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

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

package authors need to do at this time. I'll report back here on the status after the update has been rolled out. Best wishes, Mike On Tue, 11 Jun 2024 at 04:09, Xiangyu Luo wrote: > I also received the same error email for my packages BUScorrect and > HIREewas. I don't know how

Re: [Rd] using Paraview "in-situ" with R?

ry helpful. The workflow, and mind flow, for the "in situ" mode makes you wonder how you ever did without it. I will probably need to update my R interface package and MJMDatascope is hardly ideal but improving both seems worth the effort. Thanks.  Mike Marchywka  44 Crosscreek Trail Jasper GA 3

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

'::' or ':::' imports not declared from: ‘ExperimentHub’ ‘dplyr’ 'library' or 'require' calls not declared from: ‘ExperimentHub’ ‘dplyr’ That should also be fixed by putting those packages in Suggests. Cheers, Mike On Wed, 20 Mar 2024 at 09:54, Eszter Ari wrote: > Hi, > > I have a question

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

ed, RCurl doesn't get installed with xcms in a fresh R/Bioconductor install like your Docker container. Then when you load the object via data() R complains about missing the expected RCurl package. That's just an educated guess, but seems plausible to me. Best, Mike On Wed, 13 Mar 2024 at 10:1

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

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 21st) how

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

apply to other sites we host. I'll report back here if we change things. Cheers, Mike On Wed, 6 Mar 2024 at 09:00, Gábor Csárdi wrote: > Anyone know where to report issues with code.bioconductor.org? > > This is what I see from a vanilla Ubuntu 22.04 (and also from Fedora >

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

branch, but there aren't any recent updates to RELEASE_3_18. If you do make more changes, be aware it might take 15 minutes before they appear on that site. It updates frequently, so that's the longest you should need to wait. Best, Mike On Fri, 9 Feb 2024 at 03:28, Sokratis Kariotis wrote

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

to this particular issue. Cheers, Mike On Wed, 7 Feb 2024 at 16:34, Martin Grigorov wrote: > Hi Kasper, > > According to > > https://github.com/Bioconductor/BBS/blob/9ebb2cf20e70e4bebf24a2a824a67193de821b08/3.19/bioc-mac-arm64/kjohnson3/config.sh#L17-L20 > the ma

Re: [Rd] using Paraview "in-situ" with R?

ore useful on-the-fly than text or after the fact.  Mike Marchywka  44 Crosscreek Trail Jasper GA 30143 was 306 Charles Cox Drive  Canton, GA 30115 470-758-0799 404-788-1216  From: George Ostrouchov Sent: Wednesday, January 10, 2024 3:06 PM To:

[R-pkg-devel] Fw: [Rd] using Paraview "in-situ" with R?

The r-devel list suggested I try this here. Thanks. From: R-devel on behalf of Mike Marchywka Sent: Tuesday, January 9, 2024 9:20 AM To: R-devel Subject: [Rd] using Paraview "in-situ" with R? I had previously asked about R interfaces

[Rd] using Paraview "in-situ" with R?

ware of anyone doing this interface or reasons its a boondoggle? Thanks.  Mike Marchywka  44 Crosscreek Trail Jasper GA 30143 was 306 Charles Cox Drive  Canton, GA 30115 470-758-0799 404-788-1216  __ R-devel@r-project.org mailing list https://stat.ethz.c

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

much work creating the workflow: https://github.com/marketplace/actions/upstream-sync Cheers, Mike On Wed, 15 Nov 2023 at 12:22, migdal migdal wrote: > Awesome, thanks for the response! > > I think it should be possible to put what you are doing manually into > GithubActions scri

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

we take when using other packages. Generally speaking the effort saved in not reinventing all the cool stuff in Matrix & Seurat yourself is worth this hassle. Personally, I trust the Seurat developers will address this in a timely manner. Cheers, Mike On Sun, 12 Nov 2023 at 04:48, Jinjin Chen

Re: [Rd] R packages to send plottable data to external apps

ackage you mentioned maybe one interface would be to emulate that action too as that was my original interest circa 2007 lol. fwiw. Thanks.  Mike Marchywka  44 Crosscreek Trail Jasper GA 30143 was 306 Charles Cox Drive  Canton, GA 30115 470-758-0799 40

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

packages if they aren't useful to the end user of the package. However it looks like you're already excluding the raw and data-raw directories via .Rbuildignore, so I don't think you need to do more than that. Best, Mike On Tue, 5 Sept 2023 at 19:15, Ali Sajid Imami wrote: > Hi M

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

rom the package. Best wishes, Mike On Thu, 31 Aug 2023 at 20:08, Ali Sajid Imami wrote: > Hi, > > The file is downloaded and filtered from the ilincs website. Unfortunately > it is not readily available from ilincs.org itself. We have the capability > of storing the file in our S

[Rd] R packages to send plottable data to external apps

drop-in to the attached code and get something like the attached output that could also be switched to other data sources? This right now works via linux fifo and somewhat by UDP. It can queue data and stop making it if no one seems to be consuming it depending on the channel. Thanks.  Mike

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

to 1.2.1 and push that branch. Hopefully this will fix the issues there too. Best, Mike On Thu, 17 Aug 2023 at 03:47, Sokratis Kariotis wrote: > Hey all, > > I can see all is green but I still get messages about failing builds and on > the website shows build error. Do I still have to

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

; > >> > > >> > > >> > > >> > > >> > > >> > > >> *Enumerating objects: 19, done.Counting objects: 100% (17/17), > > done.Delta > > >> compression using up to 16 threadsCompressing objects: 100% (11/11),

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

them available for distribution. Perhaps you can include the git command you're running to submit the changes and a copy of the exact error you're receiving. That might help the team suggest a solution. Best regards, Mike On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis wrote: > Hey both, &g

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

-package.Rd#L28 Writing R Extensions suggests the entries in this environment should have two arguments and might not work otherwise ( https://rstudio.github.io/r-manuals/r-exts/Writing-R-documentation-files.html#lists-and-tables ). Best regards, Mike On Thu, 20 Apr 2023 at 16:14, Wiel, M.A. van de

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

if I checkout the version on the git.bioconductor.org. I don't see any problem with the way you've formatted the maintainer field, so I think if you update both the email and package version number and then push the changes to the Bioc repository you should see that error go away. Best, Mike On Wed

Re: [R-pkg-devel] CRAN Vignette pdfs garbled in Firefox pdf viewer

Awesome, thanks so much! Mike On Fri, Feb 10, 2023 at 11:22 AM Shota Ochi wrote: > I reported the bug to bugzilla. > > https://bugzilla.mozilla.org/show_bug.cgi?id=1816128 > > The bug is already fixed. > We should use higher version of firefox or firefox nightly. > >

[R-pkg-devel] CRAN Vignette pdfs garbled in Firefox pdf viewer

h a local pdf viewer. The issue was documented here: https://github.com/mikeblazanin/gcplyr/issues/112 Anyone have any suggestions for what could be causing this? Thanks! Mike Blazanin [[alternative HTML version deleted]] __ R-package-devel@r-proj

[R-pkg-devel] Help with CRAN-only Windows-only package build error: System.Rd not found

want to take up any more of the CRAN volunteers' time Thanks! Mike Blazanin [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

, and hopefully the underlying issue won't be too tricky for the Bioc team to resolve. Cheers, Mike On Fri, 11 Nov 2022 at 06:17, Stevie Pederson wrote: > Hi, > > I've just instantiated a local container for RELEASE_3_16 & have this > problem: > > library(stringi) > Error:

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

ep 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's happening. Hopefully

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

tor versions in sync a bit easier. Cheers, Mike On Wed, 9 Nov 2022 at 04:43, Stevie Pederson wrote: > Hi, > > I also can't get my github actions bioc-check workflow running for devel, > so I checked the bioc-devel docker image & can't seem to install BiocCheck > on that co

Re: [Bioc-devel] Trouble with version bump

iewed", since you've already completed the review process. Best regards, Mike On Tue, 8 Nov 2022 at 05:35, Alex Wong via Bioc-devel < bioc-devel@r-project.org> wrote: > Hi there, > > I am having difficulty bumping a new version of SpliceWiz onto devel. Below > is the err

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

, and it should be really interesting to learn more about this. Please note the meeting details have changed; We're now on Zoom: https://embl-org.zoom.us/j/99712225827 passcode: bioc-devel Looking forward to seeing people there, Best wishes Mike

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

with the default arguments to useMart(), but if biomaRt finds it's taking > 10 seconds to get a response it will see if one of the mirrors is more responsive. That's why it might take a variable number of tries before reproducing the problem. Best, Mike On Thu, 4 Nov 2021 at 20:42, Hervé Pagès wr

Re: [Rd] Segfault in setMask in R 4.1

believe reconciles these two diverged sources, includes the GE v13 changes (see https://github.com/s-u/Cairo/) and fixes my segfual. I assume this will be pushed to CRAN at some point. Thank you very much Paul, Andre and Simon for you help! Mike On Tue, Sep 21, 2021, at 2:24 PM, Paul Murrell

Re: [Rd] Segfault in setMask in R 4.1

, but the only release since 1.5-12 according to the NEWS file). The 1.5-13 tarball at https://www.rforge.net/Cairo/files/ contains no mention of strings like "setMask", "releasePattern" or "setPattern", which seem like they should be in there if that version has implemented

Re: [Rd] Segfault in setMask in R 4.1

code is presumably part of the problem. I would like to confirm that by failing to reproduce the bug in "vanilla" R 4.1 with a Cairo device. If anyone has any tips for how to do that (on Linux) or any other comments I would be very grateful. If our code is the problem then I'm still confused wh

[Rd] Segfault in setMask in R 4.1

tput of any commands. If anyone has any suggestions then please let me know! Thanks! Mike Lee Williams __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Genomics Extension for SQLite seeking R/bioC co-maintainer

On Tue, Jun 1, 2021 at 5:12 AM Vincent Carey wrote: > Thanks Mike, we're having a look. I haven't found much comparative > benchmarking data by prowling around your site ... am I missing anything? > The colab notebook is helpful. > Specifically wrt the compression layer, there's a

[Bioc-devel] Genomics Extension for SQLite seeking R/bioC co-maintainer

me if interested, on this github discussion <https://github.com/mlin/GenomicSQLite/discussions/17>, by email d...@mlin.net, or this thread. Alternatively, any feedback/ideas about how to make the project useful are most welcome! Thanks, Mike Lin <https://www.mlin.net> [[alte

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

of package, and it's something I'm happy to consider for the future. Cheers, Mike On Mon, 10 May 2021 at 09:10, Neumann, Steffen wrote: > Hi, > > this is a follow-up to a rather old thread, but with > Mike Smith's (twitter: @grimbough) > > https://code.bioconductor.org/ >

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

developer introduce some changes you have to wait for the following day's report to see their impact. Best, Mike On Fri, 23 Apr 2021 at 13:31, Ilyess RACHEDI wrote: > Dear all, > > My package has just been accepted but an error occured during the nigthly > devel build > Here the r

Re: [R-pkg-devel] Using ggplot2 within another package

Hi Kevin, I recently developed a plot function in a package that used ggplot and ran into the same problem. I overcame the problem with a first line of (useless) code as myX <- myY <- NULL I found the solution inelegant but it worked. cheers! Mike > On Apr 22, 2021, at 4:28 PM

Re: [Bioc-devel] Suppressing messages from Rprofile

Thanks both for the suggestions. I ended up piping the output to tail -n1 I've no idea how portable that is, but presumably similar to trying a grep/sed approach. Cheers, Mike On Thu, 8 Apr 2021 at 15:48, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > You could also

[Bioc-devel] Suppressing messages from Rprofile

ism entirely, etc)? Alternatively, is there anything definitive in WRE or the like that suggests printing messages Rprofile is a bad idea that I can pass on to the users? Cheers, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

niversally, rather than take that route. Mike On Tue, 23 Mar 2021 at 12:11, Murphy, Alan E wrote: > Hi, > > Thank you very much Martin and Hervé for your suggestions. I have reverted > my zzz.R on load function to that advised by ExperimentHub and had used the > ID look up (

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

ne that's in release that doesn't appear in master. This doesn't mean anything has gone wrong, the Bioconductor versioning guidelines have been followed, GitHub just likes to let you know the two branches have both diverged from their common ancestor. Best, Mike On Mon, 22 Mar 2021 at 23:59, Marcel Ra

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

' Forum. Best wishes, Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

so I imagine you want to keep them. Mike On Tue, 9 Mar 2021 at 10:09, Murphy, Alan E wrote: > Hi both, > > Thank you for your suggestions. Yes, I am still having problems with the > size of my git history in the EWCE package. To clarify, I have already > tried the BFG cleaner

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

future topics you'd like to discuss in the Developers' Forum. Best wishes, Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

you'd like to discuss in the Developers' Forum. Best wishes, Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor package CNVRanger

() arguments are no longer in the same order. I've submitted a pull request to Gviz at https://github.com/ivanek/Gviz/pull/40 which allows Gviz to pass build/check. Hopefully that'll straighten things out for you if it gets accepted. Cheers, Mike On Fri, 1 Jan 2021 at 23:38, Geistlinger, Ludwig

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

suspect that the build system warnings will persist for a while longer as the issue is still there, but I don't think there's anything you can do as a package developer, so there's no need to worry about it for now. Hopefully a fix will make it's way into R-devel fairly soon. Mike On Wed, 30 Dec 2020

[Bioc-devel] Problem with download count tables

ing the BiocPkgTools::biocDownloadStats() function. The issue also seems to be affecting the count tables for the experiment data and workflow packages. Software seems ok. Cheers, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.or

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

ing ID: 114 067 881) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

. The latest commit message to https://github.com/cboettig/knitcitations is 'prep for release', so it looks likely that the author of knitcitations is addressing the CRAN issue. I would hang tight for a while longer and hope it gets smoothed out there. Mike On Thu, 26 Nov 2020 at 04:26, Eeles, Christopher

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

Cheers, Mike On Thu, 19 Nov 2020 at 15:14, Sudeep Sahadevan wrote: > Thank you... > Perhaps I can add some additional info here. I was comparing the > sessionInfo from my local build based on RELEASE 3_12 docker image (where > the images are rendered fine) against the sessionInfo from

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

in our recent Slack survey, and it's sure to be an interesting look into some of the fundamentals of how R works. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinf

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, Raine

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

and the performance gains the package might help us realise. Please let me know if you'd like anything else added to the agenda. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

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

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." -

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

and the original error. I'm afraid that doesn't offer much guidance, but perhaps this is something more specific to the setup on nebbiolo1 ? Mike On Wed, 14 Oct 2020 at 07:52, Pages, Herve wrote: > On 10/13/20 15:18, Selles Vidal, Lara wrote: > > Hi Hervé, > > > > Thanks

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

ot;, but does seem to work for now on Ubuntu 20.04 and hasn't thrown any problems for my tests on 16.04 and 18.04. Best, Mike On Wed, 30 Sep 2020 at 21:02, Selles Vidal, Lara < lara.selle...@imperial.ac.uk> wrote: > Dear BioC community, > > We were recently informed that a mult

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

g systems. Also the get_dcf_info error actually looks like it comes from the python code that runs the build system - so it's pretty hard for you to debug directly, and might behave differently from similarly named functions in R. I'd try changing out the quotes and then giving it another try. Best, Mike On F

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

and rapid searching of the entire codebase across all packages. Please let me know if you'd like anything else added to the agenda. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https

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

this. The review process is also a dialog between the package author and reviewer, so you have a chance to explain reasons why your code may be triggering BiocCheck messages, and if the explanation is reasonable (as this sounds) then it will probably be accepted by the reviewer. Best wishes, Mike On Thu, 23 Jul

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

on Bioconductor Slack (https://bioc-community.herokuapp.com/). Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

wrong for my system: > system2('java', '-version') java version "13.0.2" 2020-01-14 Java(TM) SE Runtime Environment (build 13.0.2+8) Java HotSpot(TM) 64-Bit Server VM (build 13.0.2+8, mixed mode, sharing) Perhaps there's an issue with whatever part of the code is detecting the version o

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: ..

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

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's a simple fix in

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

[Bioc-devel] Updates to BiocStyle

via a Github issue ( https://github.com/Bioconductor/BiocStyle/issues). Cheers, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Announcement: Update to Rhdf5lib

be related to this. Best regards, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

ty.herokuapp.com/). Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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.

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

cipant 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 > March at 09:00 PST/ 12:00 EST / 18:00 CET &g

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

Slack ( https://bioc-community.herokuapp.com/). Feel free to suggest anything of interest, don't feel like you need to match with the sort of direction we've gone previously. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r

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

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 Develope

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

to raise please let me know or post in #developers-forum on Bioconductor Slack ( https://bioc-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

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

Just as a reminder, the next call is taking place today at 09:00 PST/ 12:00 EST / 18:00 CET https://bluejeans.com/114067881 (Meeting ID: 114 067 881) One topic for discussion is the new Windows toolchain being trialled on CRAN. Any other topics are welcome. See you later, Mike On Mon, 20 Jan

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

to raise please let me know or post in #developers-forum on Bioconductor Slack ( https://bioc-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

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

t.org explaining the package has been cleaned for large data files and needs to be reset.". Seems like you've done the emailing part, so I'm sure someone will be in touch soon. Mike On Thu, 19 Dec 2019 at 05:20, Saskia Freytag < saskia.frey...@perkins.uwa.edu.au> wrote: > Hi, &

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

to raise please let me know or post in #developers-forum on Bioconductor Slack ( https://bioc-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Bioc-devel] Long Tests builds

process currently is. Cheers, Mike On Thu, 5 Dec 2019 at 19:11, Pages, Herve wrote: > Hello developers, > > These builds were announced on this list in Nov. 2017 (see > https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012326.html). > > The purpose of the "Long

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

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

amp; 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, > > The next Bioconductor Developers' Forum is scheduled for Thurs

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

-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

Dear all, Just as a reminder, the next call is scheduled for today (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) Best wishes, Mike On Thu, 10 Oct 2019 at 16

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

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

anch, cram as many bug fixes as possible in the last week, or go on holiday until it's all over? More details and discussion can be found in the #developers-forum channel of the Bioconductor Slack (https://bioc-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version del

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

on object serilaisation which should cover exactly this type of issue. Best, Mike On Sat, 14 Sep 2019 at 23:26, Tiago Lubiana Alves < tiago.lubiana.al...@usp.br> wrote: > Hello, > > I am having a problem with a package submission build. > > This is the package issue:

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

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

in the #developers-forum channel of the Bioconductor Slack (https://bioc-community.herokuapp.com/) Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Biocondutor Developers Forum

date 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 Biocond

Re: [Bioc-devel] Resetting to previous commits

never passed all the checks, and so is absent from the archive at https://bioconductor.org/packages/3.9/bioc/src/contrib/Archive/biomaRt/ In theory someone could get hold of it via git, anyone doing so it probably experienced enough to look after themselves. Best, Mike On Wed, 14 Aug 2019 at 18

[Bioc-devel] Biocondutor Developers Forum

reach out to me. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] HiCBricks build error

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, and so files written

Re: [Bioc-devel] HiCBricks build error

as a package manager, but it seems I've introduced a regression. I'll look into why this is the case, I'm a bit confused as to why rhdf5 is not failing in a similar way. Mike On Mon, 29 Jul 2019 at 17:53, Koustav Pal wrote: > Hi, > > My package HiCBricks is producing build errors o

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