issue installing R packages using Neurodesk Docker

[kel-github]

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:

• installing source package ‘bayesplot’ ... package ‘bayesplot’ successfully unpacked and MD5 sums checked using staged installation R inst ** byte-compile and prepare package for lazy loading Error in element_line(linewidth = 0.3) : unused argument (linewidth = 0.3) Error: unable to load R code in package ‘bayesplot’ Execution halted ERROR: lazy loading failed for package ‘bayesplot’
• removing ‘/clusterdata/uqkgarn1/R/x86_64-pc-linux-gnu-library/4.0/bayesplot’ Warning in install.packages : installation of package ‘bayesplot’ had non-zero exit status

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:

• installing source package ‘tidyverse’ ... package ‘tidyverse’ successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading System has not been booted with systemd as init system (PID 1). Can't operate. Failed to connect to bus: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 help installing help indices copying figures building package indices installing vignettes testing if installed package can be loaded from temporary location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to connect to bus: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 testing if installed package can be loaded from final location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to connect to bus: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 ** testing if installed package keeps a record of temporary installation path
• DONE (tidyverse)

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

[stebo85]

Thank you for reporting this - I have a look at this

[stebo85]

So, right now, I think it's a bug in bayesplot and I am currenlty trying this workaround:

https://stackoverflow.com/questions/74546310/error-when-installing-brms-package-in-r-bayesplot-cannot-be-installed

[kel-github]

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:

https://stackoverflow.com/questions/74546310/error-when-installing-brms-package-in-r-bayesplot-cannot-be-installed

— Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/neurocommand/issues/133#issuecomment-1325776978, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXC34YUP73SIM5BCDSYEPLWJ2UMDANCNFSM6AAAAAASIRCS44 . 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.--

[stebo85]

yes, I ran into the same issue with devtools - I am currenlty building a new container where I can control the problematic dependencies

[stebo85]

ok, I got it to work and the new container is now building: https://github.com/NeuroDesk/neurocontainers/actions/runs/3536983328/jobs/5936550838

[stebo85]

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?

[kel-github]

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.--

[stebo85]

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 :)

[kel-github]

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: @.***>

[kel-github]

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.--

[stebo85]

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 :)

[kel-github]

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.--

[stebo85]

@kel-github - awesome :)