fidzu : debian

A new maintenance release 0.4.27 of RProtoBuf arrived on CRAN today. RProtoBuf provides R with bindings for the Google Protocol Buffers ("ProtoBuf") data encoding and serialization library used and released by Google, and deployed very widely in numerous projects as a language and operating-system agnostic protocol. The new release is also already as a binary via r2u.

This release adjusts to a change upstream. Luca Billi noticed that upstream removed some fields from FieldDescriptor, filed and issue and followed up with a spotless PR. No other changes.

The following section from the NEWS.Rd file has all details and links.

Changes in RProtoBuf version 0.4.27 (2026-04-26)

• Adjust to FieldDescriptor API changes in ProtoBuf 3.4 (Luca Billi in #114 fixing #113)

Thanks to my CRANberries, there is a diff to the previous release. The RProtoBuf page has copies of the (older) package vignette, the 'quick' overview vignette, and the pre-print of our JSS paper. Questions, comments etc should go to the GitHub issue tracker off the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. If you like this or other open-source work I do, you can sponsor me at GitHub. You can also sponsor my Tour de Shore 2026 ride in support of the Maywood Fine Arts Center.

26 Apr 2026 6:07pm GMT

The SpacemiT K1 is a rather interesting RISC-V SoC, found for instance on boards like the Banana Pi BPI-F3 board. It's one of those platforms that looked promising on paper, but took a bit of time before things really started to move upstream. Things have clearly accelerated over the last few months.

Linux 7.0 brings, among other things PCIe support, making the board quite capable as a development board. SD card, CPU thermal sensor and cpufreq support are already in the pipe.

Unfortunately the situation is less advanced on the firmware side. There is only very basic support for the SpacemiT K1 in U-Boot for the second stage, and initial SPL support has been posted on the mailing list, but has not yet been merged. In practice, this means you still have to rely on the vendor U-Boot, which is based on the rather old 2022.10 release.

On the other hand, OpenSBI does have upstream support for the SpacemiT K1, however it is not compatible with the vendor U-Boot, mostly due to device tree differences.

This can be addressed by applying a few patches to the vendor U-Boot, which I have published in a git tree in the k1-bl-v2.2.y-opensbi branch (technically this can also be handled on the OpenSBI side, but I prefer using a vanilla upstream OpenSBI version). The first two patches update the configuration to get closer to the upstream U-Boot defaults, and to enable some configuration options for the Milk-V Jupiter board, which stores its firmware in SPI NOR flash, instead of eMMC for the Banana Pi BPI-F3. The following patches update the device tree by adding extra compatible entries to several devices, as expected by the upstream kernel and OpenSBI (thanks to Troy Mitchell for the hint about the UART change) and update the CPU riscv,isa properties. Finally an additional patch adds the SpacemiT P1 PMIC to the device tree, which is required for the OpenSBI reboot patchset I recently posted (this is currently done only for the Banana Pi BPI-F3 and Milk-V Jupiter boards, but extending it to other boards should be straightforward).

Building this U-Boot version is as simple as running this command in the source directory:

make k1_defconfig && make

On a Banana Pi BPI-F3 board, the resulting U-Boot can be flashed with:

echo 0 > /sys/block/mmcblk0boot0/force_ro
dd if=FSBL.bin of=/dev/mmcblk0boot0 bs=512 seek=1
dd if=u-boot.itb of=/dev/mmcblk0p1

Building upstream OpenSBI is also fairly simple, and can be done by running this command in the source directory:

make PLATFORM=generic

On a Banana Pi BPI-F3 board, the resulting OpenSBI can be flashed with:

dd if=fw_dynamic.itb of=/dev/mmcblk0p2

Note that the vendor U-Boot version is patched to install OpenSBI in a separate partition instead of embedding, as the upstream U-Boot does. While this works well on the Banana Pi BPI-F3, the corresponding partition in the Milk-V Jupiter SPI NOR flash is too small for the upstream OpenSBI version, and can't be easily resized without breaking compatibility. To address this, the branch k1-bl-v2.2.y-opensbi-embedded contains an additional patch (a bit hackish I admit) to somehow restore the upstream approach. The build process remains simple, first build OpenSBI with the following command:

make PLATFORM=generic

Then build U-Boot, specifying the patch to the just built OpenSBI firmware:

make k1_defconfig && make OPENSBI=/path/to/opensbi/build/platform/generic/firmware/fw_dynamic.bin

On a Milk-V Jupiter board, the resulting combined U-Boot/OpenSBI can be flashed with:

modprobe mdtblock
dd bs=4k if=FSBL.bin of=/dev/mtdblock2
dd bs=4k if=u-boot.itb of=/dev/mtdblock5

This combined U-Boot/OpenSBI can also be used on a Banana Pi BPI-F3, using the same flashing procedure as above, while skipping the OpenSBI part (although running it won't cause any issue, it will simply be unused).

All of this is admittedly a bit hackish, but enabling the use of upstream OpenSBI is already one step forward. Hopefully, in a few months, we will be able to rely entirely on upstream U-Boot.

26 Apr 2026 12:13pm GMT

Review: The Genocidal Healer, by James White

The Genocidal Healer is the eighth book in James White's medical science fiction series about the Sector General hospital. As with the rest of the series, detailed memory of the previous books is not required and the books could be read out of order if you didn't mind spoilers.

I read this as part of the Orb General Practice omnibus.

Surgeon-Captain Lioren is a Tarlan doctor who was in charge of the medical response to a newly-discovered civilization. The aliens were suffering from an apparently universal plague and an ongoing vicious war waged entirely through hand-to-hand combat, putting them on the edge of extinction. Lioren rushed the distribution of a possible cure against the advice of the doctors working on developing it, with catastrophic results. As The Genocidal Healer opens, Lioren is insisting on a court-martial in the hope of receiving the sentence it believes it deserves and was denied: death.

(It pronouns are the convention in the Sector General series for all alien races and formal discussions, because even someone prone to bouts of gender essentialism such as White understood the need for avoiding gender assumptions in a science fiction medical context.)

Predictably, both Sector General and the Monitor Corps that technically runs the hospital are flatly unwilling to execute Lioren. Instead, he is assigned as a new apprentice in the psychology department under the legendary O'Mara, where he is ordered to investigate the psychological fitness of a senior doctor named Seldal. This leads him to talk to Seldal's patients, which in turn leads to a challenging set of ethical dilemmas.

The first five chapters (and more than sixty pages) are the story of Lioren's trial and a recounting of the events on Cromsag. The series is full of medical and cultural puzzles like this, and usually I like them, but I thought this one was less successful. We know the vague (and horrible) outline of the ending in advance, and the massive simplification and artificial universality that is required to make this puzzle work is particularly blatant. A universally infectious disease is more of a fiction plot than a believable biological concept, and the number of failures of communication, analysis, and misunderstanding that have to line up to create White's predetermined outcome were a bit much for me.

Once the story gets past that and into Lioren's psychological work, the novel improves. Lioren is guilt-ridden and irrational, but also rather arrogant about his guilt and his concepts of professional responsibility in a way that I think mostly worked. Most of the novel consists of Lioren slowly discovering that people like him and enjoy talking to him, much to his bafflement. In that, it has the gentle kindness and sense of universal basic decency that is characteristic of this series. There are, of course, medical puzzles to solve, although this time they are primarily psychological in nature. Various characters from previous books make an appearance, but White re-explains their background in sufficient detail that you don't need to remember (or have read) those previous books.

There are a lot of similarities between this book and the previous one, Code Blue-Emergency. Both feature nonhuman viewpoint protagonists and amusing descriptions of human facial expressions from an alien perspective. Both feature protagonists with overly rigid ethical structures that partly clash with the generally human policies of Sector General. The Genocidal Healer is a bit more subtle and nuanced, although a lot of Lioren's psychological evaluation rests on an ethical difference that I found somewhat unbelievable. This book, though, tackles a subject the previous book did not: religion. The treatment isn't horrible, but I have some complaints.

My primary issue is that Lioren, who starts as an atheist, does extensive research into religion to help a patient and then starts making statements summarizing the religions beliefs of the majority of known species that are just... Christianity. As someone raised Christian, I recognized it immediately as the sort of abstracted Christianity that Christians claim is universal while completely ignoring the opinions of the adherents of any other religion.

Key components of this majority galactic religious pattern, according to Lioren, include an omnipotent and omnibenevolent creator god, a religious figure who preaches forgiveness and mercy and is persecuted, and emphasis on redemption. This simply is not some abstract universal religion. This is just Christianity in disguise. Even in religions that have some of those elements in their traditions, they do not get the same emphasis and are not handled the way that Lioren describes them. I therefore found Lioren's extended discussions of religion rather annoying, since he kept claiming as relatively universal principles beliefs that are not even held by the majority of religious adherents on Earth, let alone a wildly varying collection of alien races with entirely different biology and societal constructions. It caused a lot of problems for my suspension of disbelief, on top of the annoyance at this repetition of, frankly, Christian propaganda.

Lioren goes, from that research, into theodicy (the problem of evil). The interesting part of this is White's earnest portrayal of a doctor's approach to societal problems: a desire to find workarounds and patches and fixes for anything that makes people unhappy, whether medical or social. It makes sense, given the horrible biologic hands that some of the aliens in this series have been dealt, that they would question the idea of a benevolent god, so this philosophical digression is justified in that sense. But you might guess that a mid-list science fiction author is not going to say something new about one of the oldest problems in Christianity, and indeed he does not. Lioren arrives at the standard handwaving about the unknowability of divine intent, which I found tedious to read but at least not fatal to the plot.

White, thankfully, doesn't take the religious material too far. The characters recognize how sensitive of an issue religion is in a hospital, Lioren never adopts religion fully, and the resolution of the plot is as much biological as philosophical. White is going somewhere with the introduction of religion, and although some of the path there annoyed me, I think the destination worked. White was from Northern Ireland, and therefore well aware of the drawbacks of religion, and he abhorred violence (hence Sector General as a setting), so the reader is in better hands with him than with most authors who might attempt this plot.

I think I know a bit too much about religion to be the best audience for this entry in the series, and I'm not sure the introductory five chapters quite worked. But as with all of the other books in the series, this kept me turning the pages and I'm glad I read it. The Genocidal Healer probably isn't worth seeking out unless you're reading the whole series, but if you're enjoying the rest of the series, you'll probably like this too.

Followed by The Galactic Gourmet.

Rating: 6 out of 10

25 Apr 2026 4:44am GMT