community commentary. Reviewers will

[Bioc-devel] web browser support missing in the build system? new package, IGV

Perhaps my newly submitted package times out because no web browser is available on the build systems? https://github.com/paul-shannon/IGV The build times out on linux and OS X at the “creating vignettes” stage. But since the package is a wrapper around igv.js running in the browser, no

Re: [Bioc-devel] new package deadline? 4/2 or 4/9

ing the typo - I'll fix that. > > The last day to submit packages is April 2. The API deadline (no new packages > added to manifest) is the 16th so we moved the last day to submit from the > 9th to the 2nd. This allows 2 weeks for the review instead of 1. > > Valerie > >

[Bioc-devel] new package deadline? 4/2 or 4/9

https://www.bioconductor.org/developers/release-schedule/ seems it bit unclear - see below. Do we have until April 9th to submit new packages? - Paul Monday March 26 • Announce new package deadline of April 9. Monday April 2 • Announce deprecated packages for BioC 3.7. The

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

and subjected to a few months of user QC. I admit that I also prefer the greater operational clarity which for me, with my plodding brain, comes from using by explicit data types and explicit constructors.) - Paul > On Mar 14, 2018, at 1:05 PM, Michael Lawrence > wrote: >

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

Hi Michael, Set me straight if I got this wrong. You suggest: > There should be no need to explicitly construct a track; just rely on > dispatch and class semantics, i.e., passing a VCF object to add_track() would > create a variant track automatically. But wouldn’t displayTrack(vcf)

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

Gabe and Levi made a good case for supporting GRanges in IGV. Looking at the GenomicRanges vignettes, it appears that many of Herve’s introductory examples have GC content as the mcols column of interest. Would that be a good test and demo for IGV? Or perhaps some other genomic quantity, o

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

t would require > it to talk to some standard API, like the old DAS. > > 2) The rtracklayer API is in rtracklayer/R/browser.R. See ucsc.R for how that > is implemented for UCSC. > > On Fri, Mar 9, 2018 at 9:59 AM, Paul Shannon > wrote: > Thanks, Levi. Your comments, a

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

plugin system. Can anyone (maybe Michael himself?) comment on how I can evaluate an rtracklayer plugin strategy for igv? - Paul > On Mar 9, 2018, at 4:15 AM, Levi Waldron wrote: > > On Thu, Mar 8, 2018 at 12:29 AM, Paul Shannon > wrote: > Thanks, Gabe. > > You ma

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

by” appropriate bioc data types? - Paul > On Mar 7, 2018, at 2:40 PM, Gabe Becker wrote: > > 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 typical

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

To avoid duplication of effort, and perhaps to attract some early reviewers, I figure I’d let this group know that I plan to submit a new package “IGV” for inclusion in the next Bioconductor release. The package will provide an interface to the excellent and quite new browser-based genome viewe

[Bioc-devel] not all bioc packages visible on github?

By example: https://github.com/Bioconductor/KEGGREST-> github project homepage displays https://github.com/Bioconductor/BrowserViz -> 404 Yet this works fine: git clone g...@git.bioconductor.org:packages/BrowserViz.git Is visibility at github.com/Bioconductor therefore conditional? M

[Bioc-devel] Classes to be supported by ggraph

Possibly of interest on this topic, though it implements a different sort of (interactive) solution, are two Bioc packages: RCyjs and RCy3. RCyjs renders to the browser, using the cytoscape.js javascript library and websockets: http://js.cytoscape.org/ RCy3 renders to Cytoscape, the matur

[Bioc-devel] possible BioGrid/psiquic bug [was Problem with constrained PSICQUIC queries]

ND species:9606 AND detmethod:(psi-mi:MI:0004 OR psi-mi:MI:0676) It is tempting - but not always correct! - to conclude that this is not my own mistake. Please forgive me if it is. I hope that the first url above will be enough for you to easily find out. Thanks! - Paul Shannon Ins

[Bioc-devel] biomaR + CosmicMart fails in devel

Hoping to use Sanger's COSMIC database ("Catalogue Of Somatic Mutations In Cancer") via biomaRt, I ran into some trouble: 'CosmicMart' connections usually fail. A few lines to replicate the problem are included below. SessionInfo output follows. - Paul library(biomaRt) tbl <- listMarts

Re: [Bioc-devel] ¿A useful addition to MotifDb package?

Hi Steve and all, MotifDb 1.1.6 (devel) now includes the transcription factor binding motifs from the stamlab footprints suggested by Steve. Thanks for that tip, Steve. The new motifs are not associated with their binding protein, as all the others motifs in MotifDb are: that information was