[Bioc-devel] Package home pages with >1 URL have broken links

Fri Oct 9 20:33:32 CEST 2026

Hi Thomas,

Thanks for reporting this. Our package pages currently take versions and files from the existing build system, but they take vignette lists from r-universe; this is a weird transition state. When r-universe can't build a package's vignettes, the list comes up empty, even though the vignette is on bioconductor.org. We'll make the pages read vignettes from the same place as everything else. It affects a couple of hundred packages, tracked here:

https://github.com/seandavi/bioc-infrastructure/issues/108

For drugTargetInteractions there's a real issue underneath. The r-universe build of 1.21.14 fails while building the vignette:

  Quitting from drugTargetInteractions.Rmd:564-570 [gtopdb_build]
  Error in `.util_download()`: bfcadd() failed

buildGtoPdbDb() downloads https://www.guidetopharmacology.org/services/interactions, and GtoPdb now requires an API key for its web services. Every /services/ endpoint returns 401 "API key is missing". The HGNC mapping file is still public.

The Bioconductor build still shows the vignette as OK, most likely because the build machines keep BiocFileCache between runs, so buildGtoPdbDb(rerun = FALSE) finds a cached copy and never downloads. r-universe starts from an empty cache every time, so it hits the 401. I'd expect the Bioconductor build to fail too once that cache is refreshed. Build machines won't have an API key, so the vignette probably needs to run without that download or needs an API key: for example a small bundled extract, or skipping the chunk when the download fails.

Separately, BiocCheck on r-universe reports one error: "At least 80% of man pages documenting exported objects must have runnable examples." The daily Bioconductor build doesn't run BiocCheck, so you won't have seen it there.

Full logs, while GitHub keeps them:

https://github.com/r-universe/bioc/actions/runs/35435072146

On the layout: I agree the landing pages matter for exactly the reasons you give. For now we're deliberately keeping them close to the old pages, but I have played with some new layouts such as https://bioconductor.org/next/bioc-release/package/drugTargetInteractions.html. Any redesign, dashboard-style or otherwise, needs proper community review first, and wasn’t something that we wanted as a side effect of the migration. I've recorded your suggestion so it's part of that discussion:
https://github.com/seandavi/bioc-infrastructure/issues/109

Thanks again,
Sean

From: Thomas Girke <thomas.girke using ucr.edu>
Date: Friday, October 9, 2026 at 14:21
To: Vincent Carey <stvjc using channing.harvard.edu>
Cc: Sean Davis <seandavi using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Package home pages with >1 URL have broken links

I didn't even know this new build report page existed. I keep looking here<https://bioconductor.org/packages/devel/bioc/html/drugTargetInteractions.html> (where top shows build ok) and here<https://bioconductor.org/checkResults/3.24/bioc-LATEST/drugTargetInteractions/> where the reports show no problems on any OS. What's then even more confusing is that the latest version did build properly on the landing page I am using but obviously it shouldn't have based on the usual policies. I also didn't get any email notification about a problem.

Sorry if I missed some important announcements about this change. But perhaps my ignorance and confusion helps others?

Thomas

On Fri, Oct 9, 2026 at 11:06 AM Vincent Carey <stvjc using channing.harvard.edu<mailto:stvjc using channing.harvard.edu>> wrote:
Thomas, have you seen

https://github.com/r-universe/bioc/actions/runs/35435072146/job/105876277171

This may be related to your finding.  The badge on the classic landing page does not
reflect this.  It would be good to find out why.

Best regards
Vince

On Fri, Oct 9, 2026 at 1:20 PM Thomas Girke via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:
Hi Sean,

Thanks for all the hard work on this transition and for explaining the
background. Moving the infrastructure while preserving the existing
functionality must have required a substantial effort.

One additional issue I'd like to report: some package pages in the devel
branch appear to be missing their vignettes or links to them. One example
(there are more) from my own packages is drugTargetInteractions
<https://bioconductor.org/packages/devel/bioc/html/drugTargetInteractions.html>.
Is this a temporary issue during the transition, or something that should
be reported separately?

Looking further ahead, would the project consider a more dashboard-like
layout for the package landing pages in the future? I understand that the
current priority is preserving the familiar layout and functionalities. As
a future enhancement, clearly labeled buttons for documentation, source
code, support, and related resources could make the pages easier to
navigate. Descriptive link labels instead of full URLs could also reduce
visual crowdedness. In addition, a dashboard would be more condensed and
scale better for a large number of links.

The package landing pages are often the first point of contact for
prospective users, permanent URLs in publications and an important place
for developers to showcase their packages. A more attractive and welcoming
layout could help visitors, particularly those less familiar with
Bioconductor, find what they need and explore the available resources. -
Just a suggestion.

Thanks again for leading this transition!

Thomas

On Thu, Oct 8, 2026 at 8:15 AM Sean Davis <seandavi using gmail.com<mailto:seandavi using gmail.com>> wrote:

> Thanks, again, Gordon, for the comments and entirely warranted questions
> about the background for the changes.
>
> The package pages weren't redone for design reasons. Until recently,
> bioconductor.org<http://bioconductor.org> was generated and served by a single server (
> master.bioconductor.org<http://master.bioconductor.org>). We are moving off that server to a more
> performant and cloud-based infrastructure; the change was necessitated by
> increasing and abrupt unsustainable traffic to the old infrastructure.
> Since late September, the site has been served from on entirely new
> infrastructure and rebuilt from the same package metadata (with the caveat
> that we are also in parallel integrating r-universe).
>
> In the move to new infrastructure, the intent was to keep the package
> pages as close as possible to the originals. The new website html
> generation process also required update, so while the website looks very
> similar, it is built from scratch to be faster and more flexible. The first
> version changed more than it should have, and that's on me.
>
> As of today, the pages are much closer to the old layout again:
>
> - Same section order: Installation, Documentation, Details (with "See
> More"), Package Archives.
> - "In Bioconductor since" uses the same source as before, so it agrees
> with the badge again (limma: BioC 1.6 or earlier, > 21.5 years).
> - The duplicate download-rank row is gone.
> - The Documentation links that led back to the same page are fixed. That
> was a bug in the tool that builds the pages, not intended behaviour.
> - NEWS, the installation pointer and the unlinked base packages (splines
> ships with R) are as they were on the old pages.
> - The code browser link returns once code.bioconductor.org<http://code.bioconductor.org>'s certificate
> problem is fixed. I have testing that runs each day that checks this.
>
> Going forward, the package pages should stay close to what you were used
> to. The new website can generate PR review sites, so we can have live
> previews of substantial changes.
>
> If you want the longer story, the plan and current status are at
> https://seandavi.github.io/bioc-infrastructure/ ("How bioconductor.org<http://bioconductor.org>
> works" and the roadmap are the best starting points). If anything else is
> missing or wrong, reply here or file a report at
> https://github.com/seandavi/bioc-infrastructure/issues. I also have a
> talk that I gave to the Bioconductor Technical Advisory Board that might be
> of interest to a few folks here:
> https://talks.seandavis.net/2026-10-01-bioc-tab/
>
> Thanks, again, Gordon for the close reading and for the questions. Please
> keep them coming.
>
> Best,
> Sean
>
>
>
> From: Gordon Smyth <gksmyth using outlook.com<mailto:gksmyth using outlook.com>>
> Date: Thursday, October 8, 2026 at 08:08
> To: Sean Davis <seandavi using gmail.com<mailto:seandavi using gmail.com>>; Kern, Lori
> <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <
> bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
> Subject: RE: Package home pages with >1 URL have broken links
>
> Hi Sean,
>
> Thanks for making updates. Looking at the limma home page, some things
> that still look odd include:
>
> - The badge and the Details give different estimates of how long the
> package has been in Bioconductor (and why give the same info twice anyway).
> - The badge and the Detail repeat downloads rank, which is unnecessary
> duplication. The later takes quite of bit of vertical space to give the
> same info, so it would be one that I would remove.
> - Under Documentation, the text "A brief introduction to limma", "limma
> User's Guide", "Reference Manual", and "NEWS" all have live links, but the
> links are degenerate because they just lead back to the same page.
> - Could the link for NEWS be HTML instead of Text?
> - Installation instructions are given twice, once under Installation and
> once under "Downloads".
> - Under Imports and Suggests, most package names come with live links, but
> the base packages do not. The 'splines' package is not part of the default
> R installation, so I wonder why it doesn't have a live link? Not that this
> is terribly important.
> - There's still no link to the code Browser, but I don't mind that. The
> git commands to access the source repository are far more important IMO.
> - There is in general much too much vertical white space on the page for
> my taste. I guess that's the current modern style to allow for thick thumbs
> and smart phone access, but to this old dinosaur the page looks rather
> sparse even on my iphone.
>
> BTW, it would be interesting to know some background information on why
> the home pages are completely redone like this. They seemed ok as they
> were, so I assume that it must have something to do with rebuilding the
> backend. What's happening? It would be interesting to know what the plans
> are.
>
> Regards
> Gordon
> https://gksmyth.github.io
>
>
> From: Sean Davis <seandavi using gmail.com<mailto:seandavi using gmail.com>>
> Sent: Thursday, 8 October 2026 1:13
> To: Gordon Smyth <gksmyth using outlook.com<mailto:gksmyth using outlook.com>>; Kern, Lori
> <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
> Subject: Re: Package home pages with >1 URL have broken links
>
> Thanks, Gordon and Oleksii, for taking the time to report. Take a look
> now. The tracking issue is here:
>
> https://github.com/seandavi/bioc-infrastructure/issues/101
>
> Sean
>
>
> From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Gordon
> Smyth <gksmyth using outlook.com<mailto:gksmyth using outlook.com>>
> Date: Wednesday, October 7, 2026 at 07:26
> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <
> bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
> Subject: Re: [Bioc-devel] Package home pages with >1 URL have broken links
> Thanks.
>
> Well, there's so many features that have been removed that I hesitate to
> list them. None are essential because the information can be found
> elsewhere, if one knows where to look, but then the home page itself is
> non-essential in that sense.
>
> Author ORCIDs are now rendered a plain text URLs instead of as links. The
> info bar at the top of the page giving package rank and time in Bioc is
> gone. Links to reference manual, NEWS, download report, and code browser
> are all gone.
>
> Cheers
> Gordon
>
> From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
> Sent: Wednesday, 7 October 2026 21:54
> To: Gordon Smyth <gksmyth using outlook.com<mailto:gksmyth using outlook.com>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
> Subject: Re: Package home pages with >1 URL have broken links
>
> I have captured the reported bug in an issue on the github.
>
> What other features are missing on the pages?  We can look to bring useful
> features back.
>
>
> Lori Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Gordon
> Smyth <gksmyth using outlook.com<mailto:gksmyth using outlook.com>>
> Sent: Wednesday, October 7, 2026 5:59 AM
> To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
> Subject: [Bioc-devel] Package home pages with >1 URL have broken links
>
> The example on page 4 of the "Writing R Extensions" manual shows that the
> URL field fo the DESCRIPTION file can contain a list of comma-separated
> URLs.
>
> Until very recently, the two URLs given in edgeR's DESCRIPTION file were
> rendered correctly on the edgeR home page. After the most recent website
> revision, though, the two URLs are now pasted together into one href URL,
> which of course fails if a users clicks on it.
>
> https://secure-web.cisco.com/17JGUUqMOZgzrDHGQ90yT7ElKp6QPbhssqJ2Qi6H5WYeJargL5Y8WOuoPOwUQUj6BH6Y6o3vNzAzGw1rbaxP-o7HLJEOUlTnuMHHrfmf8uS2ACGAphiF1G96zau5Sz14SbkEbj_JLaqUbpSHKK7zAjB_0ZsWzG0TuHqn1MLv59ec3Ija5CZ3ihjqWW1alh4eLs2yn-vmE8TLFX-68xALNVZ-2Jqt3527XLJu4ZXMlXvaxOfxvyVCrrncJIJOt4gT1pXdKZIsVUvhgm0Wrg2iSWWzqopYmjAlkxeKzYJFNZRbGHZH20FXUeeiCW2gJK52p/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.23%2Fbioc%2Fhtml%2FedgeR.html
>
> PS. I did much prefer the old home pages! A lot of features that I found
> useful have now been removed.
>
> Regards
> Gordon
>
> ---------------------------------------
> Professor Gordon K Smyth
> Lab Head, Tech Sciences Division, WEHI
> htttps://gksmyth.github.io<http://gksmyth.github.io>
>
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--
Thomas Girke, Ph.D.
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University of California
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