Re: [Bioc-devel] Error in Vignette of package

r/tokay1-buildsrc.html > > > Thanks! > Cheers, > Simina > > > > On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve wrote: > >> Great news Andrzej! We'll keep a close eye on the build reports in the >> next few days. Fingers crossed. Thanks! >> >> H. >&g

Re: [Bioc-devel] Error in Vignette of package

Andrzej Oleś wrote: > Dear Package Developers, > > BiocStyle will be patched within the next couple of days to address the > observed errors. Until then please refrain from making any changes to your > package, the issue should resolve itself once BiocStyle is updated. > &

Re: [Bioc-devel] Windows only vignette error - any ideas?

To me this issue doesn't seem to be directly linked to BiocStyle as the affected package does not depend on it. Might be still a problem with rmarkdown though. Cheers, Andrzej On Wed, Dec 4, 2019 at 10:12 PM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > We are hoping it is related to

Re: [Bioc-devel] Error in Vignette of package

Dear Package Developers, BiocStyle will be patched within the next couple of days to address the observed errors. Until then please refrain from making any changes to your package, the issue should resolve itself once BiocStyle is updated. Cheers, Andrzej On Mon, Dec 2, 2019 at 11:20 AM Andrzej

Re: [Bioc-devel] Error in Vignette of package

Hi, the error seems to be related to some recent changes in the upstream package rmarkdown v1.18. I will give you an update once I know more details. Cheers, Andrzej On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay < b2tremb...@uwaterloo.ca> wrote: > Not using

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

Hi Vince, I briefly communicated with Martin regarding this issue a few days ago. The ImageMagick convert tool called by BiocStyle through a knitr figure cropping hook can certainly be improved, as pointed out by Yihui in the in the GitHub issue linked by Christian. This is something I will look

Re: [Bioc-devel] warnings with BiocStyle pdf compilation

Hi Vince, thank you for your feedback. If the vignette compiles fine I wouldn't worry too much about these warnings. The first one "LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor', but the package

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

Dear Leo, thanks for you inquiry. Re points 2-4: there is no need to use the token file .html_output anymore. This was an intermediate solution meant for the transition period to new output format. Now all workflow vignettes for the the website are build using this new format, regardless the

Re: [Bioc-devel] release build of ChemmineR failing

Dear Kevin, thank you for reporting the problem. It is not clear to me why do you need a Makefile to build your vignette in first place, could you maybe explain the motivation behind it? Cheers, Andrzej On Wed, Feb 7, 2018 at 5:37 PM, Kevin Horan wrote: > The

Re: [Bioc-devel] workflow page reorganization

Hi Aaron, thank you for taking the lead. I've merged your suggested categories with my preliminary arrangement (which just went online). I've also included an index at the beginning of the page. Any refinements are of course welcome, e.g. via PR to

Re: [Bioc-devel] workflow page reorganization

Hi Laurent, thanks, we might consider this in the future. To get us going, for the moment we will probably just rearrange the website manually. On the technical note: even though workflows are now fully fledged packages, two documents linked from https://bioconductor.org/help/workflows are just

Re: [Bioc-devel] workflow page reorganization

Hi, Motivated by discussions with Aaron I've already started to group the workflows on the page (but this change didn't propagate to the website yet). Some common topics I was able to identify so far include: - Beginner's Worklows authored originally by the core team giving a quite broad

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Thanks for you feedback Aaron! On Tue, Dec 12, 2017 at 9:49 PM, Aaron Lun wrote: > Thanks Andrzej. > > > Thank you. I've edited the workflow index page by introducing a separate > > "Single-cell Workflows" section, and by substituting the previous link to > > your workflow by

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Hi Aaron, Thank you. I've edited the workflow index page by introducing a separate "Single-cell Workflows" section, and by substituting the previous link to your workflow by links to the individual parts. As discussed during EuroBioc, I'm happy to restructure the index page by grouping workflows

Re: [Bioc-devel] Pandoc on Build Computers

Dear Dario, not sure how the "institute" header field is supposed to work and whether this is an actual builder configuration issue. I have tested it with pandoc 1.17.2 and it doesn't produce any output, neither for `rmarkdown::html_document` nor for `rmarkdown::pdf_document`. See

Re: [Bioc-devel] Superscript in BiocStyle 2.5.39 html document seems to be not working

Hi Stefan, thanks for reporting this. Should be fixed in BiocStyle 2.5.42. Best, Andrzej On Mon, Oct 23, 2017 at 7:55 AM, Stefan Mutter wrote: > Hi, > > > I am currently writing a vignette for a package that we want to submit to > Bioconductor. I am using BiocStyle

Re: [Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

Dear Stefan, Thanks for your feedback. I didn't find the R Markdown sample document you mentioned, maybe you forgot to attach it. The following minimal example illustrates how to include figures from external files such that they are numbered and contain captions. Best, Andrzej --- output:

Re: [Bioc-devel] R: R: R: Errors updating DaMiRseq package

Thanks Hervé for troubleshooting! This should be now fixed in BiocStyle 2.5.39, for details see the discussion at https://github.com/Bioconductor/BiocStyle/issues/36. Cheers, Andrzej On Wed, Sep 27, 2017 at 8:42 PM, Hervé Pagès wrote: > It's better to discuss this on

Re: [Bioc-devel] BiocStyle not acknowledging fig.wide=TRUE in knitr

Hi Aaron, thanks fo reporting this! I've fixed it in BiocStyle 2.5.38. Best, Andrzej On Fri, Sep 15, 2017 at 9:23 AM, Aaron Lun wrote: > Dear list, > > > I'm playing around with the BiocStyle aesthetics for my csaw user's guide, > and it looks pretty good in general.

Re: [Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

Hi Mike, thanks for reporting this. Strange, not sure what the problem was because now I was able to rebuild the workflow without actually reinstalling or reconfiguring anything on the builder. Maybe this was a transient issue related to the fact that I updated the LaTeX distro on the builder

Re: [Bioc-devel] BiocStyle2: issue with wide figure command

Hi Ludwig, thank you! This sounds like an issue with your LaTeX distribution, in particular the package 'marginfix'. Please make sure that all the packages listed in the BiocStyle vignette under Appendix B "Attached LATEX packages" are installed, and possibly the up-to-date. Best, Andrzej On

[Bioc-devel] BiocStyle transition aftermath

s contain some LaTeX customizations incompatible with the current version of BiocStyle. funtooNorm Linnorm NanoStringQCPro Thank you for your understanding and cooperation. Kind regards, Andrzej Oleś [1] http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf

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

strings_2.44.2 > GenomicAlignments_1.12.2 bitops_1.0-6 > [9] grid_3.4.1 GenomeInfoDb_1.12.2 > stats4_3.4.1 zlibbioc_1.22.0 > [13] XVector_0.16.0 S4Vectors_0.14.3 > Matrix_1.2-11 BiocParallel_1.10.1 > [17] tools_3.4.1

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

ext, ...) : End of file reading 4096 bytes (got 0) I didn't look into what loadCoverage does internally, but maybe the error has something to do with the fact that the size of mean_SRP045638.bw is 7GB, while the builder vagrant box runs only on 2GB(!) of RAM. Best, Andrzej On Thu, Aug 31, 2017 at

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

Hi Leo, first of all, many thanks for your efforts in troubleshooting workflow build issues and the detailed description of your findings. Also, congratulations on the successful publication of your new workflow on the Bioconductor website! We are now beta testing a new workflow build engine

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Hi Martin, Nitesh, thanks for recreating the EBImage repo! I've noticed that even though the operation helped to fix one commit where the user was previously unknown: commit b67438e41b9b7dc62db8c403ee8afd673bd5c0a0 Author: unknown Date: Fri Apr 21 13:47:14

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Hi Martin, I've just noticed that EBImage, which is on the list of packages not to be regenerated, is actually affected too (according to the output below). Therefore, I would like to ask to have it regenerated for the sake of clean commit history. Thanks, Andrzej [oles@localhost EBImage]$ git

Re: [Bioc-devel] Updates to BiocStyle formatting

sue](https://github.com/Bioconductor/BiocStyle/issues). As a temporary solution you can still use one of the deprecated format functions (`latex_old`, `pdf_document_old` or `html_document_old`), but please be warned that the "old" functions will be made defunct after the release. Best regards, An

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

Awesome, thank you Michael! On Mon, Aug 7, 2017 at 7:27 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > I ported that over. > > On Tue, Aug 1, 2017 at 5:50 AM, Andrzej Oleś <andrzej.o...@gmail.com> > wrote: > >> Thank you Michael for updating the 3.4 b

Re: [Bioc-devel] Updates to BiocStyle formatting

the things html_document2 has to > offer. > > Best, > Leo > > On Mon, Aug 7, 2017 at 8:05 AM, Andrzej Oleś <andrzej.o...@gmail.com> > wrote: > > Dear Bioconductor Developers, > > > > We would like that in the next release most of the vignettes which use

[Bioc-devel] Updates to BiocStyle formatting

n still use the previous format function renamed to `*_old` in order to build your package. Kind regards, Andrzej Oleś [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] improving navigation within workflows

hat's exactly what I wanted, thanks. >> >> -Aaron >> >> On 04/08/17 14:19, Andrzej Oleś wrote: >> > Hi Aaron, >> > >> > I'm happy to inform that I've implemented your suggestion to add >> > navigation links at workflow pages. Feel free

Re: [Bioc-devel] improving navigation within workflows

compromise, e.g., if they can be > placed in the right margin. A simple set of three links > () beside each section/subsection heading > would probably sufficient for effective navigation, without using up too > much space. > > Cheers, > > Aaron > > On 17/07/17 00:3

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

gt; I pushed the patch to the 3.4 branch. Feel free to test. > > Michael > > On Wed, Jul 26, 2017 at 4:02 AM, Andrzej Oleś <andrzej.o...@gmail.com> > wrote: > > Hi Michael, > > > > it seems that your patch to S4 generics dispatching on `...` is still > >

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

that the broken `...` dispatch is fixed before R-3.5.0? Cheers, Andrzej On Tue, Apr 25, 2017 at 4:15 PM, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > You're right, I must have mixed up my R versions when running the example, > as the problem seems to be resolved in R-devel. > > S

Re: [Bioc-devel] improving navigation within workflows

Hi Aaron, thanks for your feedback. We are currently looking into ways of improving the building of workflows for the website in order to enable cross references, html widgets, and similar. So far these were not supported because of some technical constraints of the current implementation which

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

ed to fix it, and that example seems to work for me. It's > also a (passing) regression test in R. Are you sure you're using a new > enough R-devel? > > > On Tue, Apr 25, 2017 at 2:34 AM, Andrzej Oleś <andrzej.o...@gmail.com> > wrote: > > Hi Michael, > > > >

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

rks as the non-generic version f() ## [1] missing 'a' setGeneric("f", signature = "...") # unexpectedly fails to find 'b' f() ## Error in print(a) : object 'b' not found Any chances of fixing this? Cheers, Andrzej On Fri, Apr 21, 2017 at 11:40 AM, And

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

ich...@gene.com> wrote: > Thanks for pointing out these issues. I have a fix that I will commit soon. > > Btw, I would never have seen the post on Stack Overflow. It's best to > report bugs on the bugzilla. > > Michael > > On Thu, Apr 20, 2017 at 8:30 AM, Andrzej Oleś &l

[Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

Hi all, I recently encountered some unexpected behavior with S4 generics dispatching on `...`, which I described in http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and arguments of such

Re: [Bioc-devel] Using LaTeX packages in vignettes

Dear Roel, to override the default \bibliographystyle{unsrt} use `BiocStyle::latex(use.unsrturl=FALSE)` as documented in ?BiocStyle::latex Best, Andrzej On Mon, Apr 3, 2017 at 2:29 PM, Janssen-10, R.R.E. < r.r.e.janssen...@umcutrecht.nl> wrote: > Obenchain, Valerie writes: > > Hi, > > > > On

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

On Wed, Mar 22, 2017 at 6:12 PM, Hervé Pagès wrote: > > setClass("A", representation(stuff="numeric")) > as.vector.A <- function (x, mode="any") x@stuff > a <- new("A", stuff=c(3.5, 0.1)) > x <- numeric(10) > x[3:4] <- a > > then the code is now valid and we still

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

On Wed, Mar 22, 2017 at 10:29 AM, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > Just for the record, on R-3.3.2 Herve's code fails with the following > error: > > Error in x[TRUE] <- new("A") : > incompatible types (from S4 to logical) in subassignment ty

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

Just for the record, on R-3.3.2 Herve's code fails with the following error: Error in x[TRUE] <- new("A") : incompatible types (from S4 to logical) in subassignment type fix Cheers, Andrzej On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On

Re: [Bioc-devel] Dependency on devtools in biocLite()

Awesome, many thanks Martin for the update! Cheers, Andrzej On Thu, Jan 19, 2017 at 8:08 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/17/2017 07:15 AM, Andrzej Oleś wrote: > >> Thanks Martin! >> >> I see your point - then I suggest that at

[Bioc-devel] Dependency on devtools in biocLite()

Dear all, it's great that for some time now `biocLite()` also resolves package dependencies for GitHub hosted packages. However, as this functionality depends on devtools, an attempt to install a GitHub package when devtools is not installed results in an error > library(BiocInstaller) >

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

Dear Stian, according to https://github.com/yihui/knitr/releases/tag/v1.14 the dependency on webshot, which apparently is used to take website screenshots, is optional and knitr should use fallback mode if webshot is not available. Webshot has a list of system dependencies, not sure how hard to

Re: [Bioc-devel] BiocStyle issue

.2.2.1 Cheers, Andrzej On Wed, Nov 23, 2016 at 2:27 PM, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > Dear all, > > the compatibility issue with rmarkdown 1.2 have been resolved in > https://github.com/Bioconductor-mirror/BiocStyle/commit/307ad19 > > Guangchuang, th

Re: [Bioc-devel] BiocStyle issue

Dear all, the compatibility issue with rmarkdown 1.2 have been resolved in https://github.com/Bioconductor-mirror/BiocStyle/commit/307ad19 Guangchuang, thank you for the heads up on the problem. Even though I was aware of the incompatibility with rmarkdown release candidate, I couldn't address

Re: [Bioc-devel] odd svn event

Hi Vince, probably because of spaces in the file name, see e.g. https://bugs.launchpad.net/ubuntu/+source/apache2/+bug/1284641 I had once a similar problem with BioC svn, solved it by deleting the affected directory locally and updating. HTH, Andrzej On Sun, Oct 23, 2016 at 11:27 PM, Vincent

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

Dear all, linux builders have both IPython 3+ and Jupyter installed, see https://github.com/Bioconductor/BBS-provision-cookbook/blob/master/recipes/default.rb#L256-L264 For consistency, maybe it would make sense to have them both on Windows too. Cheers, Andrzej On Tue, Oct 4, 2016 at 6:23 PM,

Re: [Bioc-devel] Package pages: Link to NEWS gone?

Hi Henrik, thanks for spotting this and for your notification! Indeed, there seem to be some problem with building package landing pages, I will look into this. Cheers, Andrzej On Thu, Sep 22, 2016 at 1:29 AM, Henrik Bengtsson < henrik.bengts...@gmail.com> wrote: > I've noticed this for a

Re: [Bioc-devel] no build reports (nor builds) for Windows in BioC 3.4

of no builds for at least > a weak). > > > > Best, > > > > R. > > On Mon, 04-07-2016, at 13:02, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > > Hi Ramon, > > > > why do you think there have been no build in the past week? The header on > &g

Re: [Bioc-devel] no build reports (nor builds) for Windows in BioC 3.4

Hi Ramon, why do you think there have been no build in the past week? The header on the page you provided says: *This page was generated on 2016-07-03 15:29:33 -0700 (Sun, 03 Jul 2016).* >From what I see the builds are up to date and reflect recent changes to the svn. Maybe some browser caching

Re: [Bioc-devel] vignette metadata dissapeared in Sweave/PDF vignettes

Hi Robert, thank you for reporting this! I've fixed it in https://github.com/aoles/biocViews/commit/a5f3cd0 (Dan Tenenbaum CC-ed). Cheers, Andrzej On Fri, May 6, 2016 at 9:46 AM, Robert Castelo wrote: > hi, > > I have noticed that in the recent release of BioC the

Re: [Bioc-devel] build reports are not updated

Dear Ludwig, according to http://bioconductor.org/developers/release-schedule/ release (BioC 3.2) builds were to stop on April 22. That's probably why they are not updated anymore. Cheers, Andrzej On Wed, Apr 27, 2016 at 11:08 AM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote:

Re: [Bioc-devel] Package reference manuals in html

the BioC community could jump in and help them to resolve the bottlenecks and keep the website up to date. Cheers, Andrzej On Tue, Mar 8, 2016 at 4:36 PM, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > Hi Martin, > > thank you for your suggestions - I would be happy to contribute to thi

Re: [Bioc-devel] Package reference manuals in html

Hi, this is just to clarify the relation between the two github repos https://github.com/Bioconductor-mirror/BiocStyle and https://github.com/Bioconductor/BiocStyle mentioned by Martin: actually, these two are perfectly in sync right now. The "This branch is 3 commits ahead, 3 commits behind

Re: [Bioc-devel] BiocStyle markdown, pdf and html

Hi Kasper, 1. It actually does, see BiocStyle::pdf_document. 2. I think you might be right that R doesn't support that yet, but maybe this could be circumvented through a Makefile. Cheers, Andrzej On Fri, Feb 26, 2016 at 5:33 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > 1.

[Bioc-devel] Deprecation of cellHTS

Hi all, the package 'cellHTS' will be deprecated in the upcoming Bioconductor 3.3 release, with limited maintenance and support. Users of 'cellHTS' are encouraged to switch to 'cellHTS2' which offers better functionality for working with multiple screens and with multi-channel screens. Kind

Re: [Bioc-devel] Idea for improved visibility of Bioconductor packages

block > below > >> the package description, or annotating it with some metadata to exclude > it > >> from the linkedin summary (I don't know what that would be). > >> > >> On Thu, Oct 29, 2015 at 9:50 AM, Kasper Daniel Hansen < > >> kasperdanielhan

Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

Hi Leonardo, thank you for reporting your issue with BiocStyle. I haven't experienced it before. The error you're getting indicates that BiocStyle might not be loaded before processing the code from the YAML header. This is normally handled by the BiocStyle::html_document() function which loads

Re: [Bioc-devel] Idea for improved visibility of Bioconductor packages

Hi Thomas, thank you for sharing your idea! One possibility would be to include a package icon/logo next to the package name if the package provides one. This file could be saved as inst/logo.png or vignettes/logo.png, e.g. see https://github.com/aoles/EBImage/blob/master/vignettes/logo.png

Re: [Bioc-devel] Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

Hi Leonardo, thank you for considering using BiocStyle for your vignettes! Please read below. On Thu, Oct 29, 2015 at 10:17 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "lcollado" > > To: "bioc-devel"

Re: [Bioc-devel] Bioconductor Workflows: TOC and displaying document details

is a pandoc > argument that can be passed? > > I guess part of the problem is that until the document is processed into > html, there are no html headers wth ID attributes that can be linked to. > > Perhaps we should just go back to the manual TOCs. > Dan > > > >

[Bioc-devel] Bioconductor Workflows: TOC and displaying document details

Hi everyone, while browsing through http://www.bioconductor.org/help/workflows/ I've noticed some inconsistency in using TOC in workflow vignettes. As the TOC is currently not automatically generated, some authors create it manually, while others do not have it at all. I suggest to address this

Re: [Bioc-devel] Shouldn't we distinguish between package-specific and dependency errors?

riginal Message ----- > > From: "Andrzej Oleś" <andrzej.o...@gmail.com> > > To: "Wolfgang Huber" <whu...@embl.de> > > Cc: bioc-devel@r-project.org > > Sent: Thursday, September 24, 2015 5:56:20 AM > > Subject: Re: [Bioc-devel] Shouldn't we distinguish

Re: [Bioc-devel] Issues with R CMD check and an ExperimentalData package

Hi Christian, Dan, thank you for reporting your issues with using BiocStyle. I didn't experience such problems before, I use "`r pkg_ver('EBImage')`" in my package vignette and both R CMD build and R CMD check pass without errors, without the need of prepending 'BiocStyle::' to the the pkg_ver.

Re: [Bioc-devel] Announcing newtest coverage shields

- Original Message - > > From: "Andrzej Oleś" <andrzej.o...@gmail.com> > > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" < > bioc-devel@r-project.org> > > Sent: Thursday, September 10, 2015 12:35:19 AM > > Sub

Re: [Bioc-devel] Announcing newtest coverage shields

Hi Dan, I find that the coverage shields are an extremely useful metrics for both end-users and package developers, as they reflect code quality and motivate to improve package test coverage. I've noticed that the badges are not updated as frequently as I would expect. Most of the packages on

Re: [Bioc-devel] No vignette contents page/fig refs with Devtools build

Dear Steven, thank you for your inquiry. It would be helpful if you could provide more details regarding your issue. In particular, a minimal example reproducing the problem would be a great starting point. Cheers, Andrzej On Mon, Mar 16, 2015 at 4:54 PM, Steven Barrett steven.j.barr...@gsk.com

Re: [Bioc-devel] BioC 3.0 CHECK ERROR

Dear Joachim, thank you for reporting the issue with using EBImage in your package! Martin, Dan: many thanks for digging into the problem and for suggesting solutions to overcome it. I had a look into this as well and could reproduce the issue. I can also confirm that it occurs under R 3.1.2

Re: [Bioc-devel] Add a new developer/maintainer

Hi Setia, you will probably also need an account with write permissions to the package SVN for the new maintainer. For this its probably best to contact Dan Tenenbaum dtene...@fhcrc.org Cheers, Andrzej On Fri, Oct 3, 2014 at 11:48 AM, Wolfgang Huber whu...@embl.de wrote: Dear Setia just edit

Re: [Bioc-devel] RMarkdown for vignettes

Hi Gordon, James, thank you for pointing this out! At the time BiocStyle for markdown documents was developed 'rmarkdown' was not yet on CRAN and couldn't be used as a vignette builder engine. As things changed in the meantime, the approach described by Gordon should be just fine. I will update

Re: [Bioc-devel] minor suggestion for BiocStyle?

Hi Ramon, many thanks for your feedback an for your nice suggestion! Having more distinctive image captions is for sure something worth considering. I personally like the idea of having them typeset in a slightly smaller font and with boldface label. Additional margin seems reasonable as well.

Re: [Bioc-devel] daily build system behind

Dear Levi, please note that experiment data packages are now build just twice a week, on Wednesdays and Saturdays. So no need to worry. Cheers, Andrzej On Tue, Sep 9, 2014 at 5:01 PM, Levi Waldron levi.wald...@hunter.cuny.edu wrote: I just noticed that the daily build systems are several days

Re: [Bioc-devel] Submitting a workflow

Hi Mike, see also http://www.bioconductor.org/developers/how-to/workflows/ If you author your vignette in markdown you could try using BiocStyle formatting, see http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html Best, Andrzej On Wed, Sep 3, 2014 at

Re: [Bioc-devel] Distinction between release and devel package websites

Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from the devel branch. Distinct colors between release and devel make sense only if one understands their meaning, which in the end might prove not to be very useful.

Re: [Bioc-devel] Distinction between release and devel package websites

that the package at least builds. Best, Andrzej On Tue, Jul 22, 2014 at 7:57 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: James W. MacDonald jmac...@uw.edu To: Andrzej Oleś andrzej.o...@gmail.com Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring julian.gehr

Re: [Bioc-devel] Distinction between release and devel package websites

cycle anyway... Cheers, Andrzej On Tue, Jul 22, 2014 at 10:04 PM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Andrzej, On 07/22/2014 10:14 AM, Andrzej Oleś wrote: Hi all, I think having links is useful, e.g. for someone who uses BioC release but wants to install by hand a particular package from

Re: [Bioc-devel] Distinction between release and devel package websites

Hi Martin, thank you! On Tue, Jul 22, 2014 at 9:01 PM, Martin Morgan mtmor...@fhcrc.org wrote: We might tell google not to index devel packages (but then packages added during a particular release cycle aren't indexed until the next release). This adds to the complexity and I'm not sure how

Re: [Bioc-devel] Distinction between release and devel package websites

Hi Dan, Michael, Julian, Thank's for keeping the links to the tarballs! I don't argue that mixing release and devel is a good idea in general. Rather, that for some users this might be the best compromise between the following two objectives: 1. a stable working environment 2. the possibility to

Re: [Bioc-devel] r+w permissions in release branches

Dear Kasper, regarding your issue with R-2.15: I was wondering whether using an older version of Rcpp from http://cran.r-project.org/src/contrib/Archive/Rcpp/ would help? Cheers, Andrzej On Tue, Apr 22, 2014 at 2:46 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: This is because

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

Dear Hervé, just to make sure: is the the same x.y.z versioning scheme as for software packages already implemented for experiment data packages, i.e. will there be an automatic version bump for experiment packages with the upcoming BioC release? Cheers, Andrzej On Tue, Feb 11, 2014 at 7:18 AM,

Re: [Bioc-devel] BiocStyle and fonts

Hi Laurent, Martin, thank you for bringing this up! As pointed out by Martin, currently the 'helvet' package gets overridden by Sweave, so this setting affects only the knitr output. My feeling is that the default font style should be the same regardless of the engine used. Too keep thing

Re: [Bioc-devel] BiocStyle and fonts

Should we then just drop \RequirePackage{helvet} from BiocStyle? Cheers, Andrzej On Wed, Mar 12, 2014 at 3:27 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Whatever we choose, we should discourage the use of other fonts: one of the advantages of bioc style is to make it easy to