Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out Where you can see that it fails if a user don't have BiocStyle installed. I don't know

Re: [Rd] RSS Feed of NEWS needs a hand

Many thanks Duncan, I tried to look into the code but didn't manage to advance much due to some java configuration issues. To prevent being flooded by content of old versions I added a filter to only repost those that the release version of the branch is in the title of the content. Maybe this

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

Re: [Rd] RSS Feed of NEWS needs a hand

Hi! Thanks for this service! It is very helpful to know what is being developed. I distribute the content to other venues and I noticed some times that the updates are duplicated. For example, the sentence "‘is.R()’ is deprecated as no other S dialect is known to be in use (and this could only

Re: [R-pkg-devel] Package failing reverse dependency checks

tip. Out of interest, is there a way to make win/Mac > builder run revdep checks? > > Writing: wyclif.substack.com > Book: www.wyclifsdust.com > > > On Thu, 8 Feb 2024 at 10:26, Lluís Revilla > wrote: > >> Hi David, >> >> If you didn't increase the versio

Re: [R-pkg-devel] Package failing reverse dependency checks

Hi David, If you didn't increase the version number it could happen that the old version of the package was used (as CRAN might not be aware that there is a new version). The CRAN repository policy says: "Increasing the version number at each submission reduces confusion so is preferred even when

Re: [R-pkg-devel] new maintainer for CRAN package XML

Dear Uwe and the CRAN team, Many thanks for maintaining the package for so long (>10 years!). I see the latest changes are in some internal C code related to updating the libxml2 library. In CRAN's experience, is this the highest time consuming task? I have some questions about how the

Re: [R-pkg-devel] Assistance Needed for Resolving Submission Issues with openaistream Package

Hi Li Gen, This NOTE is part of the new checks on CRAN to comply with its policy. The error message was introduced in c85587 (2023/11/22), when incorporating this suggestion https://bugs.r-project.org/show_bug.cgi?id=18611. You can see the changes and checks in the browser here:

Re: [Rd] R test coverage

> > For measuring coverage of the C code in the R runtime alone you could > use gcov and run the test suite, which depending on your contribution > may be the most informative route. > > (replying for the list, accidentally replied only to Lluís the first time) > > On M

[Rd] R test coverage

Hi all, I recently proposed a change in R that has led to the addition of new code to the R source code. The code added, as far as I know, has no tests and it might affect many packages in CRAN. I was wondering if adding a test would be helpful or it is already covered by some other test. Which

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:

Re: [R-pkg-devel] Status of adbcpostgresql

Hi Dewey, Currently there are several packages on a subfolder for human inspection. I don't think you can do anything else: sending this email might help drawing attention from your reviewer to your package. There might be some issues in the package that you'll need to address, try to find them

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: [R-pkg-devel] What to do when a package is archived from CRAN

The reasons that CRAN has for this (from: https://cran.r-project.org/src/contrib/PACKAGES.in) are: X-CRAN-History: Archived on 2023-08-19 for policy violation. Downloading on installation from github. Unarchived on 2023-08-30. X-CRAN-Comment: Archived on 2023-08-31 for policy violation. .

Re: [R-pkg-devel] package submissions no auto-processed message

Hi, Are you referring to your package formods? I see it was released the same Friday 17 and it is already on CRAN. If this is not the package, it might be on the backlog of packages submitted to CRAN. You can check the queue at: https://r-hub.github.io/cransays/articles/dashboard.html Best,

Re: [Rd] Vectorize library() to improve handling of versioned deps [sprint project proposal]

Hi Gabriel, Nice idea! I have encountered this problem several times, while probably a better management of libraries could avoided the issue this is an elegant solution. How would this proposal handle arguments mask.ok, include.only and exclude? For example, in the (edge) case two packages

Re: [R-pkg-devel] Missing ggPMX causing failure for nlmixr2rpt

Dear John, I think the problem is that the package ggPMX is suggested, but nlmixr2rpt isn't prepared for when it isn't available. In such cases, a package shouldn't fail the checks. >From the CRAN policies https://cran.r-project.org/web/packages/policies.html : "A package listed in ‘Suggests’ or

[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] 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

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

Hi, I can't read any vignettes of gcplyr in Firefox 109.0.1 from a Windows 10. But sorry, I don't have any solution. On Thu, 9 Feb 2023 at 21:18, Duncan Murdoch wrote: > On 09/02/2023 10:27 a.m., Mike Blazanin wrote: > > Hi all, my package gcplyr has several vignettes which, from CRAN, appear

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: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

tually, I don’t really agree to have to resubmit, and > my time for doing so is very limited. Maybe in the next few weeks or so. > > > > Best > > > > Carsten > > > > > > Von: Lluís Revilla [mailto:lluis.revi...@gmail.com] > > Gesendet: Donnerstag, 22

Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

Hi Carsten, This seems to be an unfortunate chain of events between different packages: RcppMLPACK -> emstreeR -> wflo Package RcppMLPACK was archived on 2021-12-20 as issues were not corrected despite reminders. This resulted in the package emstreeR being archived on 2021-12-20 as requires

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

[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] 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: [R-pkg-devel] Change package maintainer

I'm ready to take over the package I will ask the CRAN team and give them more details. Many thanks to all. Lluís Revilla On Fri, 2 Jul 2021 at 08:38, Uwe Ligges wrote: > > > > On 01.07.2021 23:52, Duncan Murdoch wrote: > > On 01/07/2021 3:11 p.m., Dirk Eddelbuettel wrote: &

Re: [R-pkg-devel] Change package maintainer

Thanks Uwe for answering, I have a question related to changing maintainers. What happens when the old/current maintainer does not respond to emails or other methods of contact? Would the new maintainer need to wait until the package is removed from CRAN to submit it again? Best, Lluís PS: Not

[Rd] New post not readable

Hi all, It has come to my attention that there is a new post on The R blog: "R Can Use Your Help: Testing R Before Release". However, the link returns an error "Not found": https://developer.r-project.org/Blog/public/2021/04/28/r-can-use-your-help-testing-r-before-release/index.html Hope this

[R-pkg-devel] CRAN submissions

Hi all, Some time ago, there was a question[1] about "how long is the average waiting time when submitting a new package ("newbies") until you get a manual reply or it's on CRAN, submitting an update with all OK before it hits CRAN". I have analyzed the data provided by cransays[2] (Many

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: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

bbrev", y="Ref_ID", cex=1,gap=2.5,degree = 60, canvas.xlim = c(-5, 5), canvas.ylim = c(-3, 3), grid.col = color.grid) Hope you can solve it. Cheers, Lluís On Thu, 5 Nov 2020 at 22:00, Pablo Fonseca wrote: > > Dear Lluís Revilla, > > Thank you very much for the com

Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

Hi Pablo, "The magick package is required to crop" is related to using BiocStyle for your vignette. Not sure what causes it, but I reported this error some time ago: https://github.com/Bioconductor/BiocStyle/issues/77. On related issues and on bioc-devel mailing list

Re: [R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

Hi Anthony, I stumbled with the same issue for a package I submitted recently, the problem seems to be that LaTex doesn't know how to map this unicode character to a typesetting. My unicode character was \u2229 and I tried several ways to avoid this warning. On the vignette built with knitr I

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] 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.

[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

[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] 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

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] 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] 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] 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: >> >>

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

[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

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] 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

[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] 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

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: >&

[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

[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

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

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