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<zimoun>rekado_: Bioconductor 3.12 is released. Do you think it is affordable to try to upgrade before the Guix release? <rekado_>what I recommend (and usually do myself) is to upgrade all Bioconductor packages first, without upgrading the release number <rekado_>then upgrade the release number and do the whole thing again. <rekado_>so that the CI gets to fetch the latest tarballs <zimoun>do you upgrade manually all the Bioconductor packages? <rekado_>I do ‘./pre-inst-env guix refresh -t bioconductor -u’ <rekado_>I then review the list of proposed changes <rekado_>(like adding r-knitr to a dependency of r-knitr) <rekado_>and others are optional inputs that it tells me to remove <rekado_>once all proposals have been checked I transform the output to a list of packages and I build them all. <rekado_>if packages are affected that contained JavaScript files I check that their bundled JS is still removed and rebuilt from sources. <rekado_>some upgrades I undo, because I know that they are too difficult to complete <rekado_>e.g. r-mosaic, which depends on r-leaflet, which contains massive amounts of minified JavaScript for which there are no easily accessible sources. <rekado_>there’s another Bioconductor package that now requires keras or a similar ML framework, which we don’t have. <rekado_>unfortunately, I know now that I can’t commit that much time <rekado_>but it’s really pretty straight-forward <zimoun>thanks for all the explanations. I will try to go for it. Well, few distractions in Paris (curfew) and soon lockdown, again! The variable will be the extra-work at work because this again lockdown… <rekado_>I’ve not been paying attention to any of tis <rekado_>I don’t even know what the current status is in Berlin <rekado_>but I decided to work an hour every night on apple tree wood that I cut from a tree in our garden <rekado_>if only I never needed to return to work! <rekado_>the chunks of time are not enough for concentrated computer work, but they are enough for brute force: sawing wood, breaking off bark, carving, etc <rekado_>weirdly enough, in all my lethargy and lack of progress in the Guix world I feel oddly successful <rekado_>even though all I’ve done so far is strip bark off a log of wood and deep fry (!) a chunk of it <rekado_>but back to Guix: we can do this together <rekado_>push all of this to a new wip-r branch <rekado_>then rebase onto master, let ci build it, then merge <zimoun>yeah I was fine the previous lockdown (based on Millau south of France). Even if I was recovering from bad sport’s accident… Right arm dysfunctionnal. Sweating to recover. Well I understand your point. :-) Whatever! <rekado_>my right wrist is pretty useless these months <rekado_>I don’t recommend carrying a baby needlessly <rekado_>they are portable humans, but only barely so <zimoun>yeah the wip-r seems the good thing to do. If the merge can happen before the release, fine. Otherwise, it will be later and it will be fine too. :-) <zimoun>hehe! When in Nov. would you be back to “office”? <zimoun>I gave a look to D4. It could be interesting. I do not know how easy it would be easy to package, because of Rust. <rekado_>“Python-compatible language” smells like trouble <rekado_>I think this may come back to bite them one day <zimoun>rekado_: do you commit the upgrade package by package or all at once? <rekado_>for packages with lots of changes you may need to edit the commit message to reflow it <zimoun>thanks, I was not aware about ./etc/committer.scm <rekado_>I wrote it because I got tired of how slow magit gets when there are tens of changes, and I need to select one hunk at a time <rekado_>one caveat: committer.scm will not do the right thing when the diff contains new packages <rekado_>it figures out the changed inputs and records them in the expected format <rekado_>doesn’t do anything for other changes and it gets confused when there are completely new packages in the diff <rekado_>other than that it’s really well-suited for CRAN/Bioconductor upgrades <zimoun>yeah all the only version+hash changes. It already saves a lot of time. <rekado_>I’m not proud of the implementation, because it’s rather crude