Bioconductor
Some packages cannot be installed with BiocManager 3.22 despite the website stating it
When I tried to install PCAtools and CRISPRball (and a little earlier DESeq2) I get the message Warning message: package ‘XXX’ is not available for Bioconductor version '3.22'. These packages are not installed after this warning. The bioconductor for both packages tells they are available for BioC 3.22:
https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html https://bioconductor.org/packages/release/bioc/html/CRISPRball.html
I had to downgrade BioC to version 3.21 (BiocManager::install(version = "3.22", force = TRUE)) then install PCAtools and CRISPRball and then re-upgrade to BC 3.22. PCAtools and CRISPRball still show BioC 3.21 as source, but at least I can use them.
- Why does the website show "Bioconductor version: Release (3.22)" despite these are still only available for 3.21?
- Why do I need to downgrade to BioC 3.21 install the packages, then reinstall BioC 3.22 to use the packages with BioC 3.22 installed. Why can't BioC 3.22 not automaticall fall back to 3.21 for those packages?
CRISPRball depends on PCAtools which does not build in 3.22.
Error: processing vignette 'PCAtools.Rmd' failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building ‘PCAtools.Rmd’
Note the red dots on the right of https://bioconductor.org/checkResults/release/bioc-LATEST/CRISPRball/ . Binary package images are not produced. You do not describe the platform you are using. You have succeeded in installing packages in a non-standard way. "automatic fall back" to mix Bioconductor versions is not supported. Complications might arise from incompatibilities, depending on your platform. Perhaps you can contact the developers of ggalt and PCAtools to advise them to repair their packages, so that you can use them within 3.22.
ggalt was removed from CRAN in August: https://cran.r-project.org/package=ggalt
This breaks Bioconductor packages PCAtools and EnhancedVolcano (both maintained by Kevin Blighe), as well as any package that depends directly or indirectly on these two packages.
The PCAtools and EnhancedVolcano maintainer is being regularly reminded about this via the automatic build failure notifications sent at least once a week by the Bioconductor Build System. Unfortunately, Kevin has not taken any action to address this yet.
Maybe opening issues at https://github.com/kevinblighe/PCAtools/issues and https://github.com/kevinblighe/EnhancedVolcano/issues would help? Do you want to give it a try @gernophil ?
One more thing: both PCAtools and EnhancedVolcano only suggest ggalt, so getting rid of this dep should be easy.
Hi all, unfortunately, I virtually have no time anymore to maintain my packages. Jared (https://github.com/j-andrews7) is now maintaining EnhancedVolcano. Aaron Lun could perhaps assist for PCAtools (he is co-author) and submit a pull request.
Thanks @kevinblighe
Good to know about EnhancedVolcano.
For PCAtools, the maintainer would need to be changed to someone who is willing to actively maintain the package. Please discuss with @LTLA if he would be interested in that role. Note that the GitHub repo is out-of-sync with the repo at git.bioconductor.org so would need to be resynced before making any change.
Thanks again
FWIW, I am hoping I have fixed EnhancedVolcano just now. Installing from Github should work and hopefully the build for release is fine as well. A bit slapdash, but I'll start working on outstanding issues when I am not traveling.
I am also the developer of CRISPRball, so I need to address the issues there one way or another.
I don't really have much interest in maintaining PCAtools, I didn't contribute all that much to it anyway. If there is specific functionality that is required, I'm willing to consider migrating those useful bits to BiocSingular.
Understood - you are already involved in a lot, Aaron. @hpages , can you confirm the fix that's needed to get PCAtools re-building?
"Note that the GitHub repo is out-of-sync with the repo at git.bioconductor.org so would need to be resynced before making any change." Unsure why this is the case, but I'll check.
It just needs ggalt removed from suggests.
On Sat, Dec 6, 2025, 4:44 AM Kevin Blighe @.***> wrote:
kevinblighe left a comment (Bioconductor/BiocManager#203) https://github.com/Bioconductor/BiocManager/issues/203#issuecomment-3620181935
Understood - you are already involved in a lot, Aaron. @hpages https://github.com/hpages , can you confirm the fix that's needed to get PCAtools re-building?
"Note that the GitHub repo is out-of-sync with the repo at git.bioconductor.org http://git.bioconductor.org so would need to be resynced before making any change." Unsure why this is the case, but I'll check.
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/BiocManager/issues/203#issuecomment-3620181935, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACOAQNHJT4HTXGCXLG3V6E34ALFRDAVCNFSM6AAAAACNRXIW42VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMRQGE4DCOJTGU . You are receiving this because you commented.Message ID: @.***>
Dear @hpages @LiNk-NY @LTLA @j-andrews7 (cc: @hadley),
I have no time to maintain this package further - please set it for deprecation from Bioconductor.
Thank you and kind regards, Kevin
@kevinblighe I guess I can take on PCAtools as well, otherwise I am going to be implementing the same stuff so as not to break my packages.
If you're okay with this, I may just make a fork of it to work from so you don't have to deal with giving me permissions and all. Think it ended up being more trouble than it was worth with EnhancedVolcano.
Let me know if you're amenable, cheers.
Dear Jared @j-andrews7, I really appreciate your effort here. THANK YOU.
However, I am now requesting that both EnhancedVolcano and PCAtools are deprecated from Bioconductor.
Kind regards, Kevin
That is unfortunate, particularly given both of these packages are released under GPL-3, heavily used, and I am willing to maintain them.
That said, that is your choice. Best of luck with future endeavors.
I agree that this is unfortunate.
We will deprecate EnhancedVolcano and PCAtools in BioC devel.
However, the original issue still persists and can only be addressed by fixing PCAtools in the release (BioC 3.22). The fact that users of the current Bioconductor release cannot install the package or any of its reverse deps is not acceptable.
ggalt is only used in PCAtools::biplot() when encircle is set to TRUE, so a quick and dirty fix would be to simply fail with a "sorry, no longer supported" kind of message when the user tries to use this option, and to remove ggalt from Suggests. At least that would allow BioC 3.22 users to install PCAtools again as well as its reverse deps (CRISPRball and regionalpcs). I'll make this change to the RELEASE_3_22 branch of PCAtools.
@kevinblighe I guess I can take on PCAtools as well, otherwise I am going to be implementing the same stuff so as not to break my packages.
If you're okay with this, I may just make a fork of it to work from so you don't have to deal with giving me permissions and all. Think it ended up being more trouble than it was worth with EnhancedVolcano.
Let me know if you're amenable, cheers.
I missed this - sorry. @j-andrews7 @hpages
Can you confirm that you are going to take this on? If 'yes', then they will not need to be deprecated.
I will add you as Collaborator to both repositories.
Yes, I will take them on. Thanks Kevin, I appreciate it.
On Fri, Jan 2, 2026, 8:33 AM Kevin Blighe @.***> wrote:
kevinblighe left a comment (Bioconductor/BiocManager#203) https://github.com/Bioconductor/BiocManager/issues/203#issuecomment-3705367445
@kevinblighe https://github.com/kevinblighe I guess I can take on PCAtools as well, otherwise I am going to be implementing the same stuff so as not to break my packages.
If you're okay with this, I may just make a fork of it to work from so you don't have to deal with giving me permissions and all. Think it ended up being more trouble than it was worth with EnhancedVolcano.
Let me know if you're amenable, cheers.
I missed this - sorry. @j-andrews7 https://github.com/j-andrews7 @hpages https://github.com/hpages
Can you confirm that you are going to take this on? If 'yes', then they will not need to be deprecated.
I will add you as Collaborator to both repositories.
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For posterity, this should be fixed for PCAtools as well now in both release and devel. Next build should hopefully clear all of this up for good.