***rekado_ is now known as rekado
<rekado>zimoun: I guess we should upgrade R to 4.1.0 first and then do the Bioconductor upgrade. <zimoun>rekado: yes. I should submit the remaining Bioconductor move today, I hope. <zimoun>and yes, I agree R should be updated first, before updating Bioconductot <rekado>I feel like I should continue work on the GWL <rekado>so far there was no feedback on the DRMAA branch <rekado>so I guess I’ll just clean it up and merge it. <zimoun>ah, talking about guile-drmaa, I had a discussion with Yann from CCIPL (Nantes) using Guix on their cluster. And an potential user of guile-drmaa should be Cuirass… but not on the list of mothacehe’s stuff, yet. :-) <zimoun>I had not had the time to checkout out the branch and test it. <zimoun>So merging it seems the best move. :-) <civodul>we need training sessions! hint hint ;-) <zimoun>civodul: yeah, I spent part of this morning to do that :-) <zimoun>Almost full switch from one Conda user. ;-) Ah worse, I discovered that people are misusing Conda… the situation is even worse that I thought. ;-) <zimoun>well, I have scabality issues though. :-) *civodul .oO( how is "misusing Conda" different from "using Conda"? ) <civodul>yeah i think setting up sessions together with rekado, PurpleSym et al. would be sweet <zimoun>PurpleSym: it is related to the (private) email 86im40vycp.fsf@gmail.com. :-) <civodul>PurpleSym: introductions to Guix for reproducible science/HPC, with hands-on getting-started sessions <civodul>i think several of us did that already at work <zimoun>somehow, people are using Conda, modulefiles etc. and they need help to switch. New “paradigm”, how do I do X with Guix? etc. At the end-user level, sysadmin level, etc. <civodul>joining forces and reaching out to others could be fruitful in many ways <PurpleSym>Ah, I see. Yeah, I’ve been silent, because there’s really no-one here, who would use Guix without a big layer of GUI. <PurpleSym>Our sysadmins are moving to Docker, as far as I know -.- <civodul>right, you've developed a nice UI layer on top of Guix, so i suppose you're in a somewhat different situation <PurpleSym>We’re hiding all the nice things about guix from the user :) <civodul>perhaps that UI could also be part of a training session though, dunno <civodul>they don't even get to see parens, how sad! <PurpleSym>They don’t even know they’re using GNU Linux ;) <PurpleSym>Seriously though, the UI is being used to teach students and there’s an upcoming workshop. But we’re simply on a different level here, trying to convince people to use R instead of some proprietary statistics tool. <zimoun>PurpleSym, here it is the same. I had to explain with details why SAS is not an option; for a better or a worse, the only argument which had “worked” was money: who will pay the license? :-) <rekado>I’ve seen a number of people abandon Guix as soon as it became inconvenient <zimoun>for instance, I would like to setup something as your solution. But I am running out of time. Therefore, I would be an attendee for a training, not about using it but about help in setuping. :-) <rekado>e.g. some tool is provided via Conda and the developers of that tool recommend Conda <rekado>I don’t see much value in converting users like that. <rekado>on the other hand: one of my colleagues has finally decided to go all in with Guix <PurpleSym>zimoun: Yep, money is pretty much the only argument to use R here too. Free software? Nobody cares. <rekado>this is the result of years of sharing Guix blog posts, demonstrating reproducibility benefits, and a couple of comments about “solved problem” whenever an R upgrade would wreck their projects. <rekado>luckily people here are rather intolerant of proprietary software <rekado>they will use proprietary software in a pinch, but there’s a collective groan when a pipeline depends on proprietary tools, and an unwillingness to use it. <zimoun>what I find interesting is that using “open source” (transparency about the source) *is* the only scientific method. Otherwise, the name is not Science but cooking, artisans, etc. <civodul>rekado: yeah, i've seen that too, people who just want to get something installed, so they pick whichever tool gets them to that point <rekado>there’s a little grey area, though. There are many tools that are “academic use only”. <rekado>that’s transparent, but restrictive <civodul>would an editor be able to run the "academic-use only" software? probably not <rekado>civodul: what’s unfortunate about these users is that they attempt to mix and match — and that usually won’t work well. <civodul>i think we need to do more outreach and more reflection/self-criticism <rekado>my guix.install procedure for R was the final motivator for my colleague to make the switch <rekado>I think we need a little more of that kind of thing. To bridge the last few gaps between tools. <rekado>even though they are not strictly part of Guix <civodul>"my" new intern started this Monday! <rekado>we’re working on a new PiGx pipeline, and this time every developer uses Guix (we have a manifest with inferiors to all have the exact same environment). <zimoun>yes, I agre. On wednesday, explaining Guix a colleague said me, «I need more flexibility at the R level» and I said, yeah something exists but I was unable to reach guix.install. Well, I agree that “bridge” are missing to better fit how people concretly works. <rekado>civodul: one of the biggest problems in my experience is the glibc ABI incompatibility. There doesn’t seem to be much we can do about it. <rekado>zimoun: I want to add it to our r-minimal package. <rekado>bold move, but … that’s the best place for it, I think. <zimoun>And this same colleague installed Guix on RedHat… then “guix import cran -a bioconductor” failed (leading to a discussion on #guix about certificates ;-)), then “guix install nss-certs” failed requiring --fallback, then even with it is still failing for mysterious reasons I had solved yet. Well, if I am not at the next door, then they abandon Guix. <rekado>I often find myself posting the Application Setup URL <rekado>perhaps there’s something we could automate. ***zimoun` is now known as zimoun
<civodul>rekado: you mean the glibc locale incompatibility? or the NSS? <rekado>no, I mean the fact that mixing Guix things with non-Guix things is not possible. <rekado>Guix is completely separate from the system, which is both great and annoying :) <rekado>I’ve had a lot of problems switching to Rstudio from Guix because even with my changes to support multiple R versions I can’t let users select the system R. <rekado>this is, of course, a problem with Rstudio’s design (because they link with libR.so instead of simply spawning an R process like ESS) <rekado>I was wondering if … a “leaky build mode” could ever be made to work. <rekado>for Rstudio I’d have to build one component (the one responsible for launching the user session) in two variants: one using the system’s toolchain, and another one using the Guix toolchain. <rekado>whatever — this is just an example of the general problem, which is that the hard ABI-incompatibility boundary makes Guix rather special among package managers. <zimoun>does this “leaky build mode” could help for icc? <civodul>i agree that can be annoying, but that's also a strong point, depending on how you look at it ***Server sets mode: +nt
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<zimoun`>Tomorrow, I will start the Bioconductor update if you have not yet. <civodul>so we had: texlive-texmf-20180414/share/texmf-dist/fonts/enc/dvips/fira/fir_7gpamp.enc <civodul>is terrible, i'm stuck on texlive-2018, and the big one, even <rekado>the fira package looks like the most likely candidate. <rekado>e.g. texmf-dist/fonts/enc/dvips/fira/fir_7gskcl.enc <civodul>it's surprising that it's not in the big texlive package <civodul>"guix import texlive fira" produces something though