Re: [Bioc-devel] Code quality and bug reports

be saved from Deprecation. HTH, Lluís On 18 January 2017 at 17:52, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi, > > On 01/14/2017 03:01 AM, Lluís Revilla wrote: > > Dear Valerie and all, > > > > If I understood the page you kindly linked cor

[Bioc-devel] reusing topGO objects

Dear Adrian and all I am using the package topGO and I would like to know if you could help me to reuse the same object to perform several test, see the examples below: library("topGO") data(GOdata) geneSelectionFun(GOdata) <- function(x) {x == 1L} GOdata resultKS.elim <- runTest(GOdata,

Re: [Bioc-devel] Code quality and bug reports

nch...@roswellpark.org> wrote: > On 01/04/2017 07:53 AM, Lluís Revilla wrote: >> Dear Guangchuang and all, >> >> Quality of the packages has been a preoccupation of the project from >> the beginning (see >> https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for &

[Bioc-devel] Code quality and bug reports

Dear Guangchuang and all, Quality of the packages has been a preoccupation of the project from the beginning (see https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for more references and other discussions about bug reports.) Despite not being in a goal of the project, it is

[Bioc-devel] Commiting from git to svn

Dear all, Short problem: I am a trying to sync my new package BioCor git repository with the Bioconductor svn repository. But I am failing when I do git svn dcommit. Long history of the problem I did some changes on my master branch (where I developed until now) then I used the update_remotes.sh

Re: [Bioc-devel] Commiting from git to svn

prior history / merge conflicts" > on the git mirror page: > http://www.bioconductor.org/developers/how-to/git-mirrors/ > > Using "git cherry-pick" instead of rebase seems to avoid a lot of errors. > > Stephanie > > > On 4/5/17 8:18 AM, Lluís Revilla wrote: >&

Re: [Bioc-devel] Maintainers submit your SSH public keys

Hi, Yes, Jason your Github username is the Github id. I have a question about one social feature of github: the topics of a repository. Should we tag the repositories with packages included (or intended to be included) in Bioconductor with the tag "bioconductor" or "biocondcutor-package"? I am

Re: [Bioc-devel] Bioconductor stats

t; to dig into at some point. > > Cheers, > H. > > > On 06/27/2017 04:34 AM, Lluís Revilla wrote: > >> Hi, >> >> I have been looking at the stats of Bioconductor, and I would like to know >> more about how are they calculated. >> >> Do these stats acc

[Bioc-devel] Bioconductor stats

Hi, I have been looking at the stats of Bioconductor, and I would like to know more about how are they calculated. Do these stats account for the mirror sites? Are there any stats of the usage of mirrors? I found some packages that for the same month they have downloads in two categories. For

[Bioc-devel] BioCor devel timeout

, Lluís Revilla [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Support site question can't be edited: Language "ca" is not one of the supported languages ['en']!

This seems related to this issue: https://github.com/Bioconductor/support.bioconductor.org/issues/33 On 20 September 2017 at 11:54, Martin Morgan wrote: > On 09/19/2017 10:30 PM, Gordon K Smyth wrote: > >> As a Bioc support site moderator, I tried to edit the

Re: [Bioc-devel] Transition from Google Sheet to Web App

information in 3 places, DESCRIPTION > file, credentials app and Support Site. I think the 'if' and 'how' of > connecting these pieces needs some thought. I'll discuss with the group at > our next meeting and will follow up here. > > Thanks for bringing this up. > > Valerie > &g

Re: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

Great work and happy new year!! I checked both RSS feeds and the random links I tried all point to the home page of Bioconductor. I am unsure if the links in the feed should point to a section on the gitlog page or to any other page (or is an issue on my end). Thanks, Lluís On 2 January 2018

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

I have recently faced a similar warning. This is when a link to a help page of another package is broken (there is not such help page). Although those could be false positives: mclapply help page does exists in parallel package. as.MAList does exists in devel limma HTH On 6 April 2018 at 16:35,

Re: [Bioc-devel] Transition from Google Sheet to Web App

Hi all, I have a couple of doubts related to the new app. I've seen that one can update mail, and github id, and add new keys (Nice!). However I couldn't find if this account will be somehow linked to the user profile in the support site. Are there any plans in this direction? At the moment the

Re: [Bioc-devel] repository change after package acceptance

Dear Xu, While you, with your ssh key, keep pushing to the git.bioconductor.org it doesn't matter where else is stored. To move a repository within github you need to follow this tutorial:

Re: [Bioc-devel] Warnings in build for BioCor

nd exclude >> the function that causes the problems and then use the double-colon >> operator when referring to the package's function. >> >> Kind regards >> Matthias >> >> On 02/28/2018 11:31 AM, Lluís Revilla wrote: >> >>> Dear bioconductor

Re: [Bioc-devel] Warnings in build for BioCor

same R process, so the packages loaded in the > first vignette are available (and conflict with) packages loaded in the > second. > > Martin > > > On 02/28/2018 08:53 AM, Martin Morgan wrote: > >> >> >> On 02/28/2018 05:31 AM, Lluís Revilla wrote: >> >>

[Bioc-devel] Warnings in build for BioCor

the warning for the next release? Many thanks, Lluís Revilla [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Error building the vignette

Dear Bioconductor team and list, I found that my package on devel (BioCor) fails to build on all the OS. The error message is related to creating figures of the vignette (see below). I haven't touched the vignettes in a while. and building the package on my machine passes all the checks. In

Re: [Bioc-devel] Why bioconductor?

Some people is lost even when and how many updates are and differences between different packages. See this question for instance ( https://www.biostars.org/p/287871/) Compared to CRAN or PyPi, which don't have release cycles, Bioconductor workflow is a bit more complicated to learn. Related to

Re: [Bioc-devel] NEWS.md

Entries must be indented, and > > > > ideally use a common indentation for the item texts. > > > > > > > > > > > > > > > > > > > > Please remove the pound sign (# ) from the header entry - and use > "Changes in version&

[Bioc-devel] NEWS.md

Dear Bioconductor team, I found that the new R version 3.5.1, to be used with the new release of Bioconductor, supports the ‘NEWS.md’ files. I updated my package (BioCor) to use `NEWS.md`. However, on the devel landing page of the package stills shows the old file NEWS file. This is consistent

[Bioc-devel] Bioconductor package review

Hi, Recently I was looking how package reviews are done. Specifically those packages from developers on the Bioconductor team, or listing the Bioconductor Package Maintainer as the maintainer. Some of those packages become the backbone of other packages and perhaps there are some experiences on

[Bioc-devel] Package coverage

Dear Lori and all, Some years ago there was a coverage badge, which disappeared when transitioning to git. Afterwards there were some mails about including the coverage badge on package's landing page again ( https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012417.html), but still there

Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

Hi, The maintainer is already aware of this error. I reported it several months ago https://github.com/colearendt/xlsx/issues/132 and is reported multiple times (issues 154, 156, 159) There is a fix on the github version of the package but the maintainter hasn't updated the CRAN version yet.

Re: [Bioc-devel] Bioconductor affy author questions

Hi Henry, This information is on the landing page of the package: https: bioconductor.org/packages/affy. There are many authors, but the listed maintainer is Rafael A. Irizarry whose mail is: rafa at jhu.edu. However, if you have questions about the package, the best route would be to post them

Re: [Bioc-devel] New Package Submission Workflow Updates!

Hi Lori and Core Team, Hope this change will make it easier for all to submit packages to Bioconductor (and review them). I have a couple of comments on the documentation. I think that the extensive documentation available can be confusing and a bit circular. The README of

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

Hi Stefano, About 1) you can document internal functions but remove them from the index if you use #' @keywords internal tag. See the vignette of roxygen2 https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under Other tags. About 2) perhaps you have too many/long examples? Hope

Re: [Bioc-devel] Fwd: Bioconductor package EnMCB

Hi Xin Yu, You seem to be using the symbol ≤ somewhere on the documentation, looking at the repository on GitHub I only found that symbol on two comments: https://github.com/whirlsyu/EnMCB/blob/6124a5a237a94d42d935720dc1bf8a44b11f6966/R/metricMCB.R#L239

Re: [Bioc-devel] ERROR: More than one VignetteEngine specified.

Hi Witek, Probably it is a false positive, caused by a commented VignetteEngine on https://github.com/protViz/prozor/blob/master/vignettes/TargetDecoyFDR_Example.Rmd#L16 If you delete it (and the line below to be sure) I guess it will go away. Best, Lluís On Fri, 19 Nov 2021 at 14:33, Witold

Re: [Bioc-devel] Not receiving original posts for watched tags at bioconductor support

Hi, While checking this, I realized that https://support.bioconductor.org/mytags/ doesn't show the tags I have in my profile as "My Tags" and as "Watched Tags". Not sure if it is related. Best, Lluís On Thu, 28 Sept 2023 at 01:00, Alexey Sergushichev wrote: > Hi, > > I have a problem that I

Re: [Bioc-devel] Is my package suitable for Bioconductor?

Hi Tim, I think there is a mentorship program for cases like this (I am not sure if it still accepts mentees): https://www.bioconductor.org/developers/new-developer-program/ I also recommend the book the Bioconductor community wrote to help with submissions:

[Bioc-devel] Packages removing documentation

Dear Bioconductor community, One of the oldest requirements of Bioconductor is a vignette with some executed code. Recently I found some packages that do not have examples for some functions and vignettes with executed code in the current release while they did some versions ago. The vignette

Re: [Bioc-devel] Packages removing documentation

; Buffalo, New York 14263 > > > From: Bioc-devel on behalf of Lluís > Revilla > Sent: Monday, August 1, 2022 5:36 PM > To: bioc-devel > Subject: [Bioc-devel] Packages removing documentation > > Dear Bioconductor community, > > One o

Re: [Bioc-devel] Large vignettes

Hi all, Perhaps instead of long vignettes, it would be better to use a book hosted and in sync with the packages at Bioconductor. There are already a few: https://www.bioconductor.org/books/release/ But I was not able to find how to submit such bookdowns to Bioconductor (I briefly searched the

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

Hi Rory, There was a recent change in R devel ( https://cran.r-project.org/doc/manuals/r-devel/NEWS.html): - sessionInfo() 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,

Re: [Bioc-devel] BiocManager::install() behavior with available updates

Hi Matej, Usually when I find this kind of message it indicates that the package is installed in different libraries and you are updating in just one library. Have you checked that it is installed in multiple libraries? I usually use something similar to this to identify those packages: ip1 <-

Re: [Bioc-devel] Bioconductor 3.17 requires R 4.3?

Dear Tag, Congratulations for your successful submission of TDbasedUFE! Your package was accepted and included in the devel branch of Bioconductor: See this document about what to do now: https://contributions.bioconductor.org/bioconductor-package-submissions.html#afteraccept The devel version

[Bioc-devel] Bioconductor packages released: archive

Dear all, I'm looking into the impact of two packages and I want to check Bioconductor packages that depend on them (around 130). There are some functions to retrieve information about CRAN with the current packages and all the previous releases: tools:::CRAN_archive_db() and

Re: [Bioc-devel] Package size issue

Hi Gabriel, You can find how to use BFG and other related recommendations at the R devel book: https://contributions.bioconductor.org/git-version-control.html?q=BFG#removing-large-files-from-history-with-bfg-repo-cleaner I hope this helps with this and other questions, Lluís On Fri, 29 Mar