Re: [Bioc-devel] Help Remote Installations

> ... some GitHub packages ... In addition to what's already been said (list them under Suggests), I encourage you to make those package available via https://r-universe.dev/, instead of asking users to install them directly from GitHub (via remotes::install_github(...)). The idea is that you prov

Re: [Bioc-devel] Policies regarding forked packages

FWIW, the CRAN Repository Policies (https://cran.r-project.org/web/packages/policies.html) has the below regarding "takeovers". Maybe Bioconductor can borrow from this. "Packages should be named in a way that does not conflict (irrespective of case) with any current or past CRAN package (the Archi

Re: [Bioc-devel] file 'HilbertCurve/DESCRIPTION' does not exist

The content of the .Rbuildignore file should be regular expression, i.e. it does _not_ used fixed strings or globbing to match files and folders. From 'Writing R Extensions': "To exclude files from being put into the package, one can specify a list of exclude patterns in file .Rbuildignore in the t

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

> Secondly, does anyone have a good approach for keeping a mirror of it at the > url in the lab's github since this is the link we reference in the > publication: https://neurogenomics.github.io/MungeSumstats? Maybe an alternative is to: 1. Transfer the existing repo to your GitHub name 2. Fork

Re: [Bioc-devel] Important Bioconductor Release Deadlines

> Henrik, if Bioconductor releases weren’t tied to R releases, how could > Bioconductor test them? I guess like CRAN where as long as a package says it > depends on R >= 2.0 then you’re free to try installing on 2.0 even though the > combination has never been tested? Maybe I worry too much abou

Re: [Bioc-devel] Important Bioconductor Release Deadlines

trally maintained machines or HPC clusters, that they have no access to > the latest R versions. So sometimes even for demonstration purposes, we had > to install the package from the GitHub source, rather than from BiocManager. > > Cheers, > Anatoly > > On Fri, Apr 5, 202

Re: [Bioc-devel] Important Bioconductor Release Deadlines

Hello, these days, it's quite straight forward to have multiple versions of R installed in parallel without them conflicting with each other. I know it works out of the box on MS Windows (just install all versions you'd like), and I know there are various tools to achieve the same on macOS. I'm o

Re: [Bioc-devel] Urgent minor deployment of a release?

On Mon, Jun 19, 2023 at 5:46 PM Vincent Carey wrote: > > Hi Adam, thanks for your note. > > Changes to release branch sources must be limited to bug fixes or doc > improvement. Any new features > must be introduced only in the devel branch. I know about this, but I wanted to find what the docume

Re: [Bioc-devel] missing packages on nebbiolo1

Hello, those errors are because they forgot to declare those packages as dependencies; * eiR needs to add 'RSQLite' to Suggests: * ChemmineOB needs to add 'RUnit' to Suggests: /Henrik On Tue, Apr 11, 2023 at 1:26 PM Kevin Horan wrote: > > > The packages eiR and ChemmineOB are failing to build

Re: [Bioc-devel] Will package version 3.99.0 bump to 4.0.0?

Sunday drive-by comment: I guess that means that our affxparser package which currently has version 1.71.1 in Bioc devel, will reach 1.99.0 in 13-14 years from now because of the automatic version bumps that are done twice a year. So, if we don't touch anything, it'll roll over to 2.0 around 2037,

Re: [Bioc-devel] Error building package

Hello, add 'BiocStyle' to Suggests: in your DESCRIPTION file to fix this. For details, see /Henrik On Thu, Apr 6, 2023 at 8:12 AM ELENI ADAM wrote: > > Dear all, > > I am the creator of the hummingbird package ( > https://bioco

Re: [Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

On Tue, Apr 4, 2023 at 2:44 AM Oleksii Nikolaienko wrote: > > Hi, > maybe because BiocStyle is not listed as a dependency or suggested package > in DESCRIPTION? > More info here: https://github.com/Bioconductor/BBS/issues/248 Yes, this is why. The package needs 'BiocStyle' to build the vignette,

Re: [Bioc-devel] download stats not accessible

It's under investigation; see https://github.com/Bioconductor/bioconductor.org/issues/209#issuecomment-1474204159 /Henrik On Sun, Mar 19, 2023 at 11:02 AM Luo Weijun via Bioc-devel wrote: > > Dear BioC team, > I noticed that download stats for BioC packages are not accessible for months: > http

Re: [Bioc-devel] PeacoQC Bioc version not in line with github repo

> Indeed, although PeacoQC version on Bioc is higher (1.8) than in github repo (1.7.3), the latest commits have not been included. This is explained by Bioconductor bumping versions automatically when there's a new release cycle. So, in this case it went from something like 1.7.2 to 1.8.0 on the B

Re: [Bioc-devel] Packages failing Development build due to LaTex problem in .Rnw vignette

sionInfo() records (and by default prints) the system time zone as > part of the locale information. > It was reported a couple of days ago in the R-devel mailing list by Henrik > Bengtsson, that time zones with underscores caused problems which seems to > be your case with the New_York t

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

> Anyways, that's hundreds of \items that I need to fix in a dozen of packages. > Not fun! A great opportunity to freshen up your 'sed' skills. (I think it's possible to use 'sed' here, but 100% sure) /Henrik On Thu, Dec 1, 2022 at 12:27 PM Hervé Pagès wrote: > > Itemizing brings semantics and

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

> I think in \item{}{bar} the is not wrapped, so runs off the margin > in the devel ‘Constructor’ section. Would a hack be to split up the \code{} in multiple ones, e.g. \item{ \code{SnowParam(workers = snowWorkers(), type=c("SOCK", "MPI"),} \code{tasks = 0L, stop.on.error = FAL

Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

What about: \item{\code{show(x)}}{ Displays the first five and last five elements. } ? On Sat, Nov 26, 2022, 23:00 Dario Strbenac via Bioc-devel < bioc-devel@r-project.org> wrote: > Good day, > > For a long time, it has been a convention to document S4 methods in the > format: > > \

Re: [Bioc-devel] Interpreting BiocCheck output

I'm throwing in another 1 cent. I agree that utils::globalVariables() is risky; since it goes in the root of the package code, it applies to *all* functions in the package, which is a bit too broad of a stroke for my taste. The way I deal with false globals from non-standard evaluation (NSE), is

Re: [Bioc-devel] Use set.seed inside function

The easiest is to use withr::with_seed(), e.g. > withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6)) [1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5" > withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6)) [1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15

Re: [Bioc-devel] Package name

For CRAN packages it's easy. Packages on CRAN are eternal. They may be archived, but they are never removed, so in a sense they're always "currently on CRAN". Archived packages may still be installed, but only with some efforts of the user. Some packages go in an out of "archived" status depending

Re: [Bioc-devel] Too many dependencies / MultiAssayExperiment + rtracklayer

If you're willing to depend on R (>= 4.0.0), then tools::R_user_dir() can replace the 'rappdirs' package. /Henrik On Mon, Oct 18, 2021, 09:05 Shraddha Pai wrote: > Hi all, > Despite moving rarely-used packages to Suggests and eliminating some (e.g. > TCGAutils), the number of dependencies is st

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

In addition to checking with Valgrind, the ASan/UBsan and rchk platforms on R-Hub (https://builder.r-hub.io/) can probably also be useful; > rhub::check(platform = "linux-x86_64-rocker-gcc-san") > rhub::check(platform = "ubuntu-rchk") /Henrik On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan wrot

Re: [Bioc-devel] git: lost write access to some repos + what is my BiocCredentials email address?

> Dana Farber Cancer Institute > > > On Aug 19, 2021, at 8:08 AM, Henrik Bengtsson > > wrote: > > > > Hi, > > > > I seem to have "lost" write access to several Bioconductor git > > repositories that I had git push access for before; > &g

[Bioc-devel] git: lost write access to some repos + what is my BiocCredentials email address?

Hi, I seem to have "lost" write access to several Bioconductor git repositories that I had git push access for before; $ ssh -T g...@git.bioconductor.org | grep -E "(affxparser|aroma.light|illuminaio|QDNAseq)$" X11 forwarding request failed on channel 0 R packages/QDNAseq R packages/a

Re: [Bioc-devel] Build error "failure: length > 1 in coercion to logical" not reproducible

On Thu, Jun 17, 2021 at 2:32 AM wrote: > > Dear colleagues, > > It seems to me that, starting with the latest BioC devel branch (3.14), the > build systems have become more pedantic about logical vectors of length > 1 > in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil' >

Re: [Bioc-devel] BiocCheck and version requirement

t check under older versions. That is intentional. But > that is different from the check asking for a specific version for no > particular reason (as far as I can ascertain). > > Best, > Kasper > > On Thu, Apr 8, 2021 at 8:13 PM Henrik Bengtsson > wrote: >> >> &

Re: [Bioc-devel] BiocCheck and version requirement

> I believe in the past we tried suggesting removing a R dependency altogether > but that R CMD check complained not having an R dependency? Maybe someone > remembers more about this. There are no such requirements in 'R CMD check'. The only requirement around 'Depends: R (>= x.y.z)', if speci

Re: [Bioc-devel] Suppressing messages from Rprofile

Correcting: the env var is R_LIBS_USER and nothing else. /Henrik On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson wrote: > > Can you go via a temporary file instead, i.e. output what you want to > grab to a temporary file and pull the info from that instead? > > Side tracking ...

Re: [Bioc-devel] Suppressing messages from Rprofile

Can you go via a temporary file instead, i.e. output what you want to grab to a temporary file and pull the info from that instead? Side tracking ... > I thought about using --vanilla but I use .Rprofile to set my library path, > so ignoring that file completely defeats the point in my setup. I'

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

FWIW, I ran into a similar problem when I moved R.cache (https://cran.r-project.org/package=R.cache) from using ~/.Rcache to ~/.cache/R/R.cache (etc). I decided on making it 100%-backward compatible, i.e. if there's already a legacy ~/.Rcache cache folder, it'll keep using that, otherwise the new

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Related: Does Bioconductor support 'Additional_repositories'? From RWE: The ‘Additional_repositories’ field is a comma-separated list of repository URLs where the packages named in the other fields may be found. It is currently used by R CMD check to check that the packages can be found, at least

Re: [Bioc-devel] Rsync to Bioconductor

FYI, I just sent an email to 'maintai...@bioconductor.org' regarding this but it bounced with the below errors (I've truncated your address): From: Mail Delivery System Date: Thu, Feb 25, 2021 at 12:39 PM Subject: Undelivered Mail Returned to Sender To: ... This is the mail system at host deliv

Re: [Bioc-devel] Git pack file greater than 5MB

o the Bioconductor git > repository. > > Nitesh > > On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson > wrote: > > Doesn't a git rewrite break all existing clones, forks out there? I'm > happy to be corrected, if this is not the case. > > /Henrik > > On Thu, Oct

Re: [Bioc-devel] Git pack file greater than 5MB

Doesn't a git rewrite break all existing clones, forks out there? I'm happy to be corrected, if this is not the case. /Henrik On Thu, Oct 1, 2020, 08:16 Nitesh Turaga wrote: > Hi, > > The BiocCheck will complain on the build system about the > 5MB package > size. > > The rewrite of the history

Re: [Bioc-devel] sapply and vapply

FWIW, > sapply(X, length) - always numeric(1) (integer(1) or double(1) for vectors of > more than 2^31 - 1 elements) Actually, the length of length(x) may not be 1L, e.g. > x <- Formula::Formula(~ x) > length(x) [1] 0 1 >From help("length", package = "base"): "Warning: Package authors have wr

Re: [Bioc-devel] Possible problems with BiocParallel and R cmd check on Github

Is it relevant for a bioconductor reviewer the result of these Github > action reports? We would like to submit the package for moderation soon > but we're unsure if we can due to this problem. Thank you. > > Il 29/07/2020 19:25, Henrik Bengtsson ha scritto: > > From a very

Re: [Bioc-devel] Possible problems with BiocParallel and R cmd check on Github

>From a very quick look at this, I think you also need to explicitly install the package itself for it to be available in external R session (contrary to when using forked processing as on Linux and macOS). Something like this: - name: Install dependencies run: | remotes::install_deps(d

Re: [Bioc-devel] How I hide non-exported function from the manual

On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey wrote: > > On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > > > Hello Community, > > > > I am used to document function although hey are not exported > > > > > I suppose you are talking about tidybulk? I am somewhat mystified by the > behavior > of >

Re: [Bioc-devel] Reducing dependencies

RStudio provides pre-built R package for Linux and since a some weeks now, they can be used on GitHub Actions (https://github.com/r-lib/actions). In addition, the run-time limit on GitHub Actions is several hours compared to the 50 minutes you've' got on Travis, so even if you install from source,

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

Maybe it's related to: * The plot() S3 generic function is now in package base rather than package graphics, as it is reasonable to have methods that do not use the graphics package. The generic is currently re-exported from the graphics namespace to allow packages importing it from there to conti

Re: [Bioc-devel] Bioconductor Git: Online interface

e when reaching out to maintainers is something Bioconductor is really missing right now. This would lower the friction for contributing to packages that you don't work on on a regular basis, e.g. typos, bug fixes, etc. Henrik > > Martin > > On 2/11/20, 5:16 PM, "Bioc-devel on

Re: [Bioc-devel] Bioconductor Git: Online interface

> > I would very much appreciate this as well. Issue tracking and communicating > > with users directly in the repository would be very nice, as well as the > > ability to reference source code directly. > > > > On Thu, Oct 26, 2017 at 8:50 AM, Henrik Bengtss

Re: [Bioc-devel] New setting on devel builders will cause some new package failures

This is great news. For those who wish to reproduce this locally when running R CMD check, I suggest creating '~/.R/check.Renviron' with: ## Check for bugs like if (c(TRUE, FALSE)) ... Supported since R 3.4.0 _R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,verbose ## Check for bugs l

Re: [Bioc-devel] What are the R CMD check settings (env vars) that Bioc uses?

Thank you - sounds great. /Henrik On Tue, Dec 3, 2019 at 9:23 AM Pages, Herve wrote: > > Hi Henrik, > > On 12/3/19 09:13, Henrik Bengtsson wrote: > > I'm interested in finding out what customization Bioconductor servers > > do to R CMD check, e.g. _R_CHECK_**

[Bioc-devel] What are the R CMD check settings (env vars) that Bioc uses?

I'm interested in finding out what customization Bioconductor servers do to R CMD check, e.g. _R_CHECK_***_ settings. I think someone pointed me to some location in the past, but I cannot locate it. I think a natural place to document those would be on the 'Node Info' pages together with the exis

[Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived

In case it's not known, paraphrasing from CRAN notification email, CRAN [sic!] packages: TROM, demi, diffMeanVar, maGUI, metaboGSE risk being archived on December 7 because broken Bioconductor dependencies: Heatplus, missMethyl, oligo, oligoClasses, topGO prevent pdInfoBuilder from being in

Re: [Bioc-devel] BiocManager::install() downgrade installed packages

ally since some of them come and go depending on Bioc version. /Henrik PS. I also tried setting ditto env var because it looked more like an env var than R option name to me. > > On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson > wrote: >> >> (posting this here since I thin

[Bioc-devel] BiocManager::install() downgrade installed packages

(posting this here since I think it's not a support question per se) Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1 setup: > BiocManager::install(version = "3.10") Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y Bioconductor version 3.10 (BiocManager 1.30.9),

Re: [Bioc-devel] Reference manual as HTML

On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee wrote: > > Chiming in to say +1 to this. I also use pkgdown for the same purpose as > Laurent. With some kind of CI service you can automate the build of the > website after a successful R CMD CHECK. Not sure how tricky this would be to > integrate wit

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

Just an FYI, *if* all you're doing is rbind():ing those data frames, then you're better of doing: df <- do.call(rbind, dfs) than df <- Reduce(rbind, dfs) because the former is faster and more memory efficient: > dfs <- rep(list(iris), times=100) > bench::mark(df <- Reduce(rbind, dfs))[,1:7

Re: [Bioc-devel] Using SerialParam() as the registered back-end for all platforms

On Mon, Jan 7, 2019 at 4:09 AM Martin Morgan wrote: > > I hope for 1. to have a 'local socket' (i.e., not using ports) implementation > shortly. > > I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have > > > library(BiocParallel) > > set.seed(1); p = bpparam(); rnorm(1)

Re: [Bioc-devel] Controlling vignette compilation order

On Sat, Dec 22, 2018 at 10:56 AM Michael Lawrence wrote: > > Anything that eventually lands in inst/doc is a vignette, I think, so > there might be a hack around that. Just so this is not misread - it's *not* possible to just hack your vignette "product" files (PDF or HTML) into inst/doc and thin

Re: [Bioc-devel] choosing R version dependency for existing packages

I'm using Depends: R (>= 2.12.0) to communicate that I've tested/verified that the package works as far back as R 2.12.0. Also, since R (>= 3.5.1) and R (>= 3.5.0) has been mentioned here, in 'Writing R Extensions' there is: "It is inadvisable to use a dependence on R with patchlevel (the

Re: [Bioc-devel] NEWS.md

ource: https://github.com/wch/r-source/blob/d20943d71407f9209cb6c7581ac0fce3b3517419/src/library/tools/R/news.R#L62-L66 /Henrik On Tue, Sep 25, 2018 at 3:58 PM Henrik Bengtsson wrote: > > Note that in R-devel, we have that > (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html): >

Re: [Bioc-devel] NEWS.md

Note that in R-devel, we have that (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html): * news() gains support for ‘NEWS.md’ files. That is, news(package = pkg) not only finds NEWS.md (as before) but also parses it (into sections etc.) analogously to how it parses NEWS.Rd and NEWS. Becaus

Re: [Bioc-devel] BiocInstaller: next generation

On Thu, May 10, 2018, 00:29 Martin Morgan wrote: > Developers -- > > A preliminary heads-up and request for comments. > > Almost since project inception, we've used the commands > >source("https://bioconductor.org/biocLite.R";) >biocLite(pkgs) > > to install packages. This poses security

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

A few quick comments: * I don't think the limit was hardened in R 3.4.0; maybe you started to experience it sound then because more dependent packages started to rely on more DLLs? * The limit is OS/platform specific so it's not that R core is unwilling to fix this - I think they havejust tried t

Re: [Bioc-devel] BiocFileCache for developers

R.cache (>= 0.6.0) does the following to acquire a persistent cache (root) folder. This behavior was introduced after getting prompted by CRAN not to write to disk by default (because they found "funny" folders on their check servers) and a following email conversation with CRAN (2011-12-29), and

Re: [Bioc-devel] Query bioconductor.org for what the current release version is?

; > > Hope this is what you are looking for. > > Nitesh > >> On Nov 16, 2017, at 8:09 PM, Henrik Bengtsson >> wrote: >> >> Hi. Is there a way, without using R, to query bioconductor.org (or >> any other reliable/maintained resources) for what the curren

[Bioc-devel] Query bioconductor.org for what the current release version is?

Hi. Is there a way, without using R, to query bioconductor.org (or any other reliable/maintained resources) for what the current release version of Bioconductor is? Something like: $ curl https://bioconductor.org/api/version 3.6 or possibly something fancy like: $ curl https://bioconductor.org

Re: [Bioc-devel] any interest in a BiocMatrix core package?

As Peter points out, the 'matrixStats' package provides an API with plain functions - not generic functions. This is intentional with the main purpose of this is to keep the overhead at an absolute minimum. This is also in line with the overall philosophy of 'matrixStats' where speed is maximized

[Bioc-devel] Bioconductor Git: Online interface

Are there any plans for an online interface to https://git.bioconductor.org/? I've recently looked into solutions for an open-source in-house "GitHub/GitLab"-ish, and I've found https://gitea.io/ to be really nice. It is very easy to install. It has support for various common user authentication

Re: [Bioc-devel] EXTERNAL: R version dependence of a new package

I lean to agree with Yaoyong, because I find it helpful to specify (or read): Depends: R (>= 3.0.0) which sends a message that "the code is relying on features in R that was not available prior to R 3.0.0". Also, if that's the only dependency you have, then if it passed R CMD check on R 3.0.0 in

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

mit and how it is >> set, but that is a pretty start difference. >> >> Best, >> Kasper >> >> >> >> On Fri, Oct 6, 2017 at 3:12 AM, Wolfgang Huber > <mailto:wolfgang.hu...@embl.de>> wrote: >> >> On Mac OSX 10.1

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

ultiple libraries >> which contain, for example, different bioc versions in them. >> >> NB: switchr is subject to the caveat Martin pointed out and will fail to >> retrieve a buildable version of the package if said buildable version is not >> the first commit in SCM b

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan wrote: > On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: >> >> Is there an easily accessible archive for Bioconductor packages >> similar to what is provided on CRAN where you can find all released >> versions of a pack

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

About the DLL limit: Just wanna make sure you're aware of "new" environment variable R_MAX_NUM_DLLS available in R (>= 3.4.0). It allows you to push the current default limit of 100 open DLLs a bit higher. It can be set in .Renviron or before, e.g. $ R_MAX_NUM_DLLS=500 R This, of course, assum

[Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source code for affy 1.18.0. Here are the two approaches

Re: [Bioc-devel] NEWS, inst/NEWS, NEWS.md

Note that NEWS.md (Markdown) is only partially supported, e.g. news() does _not_ pick it up, cf. https://github.com/HenrikBengtsson/Wishlist-for-R/issues/40 /Henrik On Sat, Sep 9, 2017 at 4:43 PM, Martin Morgan wrote: > On 09/09/2017 06:11 PM, Levi Waldron wrote: >> >> What's the currently recom

Re: [Bioc-devel] Git Transition Plan

aintainers by adding a .gitauthors file to the package root (or possibly via a global Bioc one that everyone can commit to), e.g. ```r hb = Henrik Bengtsson j...@foo.com = John Doe ``` and then Bioc can use this mapping when exporting to Git? Finally, will people like me who already done the SVN-to

Re: [Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function

a myth :-/ > > H. > > > On 03/09/2017 05:38 PM, Henrik Bengtsson wrote: >> >> Hi. FYI / Is anyone else experiencing: >> >> Error in c(x, values) : >> could not find symbol "recursive" in environment of the generic function >> >>

[Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function

Hi. FYI / Is anyone else experiencing: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function errors for some Bioconductor packages when running under R 3.3.3 while they don't occur with R 3.3.2? This seems realted to the following R 3.3.3 NEWS entry:

Re: [Bioc-devel] Naming and namespace collisions for commonly-named functions

A few times I'd wish there was a way to support: pkg::fun() while _not_ "exposing" fun() on the search() path when attaching pkg. Although it would be part of the public / exported API, the only way to call the function would be via pkg::fun(). This would cover Sean's use case. It would also

Re: [Bioc-devel] GitHub and svn

Hi folks, I'm a person who prefers to use Git as my main source for my Bioc packages. These Git repositories are then synced online to GitHub for each collaboration yada yada. This also means that these days I also tend to think of the Bioconductor SVN repository mostly as a communication channel

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

On Tue, Oct 11, 2016 at 6:05 PM, Dan Tenenbaum wrote: > > > - Original Message - >> From: "Kasper Daniel Hansen" >> To: "Mike" >> Cc: "bioc-devel" >> Sent: Tuesday, October 11, 2016 5:57:02 PM >> Subject: Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0 > >> Two things. >> >>

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

I've noticed this for a while and thought it was a temporary glitch, or maybe I missed some announcement about it, but it appears that NEWS files are no longed listed on the Bioc package pages, e.g. https://bioconductor.org/packages/devel/bioc/html/Biobase.html. A mistake? /Henrik __

Re: [Bioc-devel] Is it OK for Rmd package vignettes to be rendered as PDF?

On Thu, Aug 18, 2016 at 4:45 PM, Wolfgang Huber wrote: > > >> On 17 Aug 2016, at 13:02, Henrik Bengtsson >> wrote: >> >> R CMD build, which is what triggers vignette building, only supports one >> output file (HTML or PDF) per vignette. It will basicall

Re: [Bioc-devel] Is it OK for Rmd package vignettes to be rendered as PDF?

R CMD build, which is what triggers vignette building, only supports one output file (HTML or PDF) per vignette. It will basically ignore duplicate output formats. This is by design / legacy reasons. Technically it wouldn't be hard to add support for multiple output formats, but that would require

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

-- Original Message - > > From: "Henrik Bengtsson" > > To: "Dan Tenenbaum" > > Cc: "Maarten van Iterson" , "bioc-devel" < > bioc-devel@r-project.org> > > Sent: Monday, April 11, 2016 4:01:05 PM > > Subject: Re: [

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

I *cannot* reproduce this: % R --vanilla ## The IDAT file > pathname <- system.file(package="minfiData", "extdata", "5723646053", > "5723646053_R05C02_Grn.idat") > file.info(pathname)$size [1] 8091452 > unname(tools::md5sum(pathname)) [1] "dfc33fdaf3e91d872be896643a0c837f" > packageVersion("minfi

Re: [Bioc-devel] Odd behavior by R CMD check

If you have R-devel you can get those NOTEs using: R CMD check --as-cran *.tar.gz (It's been reported by --as-cran since Oct 2015 or so). /Henrik On Fri, Mar 11, 2016 at 2:45 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote: > Thanks. I'll try that. I'm surprised, as my local R-Devel install isn't

Re: [Bioc-devel] C++ header changes in R-devel

If of any help, at least for affxparser the fix was very simple. It was just a matter of moving #include statements outside of the +extern "C" { ... }: https://github.com/HenrikBengtsson/affxparser/commit/e750159a9abeeb463661095f6c07f1bb7bf611d9 So not as scary as it first may sound. The compil

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

On Feb 26, 2016 09:23, "Andrzej Oleś" wrote: > > 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, K

[Bioc-devel] Git svn mirror: Duplicated commit entries (introduced by git svn rebase?)

Hi. I've got https://github.com/HenrikBengtsson/aroma.light which I've successfully used for years to sync to Biconductor SVN via the BiocGitHub bridge. All the time I've had the `master` branch synced to Bioc. (I've also had my own `develop` branch to which I made all the commits which I then m

Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

For your Linux problem: You might have build R differently from what you had in the past, e.g. static vs dynamic. Try to explicitly re-install those failed dependences and see if you any further. If so, you might wanna remove all your installed packages and start over with a fresh package librar

Re: [Bioc-devel] vignettes with different builders in one package?

You can mix any type and number of vignette formats in a package. What vignette engine is used is solely specified by the %\VignetteEngine{::} markup string. You don't need to specify this for the default Sweave format, but you can as: %\VignetteEngine{utils::Sweave} For your knitr vignette you'd

Re: [Bioc-devel] Make codetoolsBioC available on GitHub?

be another use case motivating that change. > > I will bring it up with the rest of the devteam today. > > Jim > > > On Fri, Jul 24, 2015 at 11:12 AM, Henrik Bengtsson > wrote: >> >> Currently, the codetoolsBioC package is available via: >> >>

[Bioc-devel] Make codetoolsBioC available on GitHub?

Currently, the codetoolsBioC package is available via: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC Can codetoolsBioC be mirrored on GitHub like the other BioC packages, or is that only possible for built and distributed BioC package? Thanks, Henrik _

Re: [Bioc-devel] Announcing newtest coverage shields

On Wed, Jun 24, 2015 at 5:42 PM, Dan Tenenbaum wrote: > Hello Bioconductors, > > We're pleased to announce a new shield to join the ones we rolled out in May. > > The new shield measures test coverage of a package, as determined by Jim > Hester's covr package. > > Coverage is a measure of the deg

Re: [Bioc-devel] Wishlist: on demand R CMD check

Kasper, correct me if I'm wrong... The way I understand it, Kasper would like a way to test on an *identical* setup such that he can reproduce the issues he sees on the Bioc servers, but that he cannot reproduce elsewhere. I've been there a few times as well and when it happens you end up spendin

Re: [Bioc-devel] upcoming changes - maintainer integration with support site

On Tue, May 26, 2015 at 2:59 PM, Dan Tenenbaum wrote: > > > - Original Message - >> From: "Henrik Bengtsson" >> To: "Dan Tenenbaum" >> Cc: "bioc-devel" >> Sent: Tuesday, May 26, 2015 2:50:43 PM >> Subject: Re: [Bioc-d

Re: [Bioc-devel] upcoming changes - maintainer integration with support site

Just got the email asking me to sign up. The thing is that I've already signed up, but using a different email address that the one listed as the maintainer of my package(s). Is there a way to have multiple associated email addresses on https://support.bioconductor.org/? I cannot find such an op

Re: [Bioc-devel] Use and Usability metrics / shields

So, lots of things are happening in a few months: Jim Hester starts working at Bioconductor, we get Bioc shields/badges, Jim's covr package is released on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenb

Re: [Bioc-devel] Use and Usability metrics / shields

Sweet; you went live with the badges/shields, e.g. http://bioconductor.org/packages/release/bioc/html/affxparser.html A positive side effect is that now there's a link from the package page to to the package's check results, which I always wanted :) Thanks for adding this /Henrik On Sun, Ma

Re: [Bioc-devel] Biobase: Imports repeats Depends

t; More generally it's about expressing intentions directly versus > expressing them in an indirect manner (e.g. by relying on side > effects). I think the latter is wrong. Hope that makes sense. Thanks for clarifying. I simply thought it was a mistake/cut'n'paste typo. H.. &

Re: [Bioc-devel] Bioc package pages: List also BugReports for a package?

Beautiful. Thxs Henrik On Mon, Apr 27, 2015 at 6:47 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Henrik Bengtsson" > > To: "bioC-devel" > > Sent: Sunday, April 26, 2015 7:14:20 PM > > Subject: [Bioc-devel] Bio

[Bioc-devel] Bioc package pages: List also BugReports for a package?

For affxparser, we've got the following in DESCRIPTION: URL: https://github.com/HenrikBengtsson/affxparser BugReports: https://github.com/HenrikBengtsson/affxparser/issues But t's only the URL field that is listed on the package page(s): http://www.bioconductor.org/packages/release/bioc/html/aff

[Bioc-devel] Biobase: Imports repeats Depends

It seems unnecessary that BiocGenerics have the same package under Imports as under Depends. The former can be dropped. > packageDescription("BiocGenerics") Package: BiocGenerics Title: S4 generic functions for Bioconductor Description: S4 generic functions needed by many Bioconductor packages. V

Re: [Bioc-devel] Dependency issue

It's a new Bioc package, correct? Then it just got into the Bioc release branch yday. That Bioc branch requires R 3.2.0 (the new recommended R version everyone "should" run) regardless what your package declares. Your package does not install on R < 3.2.0 using the Bioc installers, even if your pac

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