[Bioc-devel] outdated data package in development branch

Hi, I updated flowWorkspaceData package and bump the version 12 days (devel branch) ago but it has not been re-built so far. Isn't supposed to be built twice weekly? Thanks, Mike ___ Bioc-devel@r-project.org mailing list https://stat.et

Re: [Bioc-devel] outdated data package in development branch

Valerie At the time when I posted the question, it was still 2.9.1 and definitely wasn't built for more than two weeks. Anyway, it is now updated. Thanks, Mike On 06/17/2016 09:32 AM, Obenchain, Valerie wrote: Hi Mike, We went down to just a single build per week (Saturday I think

[Bioc-devel] BioC check error for flowClust on windows

Hi, Here is the CHECK report for flowClust on moscato1. There is not pacific error message on that page and I can't reproduce it on my local windows. Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

It does use some c++11 code and I think it is reasonable to expect relative newer gcc (>=4.8.4) to be installed. On 10/10/2016 05:42 PM, Kasper Daniel Hansen wrote: Latest version (1.39.11). My guess is that this is a case of the author using C++ stuff which is not support on 4.4.7. ** lib

[Bioc-devel] a S4 dispatching question

ry these S4 methods before any S3 gets its chance. Is there better way other than these two? 1. change 'GatingSet' to S3 class 2. use a different generic function that is not associated with any S4 methods (e.g. subset) Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] a S4 dispatching question

t; x="container", i="ANY" x="eSet", i="ANY" x="filterResultList", i="ANY" x="filterSet", i="character" x="flowFrame", i="ANY" ... > y[holycrapnothere] Error: object 'holycrapnothere'

Re: [Bioc-devel] Fwd: read fcs file from CyTOF with

'flowCore' does support CyTOF fcs as long as it follows the fcs standard.( "FCS2.0", "FCS3.0" and "FCS3.1") Based on your check by 'isFCSfile', Your fcs file is probably not any one of these. >> *From: *Hurlimann Niklaus > > >> *Subject: **[Bioc-devel] read fcs

[Bioc-devel] check warning of QUALIFIER package

Secondly, adding 'importFrom(Biobase,"sampleNames<-")' to NAMESPACE file does not resolve the issue. Any suggestion? Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages

-devel| from |bioc| (hopefully coming soon) Best, Mike ​ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages

I don't think it has been addressed yet in the later commits of R-devel. And that piece of code in flowCore package was written long time ago and there is nothing wrong with it as far as I can see. Mike On 01/20/2015 05:06 PM, Dan Tenenbaum wrote: I'm not sure if you were implying

Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages

fixed.) so that users won’t be misusing it. ​ | Mike | On 01/23/2015 10:55 AM, Martin Morgan wrote: > On 01/23/2015 10:52 AM, Michael Lawrence wrote: >> First let me apologize for my failure to read emails. There was a >> long-standing bug in the methods package where argu

Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages

and that’s why I should explicitly select the argument for callNextMethod? Thanks. Mike On 01/23/2015 11:30 AM, Michael Lawrence wrote: > The bug has existed forever. The commit log may be confusing. The > actual bug (or at least a very undesirable behavior) was in > match.ca

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

.sh fatal: refs/remotes/bioc/release-3.0: not a valid SHA1 Mike ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

release branch name, e.g. 'release-3.0^[[m', which messed up the 'svn-remote' subsection within '.git/config' file. After I changed this variable value to 'auto', the script runs successfully now. Thanks a lot! On 06/19/2015 12:25 PM, Jim Hester

Re: [Bioc-devel] Merging git mirror and previous git repo ?

Here is what I did to resolve the conflicts when merging from master to devel. git clonehttps://github.com/sneumann/mtbls2/ update_remotes.sh git checkout master making some changes and commit to master... git checkout devel git rebase git log #to get the git-s

Re: [Bioc-devel] C library or C package API for regular expressions

'flowCore:::LdFlags()' to generate the linking path automatically. See the example in 'flowWorkspace/src/Makevars.in' Once Bioconductor upgrades gcc to 4.9, all of these will be unnecessary . see https://github.com/RGLab/flowWorkspace/issues/160. Mike On 01/25/2016 04:08 AM,

Re: [Bioc-devel] Bioconductor git-svn bridge is available

I have the bridge set up between our github repository and bioconductor devel branch. Is it possible to add the second bridge to bioc release from the same git repo? or I would have to create a separate github repository for that purpose? Mike

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

Kevin's fix is already pushed to the latest bioc release and devel. Thanks, Mike On 04/10/2014 11:44 PM, bioc-devel-requ...@r-project.org wrote: > Subject: > Re: [Bioc-devel] Dependency on windowing systems in the flowCore package > From: > Kieran O'Neill > Date: >

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

curvFilter' branch of https://github.com/RGLab/flowStats) library(flowStats) dat <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) c1f <- curv1Filter(filterId="myCurv1Filter", x=list("FSC-H"), bwFac=2) ## Filteri

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

#x27;flowStats' instead(leaving 'norm2Filter' untouched). I have checked the 16 packages in the 'reverse depends list', actually only one package ('plateCore') needs minor updates in its NAMESPACE file. Thus the impact to the user package should be minimum. Mike

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

ks is required by the code copied from feature package, which has been moved to flowStats. And 'norm2Filter' is not using it. Sio with the removal of curv*Filters, flowCore should not depend on ks anymore. Mike On 04/22/2014 12:14 PM, Kieran O'Neill wrote: > Thanks all

[Bioc-devel] git svn bridge is broken

I just 'delete-and-re-create' the git svn bridge for 'flowViz', but it is still not working (I've tried to 'recreate' the bridge many times) Does anyone else experience the same lately since the bioc 2.14 release? Mike _

Re: [Bioc-devel] exonsBy dropping genes from TxDb

lts is consistent for even with the larger number of attributes > identical(df3[,1], df4[,1]) [1] TRUE And some of these transcripts are clearly not present in the first query: > length(which( !unique(df3[,"ensembl_transcript_id"]) %in% df1[, "ensembl_transcript_id"] ))

Re: [Bioc-devel] Data package timeouts

Hi Mike, I was experiencing similar problems with the BeadArrayUseCases vignette, where using getGEO() from GEOquery was getting stuck in a (seemingly) infinite loop processing a GSE series matrix file. It looks like both of your examples try to do this too, so I suspect it's a similar issu

Re: [Bioc-devel] Data package timeouts

Thanks for the speedy response Sean. I'll switch back to the version using a file name shortly. Cheers, Mike On 30 November 2017 at 11:20, Sean Davis wrote: > Thanks for the report, Mike. > > The problem was (specifically) in parsing a GSEMatrix file using a > filename. Thi

Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

Rhdf5lib is in the release branch too. I'm happy to help try and get mzR working with it. On 2 January 2018 at 21:31, Martin Morgan wrote: > On 01/02/2018 03:16 PM, Neumann, Steffen wrote: > >> Dear BioC team, >> >> a happy new year to you as well ;-) >> >> for a while we have a build error for

[Bioc-devel] Changes to rhdf5

apply. The changes are now in the Bioc devel branch (rhdf5 version 2.23.3), and should appear fairly soon. Please let me know if I can provide any more info, or things start behaving unexpectedly. I've tried to test this thoroughly, but there's always cases that I will have missed. C

Re: [Bioc-devel] Changes to rhdf5

and close files for the user, while with the H5 functions it's up to you to tidy up after yourself - just like if you're using the C library. I know h5save doesn't obey this paradigm at the moment, but if you've got any other examples I'm happy to take a look. Mike On 5

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

ich case there are some nice instructions at https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Cheers, Mike On 25 January 2018 at 03:12, Robert M. Flight wrote: > Paul, > > My understanding was that the Bioconductor github repos were going to die, > and it was up to the main

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

version it was even longer than that. I haven't been able to recreate the problem at my end, I think the time taken is related as much to the internet connection as to the query, but I'll take a look at the failing example to see if I can shed any more light on it. Mike On 2 February

Re: [Bioc-devel] rhdf5 NA's in int32

Dear Stepan, Thanks for your questions. I'll take a look at them over the next few days and get back to you with some answers. I've also opened a new issue on Github (https://github.com/grimbough/rhdf5/issues/10) with your question, so I'll post any replies there too. Than

[Bioc-devel] Support site RSS feeds

ism to list all posts identified using a tag? Thanks, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Release of R package

timetable for the next release cycle is detailed at https://www.bioconductor.org/developers/release-schedule/ and from 1st May MAGeCKFlute will be part of the release branch too. Mike On 3 April 2018 at 06:49, Watson Zhang wrote: > Hi, > > I submitted R package MAGeCKFlute last year, which

Re: [Bioc-devel] Windows

Peaks}} (I haven't actually tested this though). Mike On 16 April 2018 at 09:06, Rainer Johannes wrote: > Dear all, > > we're experiencing WARNINGS in xcms on Tokay2 that are all related to > links in Rd files to functions and methods in other packages. > Example:

Re: [Bioc-devel] Windows

Martin mentioned that he changed the wording in https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e , so more recently than your version of R-devel. Mike On 16 April 2018 at 11:57, Rainer Johannes wrote: > Thanks Mike, > > I somehow missed the discu

Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

You had the right idea with your commit https://github.com/zhushijia/GIGSEA/commit/431af209590f905452b5f10b0ad3a282ab2534e3 but the wrong version of R. You need to put Depends: R (>= 3.5) in your DESCRIPTION file and it should be good. Mike On 17 April 2018 at 10:49, Shijia Zhu wrote: &

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 Apri

Re: [Bioc-devel] biomaRt uswest mirror ERROR

t the case in the devel version, as I've disabled the geo-redirect by default after talking to the people at Ensembl, and the host argument is always obeyed. Cheers, Mike On 24 April 2018 at 17:30, Shepherd, Lori wrote: > Hello, > > > OrganismDbi is failing. > > http://b

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

s://bioconductor.org/developers/how-to/git/push-to-github-bioc/ which describes how to make sure you commit changes both to your Github repository and the version at Bioconductor. Regards, Mike On 11 May 2018 at 05:48, Pijush Das wrote: > Dear Martin Morgan, > > > I have successfully add

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

hat might be the difference between path1 and path2 below. Thank, Mike -- ## setup some HDF5 components required later flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC")) fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CRE

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

the encoding, but the combination of HDF5 & Windows fails when given UTF-8 paths. I've updated rhdf5 to try and ensure paths are encoded in Latin-1 which Windows is fine with, but it'll still go awry if you use characters outside that set. I'm still searching for a more comprehen

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

s at https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Step 4 details incorporating changes from one branch to another, and then you need to manually make sure the DESCRIPTION file for committing to the RELEASE_3_7 branch contains a 1.6.x version number. Mike On Wed, 11 Jul 201

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

uctor.org/checkResults/release/bioc-LATEST/Onassis/ For you this was Snapshot Date: 2018-07-10 16:46:08 -0400 (Tue, 10 Jul 2018) which is before your commit with the version bump. It would expect the change to propagate through sometime today. Mike On Thu, 12 Jul 2018 at 10:52, Eugenia Galeota

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

instructions at https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ might help with keeping them in sync. Mike On Thu, 12 Jul 2018 at 11:53, Jason Serviss wrote: > Mike, > > It would appear that the version on Eugenia’s RELEASE_3_7 branch on her > git repo is 1

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

oo!) but I guess the logic for allowing commits has a loophole somewhere. I'll raise a query in the Slack channel and hopefully someone with power over the git repository will get back to you soon. Mike On Mon, 23 Jul 2018 at 21:20, White, Shana (vandersm) wrote: > Hi Mike, > > >

[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

Re: [Bioc-devel] Git file size limits

Thanks Martin. I'll wait til Nitesh is back. Hopefully I've successfully reverted my changes to rhdf5 that depended on this! Cheers, Mike On Wed, 22 Aug 2018 at 19:20, Martin Morgan wrote: > exceptions can be made; this will take just a little bit of time, as our > expert (N

[Bioc-devel] Major update to rhdf5 and Rhdf5lib

1.10 provides a number of new features that you can read about at https://support.hdfgroup.org/HDF5/docNewFeatures/ If you need access to one of these and it's not obviously available via rhdf5 then again please contact me & I'll prioritise things accordingly. Thanks, Mike

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

However, perhaps a more robust solution is to enforce the use of "_" rather than "-" in column names, that way you don't have to worry about using back-ticks to quote the non-syntactic names. Best regards, Mike On Mon, 5 Nov 2018 at 14:21, Ruqian Lyu wrote: > Hi Bioco

Re: [Bioc-devel] Bioconductor git credentials

Lori, Would you be able to help with this? Thanks! Mike From: Wagner, Jake Sent: Wednesday, February 6, 2019 3:20 PM To: bioc-devel@r-project.org Cc: Jiang, Mike Subject: Bioconductor git credentials Hello, My name is Jacob Wagner and I will be helping Mike

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

have this mentioned in the check results e.g http://bioconductor.org/checkResults/devel/bioc-LATEST/beadarray/malbec2-checksrc.html . Mike On Tue, 12 Feb 2019 at 08:35, web working wrote: > Hi, > > I am developing a Bioconductor package and can not get rid of some > warning messages. Duri

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] HiCBricks build error

conda 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 pro

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

[Bioc-devel] Biocondutor Developers Forum

ioritise please 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] 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

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

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

nd 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] 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

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

will have a discussion 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. > > T

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

ew branch, 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 v

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

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

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

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] 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, > &

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] 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,

Re: [Bioc-devel] Long Tests builds

the build 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 &

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

;d like 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.

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

roject.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:

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

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

;d like 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.

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 20th February

;d like 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.

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 19th March

ers-forum on Bioconductor 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]] _

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 >

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

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

-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/listinfo/bioc-devel

[Bioc-devel] Announcement: Update to Rhdf5lib

t may 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] ShortReadQ class and memory usage

ample: https://gist.github.com/grimbough/ca9e668a5772dc00cafb Thanks, Mike -- Mike Smith Research Associate Statistics & Computational Biology Laboratory Cambridge University [[alternative HTML version deleted]] ___ Bioc-devel@r-project.or

[Bioc-devel] Updates to BiocStyle

he mailing list or 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

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

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] 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 Pic

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 Valu

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

ted This seems 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 par

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

pers-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/listinfo/bioc-devel

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

bout 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

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

repository 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.or

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

different across operating 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

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

to "DEFAULT", 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 recentl

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

d 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, > > >

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] 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

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

d 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.

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,

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

opic 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/mailm

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

Style/issues/83 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 s

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

e problem. 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

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