Re: [Bioc-devel] Error in SVMDO Package

Dear Mustafa, The contents of code.bioconductor.org updates every 15 minutes, and should automatically reflect any changes in the central git repository. It looks like your changes have been pushed to the devel and RELEASE_3_19 branches and can be seen here: https://code.bioconductor.org/browse/

Re: [Bioc-devel] Moving repository for Bioconductor package

Dear Alan, I don't think there are any formal steps required to do this. Once a package is in Biocondcutor, it is effectively decoupled from whatever Git repository it was originally submitted from. For example, you could delete the existing GitHub repository entirely, and it wouldn't affect the

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

This looks to be an issue introduced by changes in knitr 1.47.0, which lead to an incompatibility in the BiocStyle Rnw template. We're working on a patch to BiocStyle, which should be deployed on the build machines today, and will hopefully fix the issue in the affected packages. The is nothing pa

Re: [Bioc-devel] muleaData problems reported in the Build/check report for BioC 3.19 experimental data

Hi Eszter, If you're using ExperimentHub in your vignette then you need to add that to the Suggests field in your DESCRIPTION file. The R CMD check output you linked to mentions a similar issue for the code in your examples: * checking for unstated dependencies in examples ... WARNING '::' or ':

Re: [Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"

Hi Johannes, I think RCurl is imported via the package dependency chain of xcms -> SummarizedExperiment -> GenomeInfoDb -> RCurl. It looks like Hervé removed this dependency from GenomeInfoDb recently ( https://code.bioconductor.org/browse/GenomeInfoDb/commit/9562907f6800cf6052fff9fb2f85329ff4479

Re: [Bioc-devel] Possible https://code.bioconductor.org SSL certificate issue

ductor.org Cheers, Mike On Wed, 6 Mar 2024 at 16:39, Mike Smith wrote: > Maintainer of the code.bioconductor.org site here. Thanks for the > report. > > The certificate is exactly the same as the one used by all other > bioconductor.org sites, however we recently changed (February

Re: [Bioc-devel] Possible https://code.bioconductor.org SSL certificate issue

Maintainer of the code.bioconductor.org site here. Thanks for the report. The certificate is exactly the same as the one used by all other bioconductor.org sites, however we recently changed (February 21st) how it is applied to the code.bioconductor.org subdomain. Did you happen to try this more

Re: [Bioc-devel] Omada package failing due to removed dependency

gt; >> Lori Shepherd - Kern >> >> Bioconductor Core Team >> >> Roswell Park Comprehensive Cancer Center >> >> >> On Mon, Sep 11, 2023 at 10:05 PM Sokratis Kariotis < >> sokratiskario...@gmail.com> wrote: >> >>> Hey, >>

Re: [Bioc-devel] Check time on macOS (MIRit)

Hi Martin, A very short summary is that on kjohnson3 a build/check on package launched by cron takes significantly longer than if one runs the same command manually in a terminal. There's some further discussion on this at https://community-bioc.slack.com/archives/CEQ04GKEC/p1706816310942079 and

Re: [Bioc-devel] Diverging version numbering on Bioconductor RELEASE

Personally I do as Steffen mentioned, and grab the upstream changes manually. Changes not introduced by me only happen once every 6 months, and I'm involved enough with Bioconductor that I generally know when the release and version bump has occurred, so it's never quite felt like enough work to i

Re: [Bioc-devel] Package check error under BiocVersion 3.18

Hi, As you surmise, it looks like this is a conflict between Matrix and SeuratObject. It's reported in quite a few places e.g. https://github.com/satijalab/seurat/issues/7986 I don't think there's much you can do except wait for the Seurat maintainers to release an update to their package. Give

Re: [Bioc-devel] Including large files for the package

te: > Hi Mike, > > These are raw data files that I use to createte internal data. They don’t > end up being used in the final package themselves. Are you suggesting that > adding them to .Rbuildignore should be sufficient? They are in the repo > because I want to keep track of them.

Re: [Bioc-devel] Including large files for the package

Hi Ali, Looking at the files, it seems although the file extension is .xls, they're actually just plain text TSV files. They compress pretty well with standard tools and R is able to easily read a tsv compressed with something like GZIP. I wonder if you've considered just compressing the files an

Re: [Bioc-devel] Omada package failing due to removed dependency

t;> >> is not allowing me to go ahead. > >>>> >> > >>>> >> My commands: > >>>> >> git add . > >>>> >> git commit -m "Update metrics" > >>>> >> git push upstream main:devel > >>>> >>

Re: [Bioc-devel] Omada package failing due to removed dependency

> >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> *Enumerating objects: 19, done.Counting objects: 100% (17/17), > > done.Delta > > >> compression u

Re: [Bioc-devel] Omada package failing due to removed dependency

Hi Sokratis, Everything in Bioconductor is built around the central Bioconductor git repositories. The only way to get changes out to users is to commit them to git.bioconductor.org and then the build system will pick those up, run the tests and checks, create new versions of packages, and make t

Re: [Bioc-devel] Can't reproduce a latex error

Hi Mark, I don't know how to identify the Latex used on the build system, but I see the same problem with GRridge on my system that uses Latex installed via the tinytex package. I think the issue is the use of \describe{} in https://code.bioconductor.org/browse/GRridge/blob/master/man/GRridge-pac

Re: [Bioc-devel] Issue with setting Maintainer in new package submission

Hi Andrew, Perhaps I'm not understanding your workflow correctly, but it looks like your email in the DESCRIPTION that was uploaded to the Bioc submission system is an @dfci.harvard.edu one. That's what I see at https://github.com/NKInstinct/flowGate/blob/master/DESCRIPTION and it is the same if

Re: [Bioc-devel] Broken stringi install on bioconductor_docker:RELEASE_3_16

Hi Stevie, I also found this same problem after our emails yesterday and opened an issue on the Bioconductor_docker repo at https://github.com/Bioconductor/bioconductor_docker/issues/59 In the short term I think Vince's suggestion of reinstalling stringi should at least fix your workflow, and hop

Re: [Bioc-devel] BiocCheck not available in bioc-devel docker container

remove that step entirely. If you ever stop using the container you'd need to reinstate it. Cheers, Mike On Wed, 9 Nov 2022 at 12:04, Mike Smith wrote: > Hi Stevie, > > It might be helpful to link to the workflow runs so people can see exactly > what you're doing and what

Re: [Bioc-devel] BiocCheck not available in bioc-devel docker container

Hi Stevie, It might be helpful to link to the workflow runs so people can see exactly what you're doing and what's happening. Hopefully I'm looking in the right place at https://github.com/steveped/ngsReports/actions/runs I'm not sure about the error message regarding BiocCheck. However there a

Re: [Bioc-devel] Trouble with version bump

Hi Alex, Where are you pushing this too? Maybe the output from git remote -v will be helpful. The reason I'm asking is that it looks like SpliceWiz has already been accepted to Bioconductor, so I wouldn't expect to see messages like "post on the Github issue where your package is being reviewed"

[Bioc-devel] Bioconductor Developers' Forum - The R Universe Project - Thursday 18th November

Hi everyone, After a hiatus the Developers Forum will be back next Thursday 18th November at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-11 This month Jeroen Ooms will give an overview of the R Universe project ( https://r-

Re: [Bioc-devel] SSL certificate error on nebbiolo2

iomart = "ensembl", dataset = > "dmelanogaster_gene_ensembl") > > ensembl <- useMart(biomart = "ensembl", dataset = > "dmelanogaster_gene_ensembl") > Ensembl site unresponsive, trying asia mirror > Error in curl::curl_fetch_memory(url, h

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

Hi Steffen, Thanks for the feedback. I've been referencing this email thread when presenting about developing the code website, so it might be old but it wasn't forgotten! Right now I think we still don't quite meet your use case, as https://code.bioconductor.org/ currently only lists the softwa

Re: [Bioc-devel] biomaRt error during nigthly 'devel' build

Dear Ilyess, The Ensembl BioMart server seems to have been intermittent over the last few days. It looks like both conclus and biomaRt are now building successfully - hopefully it stays that way. These issues happen occasionally with packages that access internet resources, and it's normally wort

Re: [Bioc-devel] Suppressing messages from Rprofile

an set it elsewhere, e.g. ~/.bashrc, in a Linux >> > environment module that is loaded, and so on. >> > >> > BTW, using Rscript --no-init-file ... would skip .Rprofile while still >> > parsing .Renviron. >> > >> > /Henrik >> > >> >

[Bioc-devel] Suppressing messages from Rprofile

I have the following line in the configure.ac for rhdf5filters, which returns the location of the HDF5 headers distributed with Rhdf5lib: RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e 'cat(system.file("include", package="Rhdf5lib"))'` For me the output is a path like /mnt/data/R-lib/4.0

Re: [Bioc-devel] Methods to speed up R CMD Check

Hi Alan, I wonder if there are instances in your tests where you can use pseudo data or mock the behaviour of certain functions. For me the aim of unit testing is to confirm the behaviour of functions under controlled conditions, but it doesn't necessarily have to be done using 'real' data. For

Re: [Bioc-devel] EXTERNAL: Resolve mismatch between master and release branches

Hi Sarah, Just to reiterate Marcel's point, if these are new features or tweaks to your package, then they shouldn't be committed to the release branch at all. The Bioconductor ethos is that the release version of a package should remain stable for a 6 month window (the release cycle), and change

[Bioc-devel] Bioconductor Developers Forum - 18th March

Dear all, The next Bioconductor Developers' Forum is this Thursday 18th March at 09:00 PST / 12:00 EST / 17:00 CET - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-03 PLEASE NOTE: this is an hour earlier for those of us not yet in daylight savings time! - Th

Re: [Bioc-devel] Removal of large items in git history - BiocCheck warning

I've used something like this approach in the past. All the normal caveats about making sure you've got a backup apply. Find the names of largest objects in the pack file (not necessarily in size order). In this case they're almost all .rda files. git rev-list --objects --all | grep -f <(git ve

[Bioc-devel] Bioconductor Developers Forum - 25th February

Dear all, The next Bioconductor Developers' Forum is this Thursday 25th February at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite attached and at https://tinyurl.com/BiocDevel-2021-02 - This month we're going to focus on Unit Testing! We'll introduce what unit tests a

[Bioc-devel] Bioconductor Developers Forum - 21st January

Dear all, The next Bioconductor Developers' Forum is this Thursday 21st January at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite attached and at *https://tinyurl.com/BiocDevel-2021-01 * - This month we will hear from Jass Bagga and E

Re: [Bioc-devel] Bioconductor package CNVRanger

Hi Ludwig, I think this actually a result of changes in rtracklayer that aren't playing well with Gviz::IdeogramTrack(). It looks like the error message is a bit misleading, it's not really a connection issue, just that something unexpected happens because some of the rtracklayer::ucscTableQuery(

Re: [Bioc-devel] Warnings about man pages for assignment operators on Windows builds

Hi Vince and Stephanie, There was some discussion in the Bioconductor slack about these warnings, and they definitely seem to be related to a change in R-devel, which tries to create files with names that are invalid on the Windows filesystem. However, the reason you may not see them on your loca

[Bioc-devel] Problem with download count tables

Hi, It looks like there's an issue with the download count tables for the annotation packages. I get either "permission denied" or "not found" errors if I try to follow any of the links from https://bioconductor.org/packages/stats/data-annotation.html This is also breaking the BiocPkgTools::biocD

[Bioc-devel] Bioconductor Developers Forum - 10th December

Dear all, The next Developers Forum will take place next Thursday 10th Dec at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite at *https://tinyurl.com/BiocDevel-2020-12-10 * Please note this is one week earlier than originally scheduled

Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx

Hi Christopher, It looks like the knitcitations package is no longer on CRAN. Heading to https://cran.r-project.org/web/packages/knitcitations/index.html results in: Package ‘knitcitations’ was removed from the CRAN repository. Formerly available versions can be obtained from the archive.

Re: [Bioc-devel] Issues with images in vignette

Thanks for the information Sudeep. I'm not sure there should be any changes in BiocStyle between 2.18.0 and 2.19.0 (other than the version number!) but there's clearly something weird going on. I'll take a look tomorrow and report back in https://github.com/Bioconductor/BiocStyle/issues/83 Cheer

[Bioc-devel] Bioconductor Developers Forum - 19th November

Dear all, The next Developers Forum will take place this coming Thursday 19th Nov at 09:00 PST / 12:00 EST / 18:00 CET - You can find a calendar invite at *https://tinyurl.com/BiocDevel-2020-09-19 * We will be using BlueJeans and the meeting can be joined

Re: [Bioc-devel] Unable to install "msdata" package in current BioC 3.13 docker

Hi Jo, There was some discussion of a similar issue on the support forum at https://support.bioconductor.org/p/p132470/ The suggestion there was to try changing R's download.file.method option e.g. options(download.file.method = "curl") Best, Mike On Thu, 5 Nov 2020 at 13:21, Rainer Johannes

[Bioc-devel] Bioconductor Developers Forum - 22th October

Dear all, The next Developers Forum will take place this coming Thursday 22th Oct at 09:00 PDT / 12:00 EDT / 18:00 CEST - You can find a calendar invite at https://tinyurl.com/y4y2xptb We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 0

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Thanks for the self contained example Gordon. Just to add to the confusion, I'm unable to replicate this on my Windows machine. Both the toy example and running R CMD check on limma or Biobase fail to produce the NOTE. I've tried within RStudio, RGui and at the command line. The only difference

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

Well I learnt something new today! "The final character, which may also be a letter "X" representing the value "10" [..], is a MOD 11-2 check digit conforming to the ISO/IEC 7064:2003 standard." - https://en.wikip

Re: [Bioc-devel] Time-out error on Ubuntu 20.04 build

I think this information will probably just confuse the issue, but I've successfully checked out ncRNAtools and run R CMD build / check without issue on my Ubuntu 20.04 test machine. It took a couple of minutes. Rolling back to an older version prior to the SSL patch would lead to failure and the

Re: [Bioc-devel] SSL error on Ubuntu 20.04

Hi Lara, I've encountered this issue with biomaRt too. I found I could get the connection to work with the following: library(httr) url <- "https://www.ensembl.org/"; httr_config <- config(ssl_cipher_list = "DEFAULT@SECLEVEL=1") res <- with_config(config = httr_config, GET(url)) I haven't quit

Re: [Bioc-devel] Help finding helpful diagnostic info in the build results report

Hi Lillian, For the most part skipping happens because there is a hierarchy to the package testing. If you can't BUILD a package, then you automatically can't CHECK or build a binary version (BUILD BIN), so the build system will simply skip trying those steps if it fails at the BUILD stage. (The

[Bioc-devel] Bioconductor Developers Forum - 20th August

Dear all, Sorry for the short notice, the next Developers Forum will take place this coming Thursday 20th August at 09:00 PDT / 12:00 EDT / 18:00 CEST - You can find a calendar invite at https://bit.ly/3iUidMb We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114

Re: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

Hi Carlos, I don't think you need to worry about this. The 4 space indentation is a style recommendation (not a requirement), and if the only place that your code isn't meeting that recommendation is the YAML header then I can't imagine that any reviewer will worry too much about this. The revie

[Bioc-devel] Bioconductor Developers Forum - Thursday 16th July

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 16th July at 09:00 PDT/ 12:00 EDT / 18:00 CEST Calendar invite available from https://bit.ly/3gCsFXO We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881)

Re: [Bioc-devel] Unable to reproduce OS/X build error for "netDx" package

Hi Shraddha, I don't know what Java the build system uses, but I can reproduce the error with Java 13. It's fine with Java 8 as you say. I wont copy the whole error message as it's the same as I see on the build system, but I do notice that in the middle I see: Java 8 detected This seems wrong

Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

Hi Erik, I think the #' @return tag will create the \value{} section in the Rd file. Mike On Thu, 25 Jun 2020 at 17:24, Erik Christensen wrote: > Hello, > > Is there a way to add the value section in man pages using roxygen tags? I > am currently using "@section Value: ..." but this fails bioc

Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

Reading around, it looks more likely this is an issue with pandoc than LaTeX directly. I guess it'd help to know what version of pandoc is running on the build machine, I'm unable to recreate either using the pandoc supplied with RStudio. Mike On Fri, 15 May 2020 at 21:09, Sergio Picart Armada

Re: [Bioc-devel] EBImage/cytomapper check error on tokay2 i386

ly by EBImage in the failing test. On Wed, 22 Apr 2020 at 09:57, Mike Smith wrote: > I can confirm that I can reproduce this error on my own Windows machine. > My first thought is that it's related to the new Windows toolchain. I'll > try to take a look today and see if there&#x

Re: [Bioc-devel] EBImage/cytomapper check error on tokay2 i386

I can confirm that I can reproduce this error on my own Windows machine. My first thought is that it's related to the new Windows toolchain. I'll try to take a look today and see if there's a simple fix in the code. On Mon, 20 Apr 2020 at 11:12, Nils Eling wrote: > Hi all, > > the checks for my

[Bioc-devel] Updates to BiocStyle

Dear All, Andrzej Oleś and I have just added responsive layout support to the devel branch of BiocStyle. This should make the HTML vignettes produced by the package work better on small screen sizes like phones & tablets. The changes are summarised on Github at https://github.com/Bioconductor/Bi

[Bioc-devel] Announcement: Update to Rhdf5lib

Dear all, This is a heads up that I've updated the version of HDF5 distributed in Rhdf5lib to 1.10.6. The change was principally motivated to allow the use of the S3 virtual file driver allowing read access to HDF5 files stored in S3 buckets. As such the library compilation now uses the --enable

[Bioc-devel] Bioconductor Developers Forum - Thursday 16th April

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 16th April at 09:00 PDT/ 12:00 EDT / 18:00 CEST (Note: This is back to the usual time in Europe, Check here! ) We will be us

Re: [Bioc-devel] How can I maintain a stable list of source urls

I was talking with another nix user a while back about this problem, and I don't think there's a good solution at the moment. One thing that strikes me is that when release packages get updated the old versions get put in an archive and the source tarball remains available e.g. https://bioconducto

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 19th March

red in previous calls, and get participant feedback on future directions and topics for the Developers' Forum. Looking forward to it. Mike On Mon, 16 Mar 2020 at 13:27, Mike Smith wrote: > Dear all, > > The next Bioconductor Developers' Forum is scheduled for Thursday 19th >

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th March

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 19th March at 09:00 PST/ 12:00 EST / 18:00 CET We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) As part of this month's call I thought would be goo

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 20th February

obert Castelo is presenting the surprisingly tricky problem of determining the exact dependency path that leads to unexpected packages being loaded by your code Looking forward to it. Mike On Mon, 17 Feb 2020 at 15:50, Mike Smith wrote: > Dear all, > > The next Bioconductor Develo

[Bioc-devel] Bioconductor Developers Forum - Thursday 20th February

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 20th February at 09:00 PST/ 12:00 EST / 18:00 CET We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) If you have any specific topics you'd like to ra

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 23rd January

2020 at 12:56, Mike Smith wrote: > Dear all, > > The next Bioconductor Developers' Forum is scheduled for Thursday 23rd > January at 09:00 PST/ 12:00 EST / 18:00 CET > > We will be using BlueJeans and the meeting can be joined via: > > https://bluejeans.com/11406

[Bioc-devel] Bioconductor Developers Forum - Thursday 23rd January

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 23rd January at 09:00 PST/ 12:00 EST / 18:00 CET We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) If you have any specific topics you'd like to rai

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 19th December

Dear all, Just a reminder that this is happening today. It appears I am resolutely wishing for summer time still - the intended time is 09:00 PST/ 12:00 EST / 18:00 CET Best wishes, Mike On Mon, 16 Dec 2019 at 15:49, Mike Smith wrote: > Dear all, > > The next Bioconductor Develope

Re: [Bioc-devel] Question regarding pruning release of large files

Hi Saskia, There's some documentation on this at https://bioconductor.org/developers/how-to/git/remove-large-data/ I guess the most pertinent part is "The Bioconductor git server does not allow -f or to force push to the git.bioconductor.org location. Please email bioc-devel@r-project.org explain

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th December

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 19th December at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) If you have any specific topics you'd like to r

Re: [Bioc-devel] Long Tests builds

Thanks Hervé for documenting this, should be very useful. Do you think there's any merit in identifying if there are currently packages that take very close to the 40 minutes mark at the moment, and pointing this feature out to the maintainers directly? I don't know how tight for time the build p

Re: [Bioc-devel] Error in building vignette for previously stable version

Hi Jakob, This looks like the same problem a few others have reported. The latest advice was to wait for BiocStyle to be updated to reflect changes in rmarkdown, so you don't need to do anything for now: https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html Mike On Thu, 5 Dec 201

Re: [Bioc-devel] Problem with uncompressing files on tokay1?

Could this be another instance where you need to specify mode = "wb" when you call download.file()? I've seen many examples of Windows downloads being corrupted because it uses mode = "w" by default. Presumably BiocFileCache would both handle this correctly and save multiple downloads, so it's a

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 21st November

ssues and need-to-know items post BioC 3.10 release - Lori Shepherd & Hervé Pagès - Improving finability of BioC packages - Steffen Neumann - User and Developer session at EuroBioc2019 - Laurent Gatto Best wishes, Mike On Mon, 18 Nov 2019 at 10:18, Mike Smith wrote: > Dear all, > &

[Bioc-devel] Bioconductor Developers Forum - Thursday 21st November

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 21st November at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) This month we currently don't have any presenta

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 17th October

:56, Mike Smith wrote: > Dear all, > > The next Bioconductor Developers' Forum is scheduled for Thursday 17th > October at 09:00 PDT/ 12:00 EDT / 18:00 CEST > > We will be using BlueJeans and the meeting can be joined via: > > https://bluejeans.com/528142528 (Meet

Re: [Bioc-devel] download statistics for 2019?

Also, if you're interested, I've been collating the downloads recorded via bioconda at: https://github.com/grimbough/anaconda-download-stats On Thu, 10 Oct 2019 at 19:59, Sean Davis wrote: > Just a note that the BiocPkgTools package has a biocDownloadStats() > function. It doesn't do anything s

[Bioc-devel] Bioconductor Developers Forum - Thursday 17th October

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 17th October at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/528142528 (Meeting ID: 528 142 528) This month, motivated by some community suggesti

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, I suspect what has happened here is that when create the mini_pbmc3k object, you're doing this by subsetting the PBMC, 3k scRNA-seq data from ExperimenHub. The assay data for that are are actually stored in an HDF5 file which will be downloaded and stored in your ExperimentHub cache on y

Re: [Bioc-devel] new package for accessing some chemical and biological databases

I've lost track of whether the infrastructure is actually used, but certainly some package have a 'longtests' folder e.g. https://github.com/LTLA/beachmat On Fri, 13 Sep 2019 at 16:02, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > We used to have (? or at least discussed the possi

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th September

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 19th September at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/645510122?src=join_info (Meeting ID: 645 510 122) More details can be found in the

Re: [Bioc-devel] Biocondutor Developers Forum

update on the status of some of his recent work. If you have anything burning to discuss or present, please let me know. Cheers, Mike On Thu, 8 Aug 2019 at 10:31, Mike Smith wrote: > Dear all, > > I am excited to announce a new initiative within the Bioconductor project > - the Bi

Re: [Bioc-devel] Resetting to previous commits

Yes, the Bioconductor build system will only try to build the most recent version in the git repository. If it never managed to successfully build a particular version then that version should not appear anywhere on the Bioc site. For example biomaRt is now on release 2.40.3, but version 2.40.2 n

[Bioc-devel] Biocondutor Developers Forum

Dear all, I am excited to announce a new initiative within the Bioconductor project - the Bioconductor Developers' Forum. This monthly teleconference is intended as a platform for Bioconductor developers to describe existing software infrastructure to other members of the BioC community, to prese

Re: [Bioc-devel] HiCBricks build error

eports and push more changes if this doesn't fix the problem. Mike On Tue, 30 Jul 2019 at 09:53, Mike Smith wrote: > There are many other packages affected by this > e.g. biomformat, BiocSklearn, CoGAPS, ... It looks like Rhdf5lib is being > built without linking to zlib, a

Re: [Bioc-devel] HiCBricks build error

There are many other packages affected by this e.g. biomformat, BiocSklearn, CoGAPS, ... It looks like Rhdf5lib is being built without linking to zlib, and so files written with zlib compression can't be read. I've been trying to get Rhdf5lib to play more smoothly for systems that use conda as a

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

I can reproduce the error using R-3.6.0beta and running the following two steps to replicate the Bioc builder commands: R CMD build --keep-empty-dirs --no-resave-data Rdisop rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --m

Re: [Bioc-devel] ddply causes error during R check

If you're sure these are false positives (and it looks like they are) then you can use utils::globalVariables() outside of your function to get rid of the note. It might also be worth pointing out that there are also plenty of Bioconductor packages that don't do this and simply have this mentioned

Re: [Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8

Hi Ruqian, I think this is a consequence of your internal data.frames have column names that include the minus sign i.e. "-". The code clearly tries to deal with this by wrapping them in back-ticks at certain points, but I think it doesn't do this successfully in projectScoreLandscape() First, c

[Bioc-devel] Major update to rhdf5 and Rhdf5lib

Hi all, I've just submitted updated versions of rhdf5 (2.25.7) and Rhdf5lib (1.3.2) to the BioC devel branch. These represent a significant change as the underlying version of HDF5 has now changed from 1.8.19 to 1.10.2. This has been done in response to an increasing prevalence of files that can

Re: [Bioc-devel] Git file size limits

itesh) is out of communication for a bit... > > On 08/22/2018 10:01 AM, Mike Smith wrote: > > Hi, > > > > I'm trying to commit an update to Rhdf5lib but run into the 5MB file size > > restriction. The file in question is the pre-compiled Windows binary so &g

[Bioc-devel] Git file size limits

Hi, I'm trying to commit an update to Rhdf5lib but run into the 5MB file size restriction. The file in question is the pre-compiled Windows binary so I'm not sure there's anything I can do to make it smaller. Is is possible to make exceptions on a per-package basis? Thanks, Mike [[alte

Re: [Bioc-devel] Synching version numbers went wrong

> > > Shana White > Ph. D Candidate - Biostatistics + Bioinformatics > <https://med.uc.edu/eh/divisions/bio> > Predoctoral Fellow - MECEH > <https://med.uc.edu/eh/divisions/epi/programs/meceh> > Room 318 Kettering Labs > vande...@mail.uc.edu > 937-657-82

Re: [Bioc-devel] Fixing bugs in release version

.3.1 ( > https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01) > so why is it 1.2.1 on the Bioconductor repo? > > p.s. have recently been struggling with a similar issue so, just asking to > try to get a better understanding > > Kind Regards, > Jaso

Re: [Bioc-devel] Fixing bugs in release version

It looks to me like you have made the changes correctly. When I checkout your packages you have versions 1.3.1 and 1.2.1 for the master and RELEASE_3_7 branches respectively. -> % git checkout --quiet master && cat DESCRIPTION | grep Version Version: 1.3.1 -> % git checkout --quiet RELEASE_3_7 &

Re: [Bioc-devel] Synching version numbers went wrong

Hi Shana, It looks like the release version of KEGGlincs is 1.6.x and the devel version should be 1.7.x.When you're committing to the master branch of git.bioconductor.org this equates to the devel version and there's a check in place to prevent even version numbers being committed here. My r

Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

sive solution. Thanks, Mike On Thu, 31 May 2018 at 20:09, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Mike, > Is this still an issue or has it been resolved? > Val > > > On 05/22/2018 02:19 PM, Mike Smith wrote: > > In trying to diagnose this

[Bioc-devel] Windows, normalizePath(), and non-ASCII characters

In trying to diagnose this issue at https://support.bioconductor.org/p/108548/ I've found some weird behaviour with Windows, normalizePath(), and non-ASCII characters. Essentially, if I run normalizePath() recursively on a path that contains 'é' (I haven't tried other characters) something 'chang

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Dear Pijush, Once a package has been accepted to Bioconductor, a copy is made in Bioconductor's own git repository and this is the source from which the packages are made available to users. Any change you make in Github won't be automatically reflected there, you have to explicitly make the chan

Re: [Bioc-devel] biomaRt uswest mirror ERROR

Hi Lori, There should be no issue with switching to an alternative mirror with regards to the content. However, in the current release you will also need to set the argument ensemblRedirect = FALSE otherwise it'll end up at the uswest mirror regardless of the host you specify. This is not the ca

Re: [Bioc-devel] Subsetting Multiple platform build/check report

I do something similar and have a local 'dashboard' page populated with the build status shields pulled from the package landing pages e.g. http://bioconductor.org/shields/build/devel/bioc/biomaRt.svg Then I can glance at that to see if anything isn't green. Mike On 20 April 2018 at 10:06, Kasper

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