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

Thu Oct 8 17:11:55 CEST 2026

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 was generated and served by a single server (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'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 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>
Date: Thursday, October 8, 2026 at 08:08
To: Sean Davis <seandavi using gmail.com>; Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <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>
Sent: Thursday, 8 October 2026 1:13
To: Gordon Smyth <gksmyth using outlook.com>; Kern, Lori <Lori.Shepherd using RoswellPark.org>; 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> on behalf of Gordon Smyth <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 <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>; 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> on behalf of Gordon Smyth <gksmyth using outlook.com>
Sent: Wednesday, October 7, 2026 5:59 AM
To: bioc-devel using r-project.org <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

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