Accessible cluster for running Biogeobears

[Peter Löwenberg Neto]

Dear all,

Four weeks ago I started to install all the packages needed to run BioGeoBears in a HPC-cluster (slurm) at my university. 

During the installation of a devtools dependency (fs package) an error  (fatal error sys/eventfd.h no such file or directory). 

The HPC manager told me there is an incompatibility with the OS and I will not be able to install BioGeoBears.

Two questions:

1) Does it make sense (the incompatibility)?

2) Does anyone know any HPC cluster that I can run a BioGeoBears analysis?  

Best regards,

Peter

[Nick Matzke]

Hi -- well, the only reason you need devtools is to install BioGeoBEARS from GitHub, so an alternate method might be to download the package manually from GitHub via the website, and install it manually.

Cheers,

Nick

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[peter.lowe...@gmail.com]

Hello Nick,

 

1) I’ve downloaded the BioGeoBEARS code at your github page as a .zip file and then I have converted to .taz.gz.

 

 

2) I tried to install manually today and I got this ERROR:

dependencies ‘phytools’, ‘FD’, ‘devtools’ are not available for package ‘BioGeoBEARS’

 

 

Thanks for your attention.

 

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/CAJdu7BAfe5F%3D3aTtvrzbWd%2BVQ3oqzd-2%3Dvam8yw99iJtcNR%2B-w%40mail.gmail.com.

[joel...@gmail.com]

Hi Peter,

I have an idea for a possible work-around. Are you able to use conda on your cluster?

If so, there is a conda package for R with devtools installed.

You could create a conda environment like this: conda create -n devtools -c conda-forge r-devtools

[joel...@gmail.com]

(...sorry, I wasn't done yet, but somehow managed to hit "Post message")

After you create the environment, activate it with: conda activate devtools

From there, enter the R console with "R", then run devtools::install_github("nmatzke/BioGeoBEARS")

That worked for me. If you use this method, you will need to activate the conda environment each time to use BioGeoBEARS, but it should avoid having to request your admin to install various dependencies.

Best,

Joel

[Nick Matzke]

On Fri, Jun 18, 2021 at 1:20 AM <peter.lowe...@gmail.com> wrote:

Hello Nick,

 

1) I’ve downloaded the BioGeoBEARS code at your github page as a .zip file and then I have converted to .taz.gz.

 

 

2) I tried to install manually today and I got this ERROR:

dependencies ‘phytools’, ‘FD’, ‘devtools’ are not available for package ‘BioGeoBEARS’

Others have answered on devtools, but phytools and FD are standard R packages on CRAN, so just install them in the usual way, then re-try BioGeoBEARS.  Repeat as needed if other dependencies come up.

Cheers,

Nick

 

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/002a01d7637b%2494a97620%24bdfc6260%24%40gmail.com.

[Peter Löwenberg Neto]

Dear Joel,

thanks for sharing your method.

I followed just what you described and I got this when trying to run R from the conda env (devtools):

Peter

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[joel...@gmail.com]

It looks like glibc also is available through conda: https://anaconda.org/rmg/glibc

You should be able to add it to your environment with conda install -c rmg glibc

Or perhaps glibc is something you will need to ask your admin to install for you.

[Peter Löwenberg Neto]

Joel, Am I missing something?

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/1e0f2b6f-60c7-4803-998a-26921197910en%40googlegroups.com.

[Nick Matzke]

Hi -- try 

library(devtools)

...before devtools:install_github etc.

Cheers,

Nick

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/CAGEumx3adRgNpu9a3ArN4GjsJOS3SbNo1ogoDeSxYQrAE7h17Q%40mail.gmail.com.

[Peter Löwenberg Neto]

Hello Nick, Joel and others,

library(devtools) did not work in conda env.

 

I am putting aside "the conda solution" (though I think it is a very nice idea) because the cluster manager decided to help me and installed the BioGeoBEARS.

Now I am trying to check if it is all right.

I could load all needed libraries and assemble the model (Tutorial, Psychotria, unconstrained).

But when I tried to run, I got this message:

Could you help me to solve this issue?

Thank you for your attention.

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/CAJdu7BDMXkZzHF5MtyzDLesHXo-5c1RHMVwuym4RBArmdcSa4w%40mail.gmail.com.

[Nick Matzke]

Hi -- this "Error in assign("last.warning..." error message is apparently due to the new version of R4.1 on some operating systems, it has just been fixed on GitHub, so re-install from GitHub.

See: 

https://groups.google.com/g/biogeobears/c/IzQaPLQp2AM

...for explanation.

Cheers,

Nick

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/CAGEumx2YT47Ngt%3DUr3UYQSzekWMAjhZxMPMWVy0pKU7KwMh%2BLA%40mail.gmail.com.

[peter.lowe...@gmail.com]

Hello Nick,

 

I am going to ask the cluster manager to reinstall the package.

Thank you for your attention.

 

Peter

 

De: bioge...@googlegroups.com <bioge...@googlegroups.com> Em nome de Nick Matzke
Enviada em: sábado, 19 de junho de 2021 18:38
Para: bioge...@googlegroups.com
Assunto: Re: [BioGeoBEARS] Accessible cluster for running Biogeobears

 

Hi -- this "Error in assign("last.warning..." error message is apparently due to the new version of R4.1 on some operating systems, it has just been fixed on GitHub, so re-install from GitHub.

 

See: 

 

https://groups.google.com/g/biogeobears/c/IzQaPLQp2AM

 

...for explanation.

 

Cheers,

Nick

On Sat, Jun 19, 2021 at 6:20 AM Peter Löwenberg Neto <peter.lowe...@gmail.com> wrote:

Hello Nick, Joel and others,

 

library(devtools) did not work in conda env.

 

 

I am putting aside "the conda solution" (though I think it is a very nice idea) because the cluster manager decided to help me and installed the BioGeoBEARS.

 

Now I am trying to check if it is all right.

I could load all needed libraries and assemble the model (Tutorial, Psychotria, unconstrained).

 

But when I tried to run, I got this message:

Could you help me to solve this issue?

 

Thank you for your attention.

 

Peter

Em qui., 17 de jun. de 2021 às 22:06, Nick Matzke <nickmat...@gmail.com> escreveu:

Hi -- try 

 

library(devtools)

 

...before devtools:install_github etc.

 

Cheers,

Nick

 

On Fri, Jun 18, 2021 at 12:56 PM Peter Löwenberg Neto <peter.lowe...@gmail.com> wrote:

Joel, Am I missing something?

Em qui., 17 de jun. de 2021 às 21:22, joel...@gmail.com <joel...@gmail.com> escreveu:

It looks like glibc also is available through conda: https://anaconda.org/rmg/glibc

You should be able to add it to your environment with conda install -c rmg glibc

Or perhaps glibc is something you will need to ask your admin to install for you.

On Friday, June 18, 2021 at 8:52:02 AM UTC+9 peter.lowe...@gmail.com wrote:

Dear Joel,

 

thanks for sharing your method.

 

I followed just what you described and I got this when trying to run R from the conda env (devtools):

 

 

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/biogeobears/CAJdu7BCBVjKfHftjW_2QsMYrguo5j-krC9qoMUY%2BRDDxZQ%3DLZg%40mail.gmail.com.