Closed kel-github closed 1 year ago
Thank you for reporting this - I have a look at this
So, right now, I think it's a bug in bayesplot and I am currenlty trying this workaround:
Ah, sorry I didn't find that intel. I also started giving the solution a go but ran into issues when installing devtools. Let me know if it's helpful to keep pursuing or if it's better to hold off :)
On Thu, 24 Nov 2022 at 09:48, Steffen Bollmann @.***> wrote:
So, right now, I think it's a bug in bayesplot and I am currenlty trying this workaround:
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-- Kelly Garner, PhD, she/her Postdoctoral Research Fellow
Google Scholar https://scholar.google.co.uk/citations?user=nmeSlZkAAAAJ&hl=en ResearchGate https://www.researchgate.net/profile/Kelly_Garner
*UQ ALLY :: Supporting the diversity of sexuality, sex and gender at UQ.*
--I acknowledge the Traditional Owners of the land upon which I live and work. I pay my respects to Elders past, present and emerging.--
--I seek to maintain a good work-life balance. If you receive this email outside office hours then don’t feel you have to respond. Please expect the like from me.--
yes, I ran into the same issue with devtools - I am currenlty building a new container where I can control the problematic dependencies
ok, I got it to work and the new container is now building: https://github.com/NeuroDesk/neurocontainers/actions/runs/3536983328/jobs/5936550838
can you send me a little test code snippet for brms so I can test if it indeed works in the new container before releasing it?
This should work (I copied it from a tutorial):
library(brms)
bdata <- data.frame(y = c(1, 0, 1, 0, 0, 0, 1,
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb22-2>0, 0,
1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0))
fit <- brm(data = bdata,
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-2>
family = bernoulli,
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-3>
y ~ 0 + Intercept,
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-4>
prior = c(prior(normal(-0.400, 0.654),
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-5>
coef = Intercept)),
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-6>
iter = 1000,
<https://bayesball.github.io/BRMS/binomial-modeling.html#cb23-7>
refresh = 0)
On Thu, 24 Nov 2022 at 11:43, Steffen Bollmann @.***> wrote:
can you send me a little test code snippet for brms so I can test if it indeed works in the new container before releasing it?
— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocommand/issues/133#issuecomment-1325843128, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC34YDVYBNTAJWASEILJTWJ3B5XANCNFSM6AAAAAASIRCS44 . You are receiving this because you authored the thread.Message ID: @.***>
-- Kelly Garner, PhD, she/her Postdoctoral Research Fellow
Google Scholar https://scholar.google.co.uk/citations?user=nmeSlZkAAAAJ&hl=en ResearchGate https://www.researchgate.net/profile/Kelly_Garner
*UQ ALLY :: Supporting the diversity of sexuality, sex and gender at UQ.*
--I acknowledge the Traditional Owners of the land upon which I live and work. I pay my respects to Elders past, present and emerging.--
--I seek to maintain a good work-life balance. If you receive this email outside office hours then don’t feel you have to respond. Please expect the like from me.--
Dear @kel-github ,
I think I fixed it :) There is now a new container in version 2022.07.02
Can you test on the https://bhsydney.neurodesk.org instance if your example is nicely working?
If everything is working than @aswinnarayanan can update the containers on CVL@Wiener :)
Hey Steffen,
Woot! I'll test this tomorrow :)
On Wed, Nov 30, 2022, 10:05 Steffen Bollmann @.***> wrote:
Dear @kel-github https://github.com/kel-github ,
I think I fixed it :) There is now a new container in version 2022.07.02
Can you test on the https://bhsydney.neurodesk.org instance if your example is nicely working?
[image: image] https://user-images.githubusercontent.com/4021595/204667363-87ac5d36-ba64-48df-8843-a7ae347c94bb.png
If everything is working than @aswinnarayanan https://github.com/aswinnarayanan can update the containers on @.*** :)
— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocommand/issues/133#issuecomment-1331430641, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC342AETC6FE6GVQWTLYLWK2D2JANCNFSM6AAAAAASIRCS44 . You are receiving this because you were mentioned.Message ID: @.***>
Hey folks,
I followed the link above and then clicked on the neurodesktop icon. I then get this window/message: [image: image.png] Have I erred?
Kel
On Thu, 1 Dec 2022 at 18:29, Kelly Garner @.***> wrote:
Hey Steffen,
Woot! I'll test this tomorrow :)
On Wed, Nov 30, 2022, 10:05 Steffen Bollmann @.***> wrote:
Dear @kel-github https://github.com/kel-github ,
I think I fixed it :) There is now a new container in version 2022.07.02
Can you test on the https://bhsydney.neurodesk.org instance if your example is nicely working?
[image: image] https://user-images.githubusercontent.com/4021595/204667363-87ac5d36-ba64-48df-8843-a7ae347c94bb.png
If everything is working than @aswinnarayanan https://github.com/aswinnarayanan can update the containers on @.*** :)
— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocommand/issues/133#issuecomment-1331430641, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC342AETC6FE6GVQWTLYLWK2D2JANCNFSM6AAAAAASIRCS44 . You are receiving this because you were mentioned.Message ID: @.***>
-- Kelly Garner, PhD, she/her Postdoctoral Research Fellow
Google Scholar https://scholar.google.co.uk/citations?user=nmeSlZkAAAAJ&hl=en ResearchGate https://www.researchgate.net/profile/Kelly_Garner
*UQ ALLY :: Supporting the diversity of sexuality, sex and gender at UQ.*
--I acknowledge the Traditional Owners of the land upon which I live and work. I pay my respects to Elders past, present and emerging.--
--I seek to maintain a good work-life balance. If you receive this email outside office hours then don’t feel you have to respond. Please expect the like from me.--
Dear @kel-github,
That's a bug we are currently trying to fix :/ The workaround for now: Click on File -> Hub Control Panel -> Stop my server -> Start my server -> then it should work again :)
I tested the brms package with my code and it works like a charm - thanks! :)
On Fri, 2 Dec 2022 at 09:19, Steffen Bollmann @.***> wrote:
Dear @kel-github https://github.com/kel-github,
That's a bug we are currently trying to fix :/ The workaround for now: Click on File -> Hub Control Panel -> Stop my server -> Start my server -> then it should work again :)
— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocommand/issues/133#issuecomment-1334521293, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC342WSJ4SALFKNX4D7YDWLEQAXANCNFSM6AAAAAASIRCS44 . You are receiving this because you were mentioned.Message ID: @.***>
-- Kelly Garner, PhD, she/her Postdoctoral Research Fellow
Google Scholar https://scholar.google.co.uk/citations?user=nmeSlZkAAAAJ&hl=en ResearchGate https://www.researchgate.net/profile/Kelly_Garner
*UQ ALLY :: Supporting the diversity of sexuality, sex and gender at UQ.*
--I acknowledge the Traditional Owners of the land upon which I live and work. I pay my respects to Elders past, present and emerging.--
--I seek to maintain a good work-life balance. If you receive this email outside office hours then don’t feel you have to respond. Please expect the like from me.--
@kel-github - awesome :)
Hey team Neurodesk folks,
I am using Neurodesk on the CVL on Wiener. I am trying to install the package "brms" https://www.jstatsoft.org/article/view/v080i01
The steps I take are: i) open rstudioGUI 1.4.11 ii) install.packages("rstan") # this step works fine iii) install.packages("brms")
Which gives the error:
iv) element_line(linewidth=0.3) are ggplot2 functions. I therefore next tried installing the tidyverse package, which does install but with the following messages:
The downloaded source packages are in ‘/tmp/RtmpaL91BZ/downloaded_packages’
v) and when I seek to subsequently install brms, I get the same error as previously.
I've tried googling the error to see if others have run into the same issue, but am not finding much.
Any help/info is much appreciated! Kel