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

[Vincent Carey]

On Fri, Oct 9, 2026 at 2:48 PM Thomas Girke <thomas.girke using ucr.edu> wrote:

> Hi Sean and Vincent,
>
> Thank you for the detailed explanation. This information is important to
> me because I spent considerable time over the summer improving and
> extending several packages while relying on the existing Bioconductor build
> reports, but I just learned that they are failing.
>
> With the new release approaching, could you clarify whether these
> r-universe failures affect the package’s inclusion? Would it be possible to
> retain the package in the upcoming release based on the existing
> Bioconductor build results?
>

Hi Thomas,

As long as we have an indication that you will rectify the problem as soon
as time permits, package build/check failure at version
transition will not lead to removal from Bioconductor.


> I understand that these issues need to be resolved and I am committed to
> do so. My concern is the timing: faculty workloads vary considerably over
> the academic year, and October is particularly difficult for me to
> accommodate unexpected maintenance work on such short notice. Knowing what
> is required before the release, and what could be addressed afterward,
> would help me prioritize.
>
> Thanks again for your help and for recording the layout suggestion. Your
> example layout looks great.
>
> Best,
>
> Thomas
>
> On Fri, Oct 9, 2026 at 11:33 AM Sean Davis <seandavi using gmail.com> wrote:
>
>> 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>
>> 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> 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> 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 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
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> >
>> >
>> https://secure-web.cisco.com/1yf_b9k6QKTkqZtSQy2IjM79u_W10D2n9mlo4fTEVMcRohhnyzr9K-VsFL1Zq-_SK5x1fdzWCT_ef3flDefGHr6TF4p74u6hQAj1zSij0swUpiLpSSJZ_Fr6yObI727OHbMrN3dHSyQQb4Wt3qUNgSDiEdeFoAWK98rrxxxeoyHeT0ApqykWwzj0NjpXSpLt9O7TMmClpe7nPJAfoNGm0WpdUJJNNV_oeciYUy8RUPJ3qTpneWAsDUu8g1WFqsikbxlAvGG_KtcXb0_eA-YyC70HtfY4wJQOmC8_dL26Ob4_DJlu0yhMg5UmeWN7RXM0f/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information. If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > distribution, or use of this email message is prohibited. If you have
>> > received this message in error, please notify the sender immediately by
>> > e-mail and delete this email message from your computer. Thank you.
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>> --
>> Thomas Girke, Ph.D.
>> Professor of Bioinformatics
>> Director of High-Performance Computing Center (HPCC)
>> 1207F Genomics Building
>> University of California
>> Riverside, CA 92521
>>
>> E-mail: thomas.girke using ucr.edu
>> URL: https://girke.bioinformatics.ucr.edu
>> Phone/Cell/Text: 951-732-7072 <(951)%20732-7072>
>> Fax: 951-827-4437 <(951)%20827-4437>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> The information in this email is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> email contains patient information, please contact the Partners
>> Compliance HelpLine at http://www.partners.org/complianceline . If the
>> email was sent to you in error but does not contain patient information,
>> please contact the sender and properly dispose of the email.
>>
>>
>>
>> --
>> Thomas Girke, Ph.D.
>> Professor of Bioinformatics
>> Director of High-Performance Computing Center (HPCC)
>> 1207F Genomics Building
>> University of California
>> Riverside, CA 92521
>>
>> E-mail: thomas.girke using ucr.edu
>> URL: https://girke.bioinformatics.ucr.edu
>> Phone/Cell/Text: 951-732-7072 <(951)%20732-7072>
>> Fax: 951-827-4437 <(951)%20827-4437>
>>
>
>
> --
> Thomas Girke, Ph.D.
> Professor of Bioinformatics
> Director of High-Performance Computing Center (HPCC)
> 1207F Genomics Building
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke using ucr.edu
> URL: https://girke.bioinformatics.ucr.edu
> Phone/Cell/Text: 951-732-7072 <(951)%20732-7072>
> Fax: 951-827-4437 <(951)%20827-4437>
>

-- 
The information in this email is intended only for the p...{{dropped:15}}