[Bioc-devel] Remote BigWig file access

at some point and when it does, those packages will work again with remote BigWig files as if nothing ever happened. But I wanted to check in if this is what others who use BigWig files are thinking of doing. Thanks! Best, Leo Leonardo Collado Torres, Ph. D. Investigator, LIEBER INSTITUTE for BRAI

Re: [Bioc-devel] Availability of DropletUtils on BBS for an experiment package

Thank you Jennifer! I just made that change on both release and devel. https://github.com/LieberInstitute/spatialLIBD/commit/94048657dd0cf134b8e2347933e4302f75cec415 Best, Leo Leonardo Collado Torres, Ph. D. Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT Assistant Professor, Department

[Bioc-devel] Availability of DropletUtils on BBS for an experiment package

see that all binaries and the source package are available. Thanks, Leo Leonardo Collado Torres, Ph. D. Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT Assistant Professor, Department of Biostatistics Johns Hopkins Bloomberg School of Public Health 855 N. Wolfe St., Room 385 Baltimore, MD

[Bioc-devel] TREG git push request access

Hi bioc-devel, Similar to my qsvaR email, can you give me git access to TREG? Louise is still the primary maintainer, but I'm helping her here and there. Thanks, Leo Leonardo Collado Torres, Ph. D. Investigator LIEBER INSTITUTE for BRAIN DEVELOPMENT 855 N. Wolfe St., Suite 300 Baltimore, MD

[Bioc-devel] qsvaR git access update request

and there. Hédia, from https://contributions.bioconductor.org/git-version-control.html?q=DENIED%20by%20fallthru#faq you'll need to submit your information to https://git.bioconductor.org/BiocCredentials/. Thanks, Leo Leonardo Collado Torres, Ph. D. Investigator LIEBER INSTITUTE for BRAIN DEVELOPMENT 855 N

Re: [Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files

openssl@3/3.0.5/lib/libcrypto.a > > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > > -Wl,CoreFoundation > > > > > > We have not made any recent changes to these binaries but these are the > > first ones we made available for M1 Macs. > >

[Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files

uce(range), as = "RleList") > packageVersion("rtracklayer") [1] ‘1.58.0’ I'm not sure what else I can do to help. As noted at https://github.com/lawremi/rtracklayer/issues/83#issuecomment-1437585161, recount / rtracklayer versions from BioC 3.11 do work with the same links.

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Thanks! This will also help me ^^ https://orcid.org/-0003-2140-308X Best, Leo Leonardo Collado Torres, Ph. D. Investigator LIEBER INSTITUTE for BRAIN DEVELOPMENT 855 N. Wolfe St., Suite 300 Baltimore, MD 21205 lcolladotor.github.io lcollado...@gmail.com On Mon, Oct 19, 2020 at 7:43 AM

[Bioc-devel] Rmd vignette failures

/runs/1152833313). Are you aware of any change to pandoc or markdown that might be related to this issue? I don't see anything at rstudio/rmarkdown https://github.com/rstudio/rmarkdown/issues?q=argument+is+of+length+zero. Best, Leo Leonardo Collado Torres, Ph. D. Investigator LIEBER INSTITUTE

[Bioc-devel] A pie in the sky idea/wish: DifferentialExpressionSummarizedExperiment clas

Hi, The tidybulk [1] workshop yesterday and Sean Davis & Levi Waldron's & Benjamin Haibe-Kains workshop [2] got me thinking today in the morning of a pie in the sky idea. Just like SummarizedExperiment has helped many of us to organize our data, it would be awesome if there was something like a

Re: [Bioc-devel] regutools: request to add more git push access

entials accounts >> for you. >> >> >> Nitesh >> >> On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote: >> > Hi Nitesh, >> > >> > Could you add me (l.collado-torres) and Alejandro Reyes (what's your >> > svn username Alej

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

the problem by eliminating from 'deps' the > packages that do not contribute to the problem. So I wonder what a minimal > 'deps' looks like? This would be much more helpful for understanding the > problem than many 1000's of lines of output from CI. > > This might help to come up

[Bioc-devel] TxDb.Hsapiens.UCSC.hg19.knownGene fails to install unless you manually install GenomeInfoDbData first

Hi Bioc-devel, Similar to the message I just sent about GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene, I found that TxDb.Hsapiens.UCSC.hg19.knownGene will fail to install on both macOS and Windows with a fresh R 4.0 and BioC 3.11 installation unless GenomeInfoDbData is installed manually

[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi Bioc-devel, I think that there's a potential issue with either GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package. On a fresh R 4.0 Windows installation with BioC 3.11, I get the following error message when installing TxDb.Hsapiens.UCSC.hg19.knownGene as shown at

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Hi, This seems related https://twitter.com/opencpu/status/1253649367946444802?s=21 Best, Leo On Wed, Apr 22, 2020 at 6:54 AM Gordon K Smyth wrote: > Hi Herve, > > > Are you saying that 'R CMD config CC' returns > > /mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest > > Windows build of

Re: [Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

.github.com/lcolladotor/73db141aea3c7d9540ecd18b9b253e40 [17] https://twitter.com/tslumley/status/1253505155523178496?s=20 On Thu, Apr 23, 2020 at 10:03 PM Leonardo Collado Torres wrote: > > Hi, > > I went to google again and maybe > https://github.com/phw/peek/issues/112#issuecomment-296690302 is

[Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

Collado Torres, Ph. D., Research Scientist Lieber Institute for Brain Development 855 N Wolfe St, Suite 300 Baltimore, MD 21205 http://lcolladotor.github.io ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

recent fix. > > Michael > > On Thu, Apr 9, 2020 at 7:11 AM Leonardo Collado Torres > wrote: >> >> Hi BioC-devel, >> >> I was able to trace a regionReport error back to ggbio & biovizBase. >> However, I'm completely clueless as to why (a) it only a

[Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

tent with regionReport and the ggbio reprex. However, I then don't understand why this hasn't failed in the BioC builds. Best, Leo Leonardo Collado Torres, Ph. D., Research Scientist Lieber Institute for Brain Development 855 N Wolfe St, Suite 300 Baltimore, MD 21205 http://lcolladotor.github.io On

[Bioc-devel] regionReport error: leads to potential disk space issues for ImageMagick

Hi BioC-devel, I spent some time yesterday getting my Windows laptop ready to debug a Windows OS-only issue in regionReport (bioc-release 3.10), but ultimately I couldn't reproduce it. Since the error seems to be some type of cache, I bumped the version number but it still failed today and it

[Bioc-devel] [rOpenSci] Community Call: Maintaining an R Package

Hi BioC-devel, Since 2018 I've been interacting with rOpenSci's organizers. For those that don't know, rOpenSci https://ropensci.org/ is a non-profit that aims to > make scientific data retrieval reproducible. Over the past seven years we > have developed an ecosystem of open source tools, we

Re: [Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis

Hi, I should clarify that this workshop will be held in Cuernavaca, Morelos, Mexico during August 3rd to the 7th, 2020. Best, Leo On Thu, Mar 5, 2020 at 10:05 PM Leonardo Collado Torres wrote: > > Hi BioC-devel! > > We just made the announcement of our CDSB 2020 worksho

[Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis

ding the word around. Also, if you have any contacts that you think might be interested in sponsoring the workshop, please let us know. At https://comunidadbioinfo.github.io/niveles-de-patrocinio/ we answer the question why should you support us? Thanks! Best, Leo Leonardo Collado Torres, Ph. D., S

[Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages

Hi, When installing BiocNeighbors (1.4.1, latest release from Bioconductor version 3.10) from source on linux I noticed the issue as a few hours ago it all worked fine but now it doesn't. Locally, I noticed that I had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I can install

Re: [Bioc-devel] Error unable to find image

ductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ---------- > *From:* Bioc-devel on behalf of > Leonardo Collado Torres > *Sent

Re: [Bioc-devel] Error unable to find image

Hi, Thanks for the links! Should we wait for the knitr fix to be available through CRAN or edit our DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub? Best, Leo On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan wrote: > This seems to be a problem with a recent change

Re: [Bioc-devel] Request R code this paper

Hi Joris, I think that it's a spam email. I've gotten a similar if not the same version directly already. Best, Leo On Tue, Jan 7, 2020 at 10:48 AM Joris Meys wrote: > Dear, > > you mailed the developers mailing list of Bioconductor, i.e. the list for > people who develop packages for the

Re: [Bioc-devel] package download stats seem unavailable

al > channel). > > Thanks for your patience, > > H. > > On 11/11/19 10:23, Leonardo Collado Torres wrote: > > Hi, > > > > The tabular files with the Bioconductor package statistics seem broken > > right now. For examp

[Bioc-devel] package download stats seem unavailable

Hi, The tabular files with the Bioconductor package statistics seem broken right now. For example, http://bioconductor.org/packages/stats/bioc/recount/ links to http://bioconductor.org/packages/stats/bioc/recount/recount_stats.tab which right now redirects to a "page not found" message at

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

on this a year ago! If any of you have other solutions, we'd love to learn about them. Best, Leo On Thu, Aug 2, 2018 at 2:22 PM Leonardo Collado Torres wrote: > > Thanks Hervé and no problem about the Windows binary. > > Richard did get DelayedArray installed today (I think us

Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

1.45.32019-08-22 [1] Github (lawremi/rtracklayer@2dac472) Best, Leo On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence wrote: > > Sorry, please try 1.45.3. If that works then I'll push it over to release. > > On Wed, Aug 21, 2019 at 11:48 AM Leonardo Collado Torres >

[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

Dear Bioc-devel, In BioC 3.9 and 3.10 I've noticed some errors on recount which today I finally traced. It looks like the internals of rtracklayer::import.bw() changed (or mabye S4Vectors:::normarg_names) in such a way that if you specify as input to rtracklayer::import() the "selection" argument

Re: [Bioc-devel] Canceled event: Biocondutor Developers Forum @ Thu Aug 15, 2019 12pm - 1pm (EDT) (bioc-devel@r-project.org)

Hi everyone, I think this caused a bit of confusion. My understanding was that Sean created a google calendar event and cc'ed the bioc-dev mailing list. In any case, from what I can see at the BioC slack in the #general channel, the forum is still scheduled for tomorrow Thursday August 15th.

Re: [Bioc-devel] Event addition request: CDSB Workshop 2019 in Cuernavaca, Mexico

14263 > > ________ > From: Bioc-devel on behalf of Leonardo > Collado Torres > Sent: Monday, June 10, 2019 2:50:14 PM > To: Bioc-devel > Subject: [Bioc-devel] Event addition request: CDSB Workshop 2019 in > Cuernavaca, Me

[Bioc-devel] Event addition request: CDSB Workshop 2019 in Cuernavaca, Mexico

Hi, Would it be possible to add a link like "[CDSB Workshop 2019](https://comunidadbioinfo.github.io/post/building-tidy-tools-cdsb-runconf-2019/#.XP6kUNNKi52) July 29-August 2, 2019, Cuernavaca, Mexico" at http://bioconductor.org/help/events/? It's a one week workshop where Alejandro Reyes, me

Re: [Bioc-devel] Procedure for changing email

ur old email is registered to the BiocCredentials app, then you'd have > to change that too. > > If you reply with that email, a Bioc admin can change it for you (me). > > Best > > Nitesh > > Get Outlook for Android > > ____ > From: Bio

[Bioc-devel] Procedure for changing email

Hi, I couldn't find at http://bioconductor.org/help/support/ or at the support website ("change email" search) the steps for changing an email. My understanding is that this requires changing the email in 4 locations: * bioc-devel mailing list through

Re: [Bioc-devel] Packages with broken unit tests because of sample() change in R 3.6

Thanks Hervé, I also found this tweet by John Muschelli useful for this situation https://twitter.com/StrictlyStat/status/1103303028751372289 where he suggests using suppressWarnings(RNGversion("3.5.0")) That's what I did for example in

Re: [Bioc-devel] GenomicFeatures export request

; > > On 11/15/18 09:25, Leonardo Collado Torres wrote: > > Hi Hervé, > > > > Looking into the details of GenomicFeatures::exonicParts() I see that > > this function runs GenomicFeatures:::.tidy_exons(). Would it be > > possible to export this function? Looks like

[Bioc-devel] GenomicFeatures export request

Hi Hervé, Looking into the details of GenomicFeatures::exonicParts() I see that this function runs GenomicFeatures:::.tidy_exons(). Would it be possible to export this function? Looks like it'll be useful for some work we are doing. We can start using it without the function being exported, and

Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

roblem of understanding your package dependency structure, > see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html. Thanks for the link! > > > On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan wrote: >> >> >> >> On 11/5/18, 5:11 PM, "Bioc-devel o

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Thanks for fixing this Nitesh and Sam! I wrote that R check and forgot that it depended on the Gencode url. I had to fix this too for recount https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e. Best, Leo On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh wrote: >

[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

Hi bioc-devel, recount is getting a warning on Bioc 3.9 (devel) on macOS: * checking whether package ‘recount’ can be installed ... WARNING Found the following significant warnings: Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found I'm not sure how to trace

Re: [Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

> https://cran.r-project.org/doc/manuals/r-devel/R-admin.html Ahh, I didn't know about this section of the manual. Thanks! > in section C.3: > > sudo installer -pkg \ > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > -target / > &g

[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

Hi, I was about to send the email below, but eventually I got it to work. I'm sharing it anyway since others might run into similar issues. Basically, I needed the latest macOS command line tools installed, but getting them installed was tricky. I installed Xcode 10.1 (10B61) from the Mac App

Re: [Bioc-devel] Roxygen documentation under windows

Hi, Adding the -class part will help for most. To get the correct name, check the top left part of the help page for the function you want to link to. For example, if you type library(GenomicRanges) ?GRanges you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac right now).

Re: [Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

changes (but I could be wrong). > > Nitesh can elaborate a bit more on this. > > We will look into it on our end. > > Regards, > > Marcel > > > > > On 09/24/2018 10:54 AM, Leonardo Collado Torres wrote: > > Hi, > > > > Marcel Ramos told me

[Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

Hi, Marcel Ramos told me a few months ago (July 24, 2018) that experiment data packages are now controlled the same way as software packages via GitHub. Today I finally tried synching the repos following these instructions

Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

ommit > check, but it should only be a worst case. I don’t recommend this for your > repo because there are very few issues and it seems we can resolve them. I > reserve this option for packages which have extensively fractured their git > history. > > > Best regards, > > Ni

Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

ts was pre-git era, we can just ignore the > duplicates. It is pretty straightforward to disable the duplicate commit > check, but it should only be a worst case. I don’t recommend this for your > repo because there are very few issues and it seems we can resolve them. I > reserv

[Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

Hi, I'm having trouble with synching a github repo with Bioc. At https://github.com/jtleek/sva-devel/commits/master we have 3 recent commits by Claire that we want to sync with Bioc. I followed the instructions at http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ and then

Re: [Bioc-devel] EXTERNAL: Re: Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

blems. > > Just to let you that I fixed the DelayedArray timeout on > > Windows and the zip files are now available for this > > platform: > > > >https://bioconductor.org/packages/DelayedArray > > > > Sorry for the inconvenience. > > > &

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

ou that I fixed the DelayedArray timeout on > Windows and the zip files are now available for this > platform: > >https://bioconductor.org/packages/DelayedArray > > Sorry for the inconvenience. > > Cheers, > H. > > > On 08/01/2018 02:23 PM, Leonardo Collado T

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

; > On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres > wrote: >> >> From Richard: >> >> > BiocManager::install("DelayedArray") >> >> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23) >> >> Installing pa

[Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

Hi bioc-devel, A co-worker of mine (Richard) tried several times to install the DelayedArray package. We got a couple of errors but it ultimately looks like it's an internet connection problem. The truth is that might be something affecting us on our side since I can't access

Re: [Bioc-devel] BiocManager now on CRAN

Hi Marcel, I noticed that https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653 doesn't include the experiment data and workflow packages. I updated mine preemptively (derfinderData and recountWorkflow). By the way, how do I sync experiment data package updates? I forgot how to do so.

[Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages

Hi, Two of my Bioconductor packages (regionReport and derfinderPlot) use ggplot2 via ggbio. Since other packages import/suggest ggbio http://bioconductor.org/packages/release/bioc/html/ggbio.html I'm curious if you've taken a look at the email from Hadley Wickham and the upcoming update to

Re: [Bioc-devel] Submit package under a Github organization

Hi, I don't think that anything changes. At least, I don't remember that being the case (I have a few packages hosted in organization accounts). If it does break, share the github url to bioc-devel to get more specific feedback. Best, Leo On Wed, Jun 6, 2018 at 11:52 AM, Diogo P. P. Branco

Re: [Bioc-devel] Suggested edits to support site posting guide

Hi Mike, Lori and everyone else, I recently saw this tweet https://twitter.com/aprilwensel/status/989248246878035972 that links to https://medium.com/compassionate-coding/its-time-to-retire-rtfm-31acdfef654f#---0-162 First, I'm curious if you've read it and if you like it. Second, maybe we

Re: [Bioc-devel] Bioconductor 3.7 release: 3.7 branch created

Awesome! Congrats and thanks to everyone involved in the new release! Best, Leo On Mon, Apr 30, 2018 at 12:49 PM, Obenchain, Valerie wrote: > > The Bioconductor 3.7 branch is now ready. If all goes well over the next 24 > hours we'll announce the official

Re: [Bioc-devel] Web App for SSH keys

Hi Valerie, Thanks for the reply and the doc changes ^^. I added a few short replies below. Best, Leo On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org> wrote: > Hi Leo, > > Great feedback, thanks. > > On 04/19/2018 08:04 AM, Leonardo

Re: [Bioc-devel] Web App for SSH keys

This looks great Valerie, congrats to all of those involved in making the web app! I hope that it leads to less questions/confusion. Here are some minor comments, mostly about including some links/docs. * Under the which packages we have access to, I noticed that it's not showing the

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

e `output` setting > in the vignette YAML header. Note that the format set in the vignette is > still used to render the document distributed with the package tarball. > > Cheers, > Andrzej > > > On Mon, Apr 2, 2018 at 4:32 PM, Leonardo Collado Torres <lcoll...@jhu.edu> >

Re: [Bioc-devel] Suggested edits to support site posting guide

Hi Mike, I just added a few comments to your google doc. Thanks for doing this! Best, Leo On Thu, Apr 12, 2018 at 11:23 AM, Michael Love wrote: > > > dear all, > > I've edited the text from the posting guide >

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Hi, Thank you for all the work in this transition Andrzej, Lori, Valerie, Nitesh and Hervé! I have a few questions about the new system. 1) I already had a github repo (that I manually kept in sync with the subversion one) for the recountWorkflow. Should I just follow the instructions at

Re: [Bioc-devel] Nightly builds

On Wed, Feb 7, 2018 at 10:36 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > Hi, > > I try to follow all the best practices but sometimes I end up relying > on the Bioc nightly build. > > Anyhow, I personally use r-travis** for quick checks to detect broken > c

Re: [Bioc-devel] Nightly builds

Hi, I try to follow all the best practices but sometimes I end up relying on the Bioc nightly build. Anyhow, I personally use r-travis** for quick checks to detect broken commits instead of running R CMD check/build on my laptop. This way I can submit a new commit that fixes a broken commit

Re: [Bioc-devel] Missing link files in Windows (release and devel)

Thank you Jim! I changed it to \link[Rsamtools:BamFile-class]{BamFile}. Best, Leo On Wed, Jan 17, 2018 at 11:56 AM, James W. MacDonald <jmac...@uw.edu> wrote: > > On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Than

Re: [Bioc-devel] Missing link files in Windows (release and devel)

org> wrote: > > > On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I have been seen warnings in several of my packages on both release >> and devel only in the Windows build machines in relation to missing >> link files

[Bioc-devel] Missing link files in Windows (release and devel)

Hi, I have been seen warnings in several of my packages on both release and devel only in the Windows build machines in relation to missing link files. Is this something that I can address from my side or a more widespread issue? If it matters, I use roxygen2 for making my Rd files. Best,

Re: [Bioc-devel] Data package timeouts

bindr_0.1tibble_1.3.4 On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > > Thanks Sean! I was seeing timeouts also in recount related to GEOquery which > I just recently looked into. > > On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis &

Re: [Bioc-devel] Data package timeouts

Thanks Sean! I was seeing timeouts also in recount related to GEOquery which I just recently looked into. On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis wrote: > > On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith wrote: > > > Thanks for the speedy response

Re: [Bioc-devel] Encoding issues with citations (Windows only)

suecomment-337248710 Best, Leo On Mon, Oct 2, 2017 at 7:43 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > Hi, > > I've been using knitcitations for a while to handle citations in HTML > vignettes. I had been using knitcitations::read.bibtex() until I > rea

Re: [Bioc-devel] Workflow builder failing at postprocessing step

unt for the now missing Mac tar balls. I will look into this. > > Cheers, > Andrzej > > On Wed, Oct 11, 2017 at 8:09 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Hi, >> >> I recently pushed some changes to recountWorkflow** that triggered new

[Bioc-devel] Workflow builder failing at postprocessing step

Hi, I recently pushed some changes to recountWorkflow** that triggered new "postprocessing" jobs by the workflow builder. The last few (#412 up to 415) failed and I can see at http://docbuilder.bioconductor.org:8080/job/postprocessing/label=master/415/console that the error is related to the

[Bioc-devel] Encoding issues with citations (Windows only)

Hi, I've been using knitcitations for a while to handle citations in HTML vignettes. I had been using knitcitations::read.bibtex() until I realized that it no longer reads the entries in the order that were given in the bib file**. So I made a change and it all works... except on Windows. I

Re: [Bioc-devel] Package DMCHMM is not installed

ioconductor.org/packages/release/BiocViews.html#___Software > Sorry this is first time I submitted a package to bioconductor and I am not > so familiar with instructions. > > > On Sep 11, 2017, at 11:31 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: > > It's only a

Re: [Bioc-devel] Package DMCHMM is not installed

It's only available on bioc-devel, not bioc-release. See http://bioconductor.org/packages/devel/bioc/html/DMCHMM.html and http://bioconductor.org/developers/how-to/useDevel/ On Mon, Sep 11, 2017 at 7:17 PM, Farhad Shokoohi wrote: > Hello, > > I tried to install my package on

Re: [Bioc-devel] workflow building issues on mac and windows

uilder issues: I've deleted the /tmp/udcCache dir on Mac, >> but it didn't help. I'm not sure yet what could be the problem there. The >> citeproc conversion error on Windows might be because of the older pandoc >> version (1.17.2), will look into this. The convert warnings appear be

[Bioc-devel] workflow building issues on mac and windows

hem. Regardless, I'm happy that I got http://bioconductor.org/help/workflows/recountWorkflow/ up and looking good ^^. It's just the links to the Mac/Windows binaries... Thank you, Leo ** I've been pushing changes via svn, I know that workflows are not part of the git transition. I just keep every

Re: [Bioc-devel] Updates to BiocStyle formatting

Hi Andrzej, Could you let us know when you make the change which BiocStyle version implemented the change? That way we can update our description files. In the meantime, I switched my vignettes to use BiocStyle::html_document2 although I need to use figure captions and references to take

[Bioc-devel] Minor doc change about update_remotes.sh

Hi, I used today http://bioconductor.org/developers/how-to/git-mirrors/ for updating https://github.com/jtleek/sva-devel and I was getting weird results when running the update_remotes.sh script https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh. It wasn't until I

Re: [Bioc-devel] github mirror out of sync for ensembldb

t;> On 3 May 2017, at 19:51, Martin Morgan <martin.mor...@roswellpark.org> wrote: >> >> On 05/03/2017 01:10 PM, Leonardo Collado Torres wrote: >>> Hi, >>> >>> I don't think that any of the Bioconductor-mirror repos have been >>> updated to m

Re: [Bioc-devel] github mirror out of sync for ensembldb

Hi, I don't think that any of the Bioconductor-mirror repos have been updated to match the current bioc-devel branch. For example, look at https://github.com/Bioconductor-mirror/aCGH/blob/master/DESCRIPTION#L4 which is one of the first packages by alphabetical order. My guess is that they are

Re: [Bioc-devel] questions about windows build execute permissions and R version dependency

You can also test your package on R Travis against R 3.4 as shown at https://travis-ci.org/leekgroup/recount#L518. Just use this on your .travis.yml file https://github.com/leekgroup/recount/blob/master/.travis.yml#L3 On Thu, Mar 23, 2017 at 4:26 AM, Martin Morgan

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

t; Thanks for hunting down and isolating that bug! I tried to >> simplify >> >>> your code even more and was able to get a segfault with just: >> >>> >> >>> setClass("A", representation(stuff="numeric")) >> >

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

You can include both like I do in https://github.com/leekgroup/derfinderPlot/blob/master/inst/CITATION which is similar to what Xie's knitr does. On Wed, Mar 22, 2017 at 12:53 PM, Gabe Becker wrote: > Alina, > > Typically in cases like the one you describe, people want

[Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

Hi bioc-devel, This is a story about a bug that took me a long time to trace. The behaviour was really weird, so I'm sharing the story in case this helps others in the future. I was originally writing it to request help, but then I was able to find the issue ^^. The story ends right now with code

Re: [Bioc-devel] badges for Bioconductor package

This is cool! Thanks Guangchuang! On Wed, Mar 8, 2017 at 10:18 PM, Yu, Guangchuang wrote: > > Dear all, > > I have some simple functions to create badges for using in README or github > pages. > > See ggtree project website and >

[Bioc-devel] User has issue with importing a BigWig file with rtracklayer despite having a recent openssl and latest R packages

Hi, I'm trying to figure out what is going wrong in https://support.bioconductor.org/p/93182/. Mustafa is using recount to load a bigwig file from the web. The code in recount relies on some code in derfinder, and the actual importing is done by rtracklayer::import(). >From looking at the R

[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

Hi, I think that a recent change in S4Vectors broke GenomicFeatures::makeTxDbFromGFF(). I ran this code about a week ago without problems, but it's failing now. Best, Leo ## Unevaluated code library('GenomicFeatures') library('devtools') txdb <-

Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

Hi Stian, Install BiocStyle 2.3.20 or newer and that error will go away. See https://github.com/Bioconductor/BiocStyle/issues/20 for details. Best, Leo On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad wrote: > Hi, > > Could someone please advice me on the errors I'm

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Jurat, Maybe it'll be helpful to you if you see how other packages have their data. For example, take a look at one of my packages: https://github.com/lcolladotor/derfinder You'll see that I have two directories inside /inst/extdata with some files that I use in my vignette code. See

Re: [Bioc-devel] Error processing scater vignette Mac OS X Sierra

Hi Davis, Update your BiocStyle package to 2.2.1 (release) or 2.3.12 (devel) which I see you are using at https://github.com/Bioconductor-mirror/scater/blob/master/DESCRIPTION#L24. See https://stat.ethz.ch/pipermail/bioc-devel/2016-November/010168.html for details Best, Leo On Wed, Nov 30, 2016

[Bioc-devel] Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

Hi, The latest build report for derfinderPlot (1.9.2) shows the following error: Quitting from lines 188-190 (derfinderPlot.Rmd) Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics: could not find function "aes" I traced it down to biovizBase::parseArgsForAes() as shown

Re: [Bioc-devel] BiocStyle issue

Guangchuang, you can see at https://github.com/Bioconductor/BiocStyle/issues/19 (the main github repo for this package) that this issue is already been reported and will be addressed asap by BiocStyle's maintainer. On Tue, Nov 22, 2016 at 9:46 PM, Yu, Guangchuang wrote: > >

Re: [Bioc-devel] Coverage test badge not updating

restore package coverage for > > release. If, for whatever reason, this is not possible or is too > > complicated, we'll remove the badges from the release landing pages. > > > > Thanks for the reminder! > > > > Cheers, > > H. > > > > On 11/01/2016 1

Re: [Bioc-devel] Availability shield URLs

Awesome, thanks Dan! On Tue, Nov 8, 2016 at 9:40 AM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > On 11/02/2016 11:54 AM, Leonardo Collado Torres wrote: > >> Hi, >> >> I'm just curious why >> http://www.bioconductor.org/shields/availability/rel

Re: [Bioc-devel] Coverage test badge not updating

, then it might be best to leave them in Bioc-devel (given Jim's arguments earlier) and remove them from Bioc-release. Best, Leo On Mon, Nov 23, 2015 at 4:25 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > > Thank you for fixing this Jim! I noticed it working now on devel. > How

Re: [Bioc-devel] github-mirror of ensembldb out of sync with BioC svn

Hi, The same is true for recount and regionReport. derfinder and my other packages are in sync though. Best, Leo On Wed, Oct 19, 2016 at 3:34 AM, Rainer Johannes wrote: > I just wanted to report that the github-mirror for ensembldb is out of > sync with the BioC

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