Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • 06:14
    betatim commented #768
  • 06:13

    betatim on master

    Add support for Julia 1.2.0 Merge pull request #768 from da… (compare)

  • 06:13
    betatim closed #768
  • 04:47
    davidanthoff opened #768
  • Aug 23 22:22
    rschmaelzle opened #767
  • Aug 23 21:15
    betatim closed #816
  • Aug 23 21:15
    betatim commented #816
  • Aug 23 20:48
    betatim commented #661
  • Aug 23 20:41
    betatim commented #1124
  • Aug 23 17:37
    sblack-usu opened #766
  • Aug 23 16:12
    choldgraf commented #1124
  • Aug 23 15:01
    jdblischak commented #661
  • Aug 23 07:41
    betatim commented #1124
  • Aug 23 06:27
    sgibson91 commented #1124
  • Aug 23 06:16
    sgibson91 commented #1124
  • Aug 23 05:43
    betatim labeled #765
  • Aug 23 05:43
    betatim labeled #765
  • Aug 23 05:43
    betatim labeled #765
  • Aug 23 05:43
    betatim unlabeled #765
  • Aug 23 05:43
    betatim labeled #765
SEOGI KANG
@sgkang
I was using environment.yml
to deploy
Wayne's Bioinformatics Code Portal
@fomightez
I have seen it with those . The one that was built to launch in past at google may work. Then the new one at OVH fails.
SEOGI KANG
@sgkang
Exactly
so, I was wondering if I have a handle that I can choose where to send ...
Wayne's Bioinformatics Code Portal
@fomightez
So you have some options. If you just need it to work now for yourself. you can specify the launch source.
Exactly.
Let me grab an example.
SEOGI KANG
@sgkang
Thanks a lot!
Wayne's Bioinformatics Code Portal
@fomightez
So you can go to directly to the google one using http://gke.mybinder.org and make your address using the form there.
Keep in mind this is not to be suggested beyond troubleshooting/workaround terms specifically by you because the operators of MyBinder want to divide up the traffic.
For OVH, just change gke to ovh.
Whoops. They generalized the form produced now.
I think if you just append the three letters yourself it will work.
Wayne's Bioinformatics Code Portal
@fomightez
Tested. That is what you do. Put those three letters followed by a period in front of the mybinder.org part of your url.
If you are experiencing what I saw, you'll see the old build will work but the newer one won't.
SEOGI KANG
@sgkang
I am deploying now. Will let you know :)
Wayne's Bioinformatics Code Portal
@fomightez
Not a 100% solution because if the old build gets erased then you won't get a working launch for now. However, conda may fix things soon and so sometimes you are better off using the one that works for now and waiting. If you want to play around with restoring it working at either place and keep the one that works, I suggest you make a new repo and try things there. That way you hang on to the one that works. For getting the new builds back to working it seems you usually are better off unpinning any versions. Unless unpinned is the one failing now. Then you are better off determining what version works and pinning to that and see if the new build works.
SEOGI KANG
@sgkang
Sounds good.
Tim Head
@betatim
do you have a link to your repository @sgkang ? that would help track this down. In general both clusters start from the same base docker image so should have the same things installed
for debugging builds i find it super useful to run https://repo2docker.readthedocs.io/ locally. faster turn around and easier to read logs. The master version of repo2docker is what runs on all clusters behind mybinder.org
SEOGI KANG
@sgkang
Hi @betatim and @fomightez, I tried both ovh and gke, my deployment seems not working.
The package causing issue is:
For simpegEM1D repo, binder is working well, however when I am pip installing simpegEM1D in simpeg-research/kang-2018-AEM I am having error that there is no fortran compiler
Tim Head
@betatim
ok, you need to install fortran inn your repository as well by listing it in a file called apt.txt like the original repository does. Take a look at https://repo2docker.readthedocs.io/en/latest/config_files.html#apt-txt-install-packages-with-apt-get for details on that config file and the others supported
SEOGI KANG
@sgkang
Thanks @betatim for pointing good resources. I'll follow those instructions.
SEOGI KANG
@sgkang
Ah, I got it working! Thanks a lot for both of @betatim and @fomightez !
flyzero
@lhc-tju
help me! urgent! How can I upload local files to jupyter notebook on Binder???
Anybody there? please help me! urgent! How can I upload local files to jupyter notebook on Binder?
Sarah Gibson
@sgibson91
The best way is to add a postBuild file to your repo that uses, e.g., wget to pull the files in https://mybinder.readthedocs.io/en/latest/config_files.html#postbuild-run-code-after-installing-the-environment
Arturo
@arturomoncadatorres
@sgibson91 A-ha, thanks! I corrected that, but I am still having some issues. I opened a thread in the Jupyter discourse https://discourse.jupyter.org/t/creating-a-shareable-bokeh-dashboard-with-binder/1962
Sarah Gibson
@sgibson91
Good idea @arturomoncadatorres :+1:
rschmaelzle
@rschmaelzle
Dear all, I have a question about binder and R. Specifically, I am trying to fire up this repository (https://github.com/nomcomm/ch2), which uses R. However, the command install.packages("bootnet") produces a non-zero exit - and i am unable to figure out a way to get this particular packages installed. From other machines (locally) I know that there were issues with the g++ compiler, but I am not an expert on that. Any ideas how I could get this working in binder? thank you and best r
Tim Head
@betatim
I'd run https://repo2docker.readthedocs.io/ locally so the logs are easier to read. See what the error message is and then google about bootnet and what kinds of dependencies it has. repo2docker is the tool that mybinder.org runs to build repos into images
we run master of repo2docker so i'd install directly from the repository as well to get all the latest updates
rschmaelzle
@rschmaelzle
i tried to do as you said (install repo2docker) and ran, but i got stuck early on
""Step 13/66 : RUN adduser --disabled-password --gecos "Default user" --uid ${NB_UID} ${NB_USER}
---> Running in 73e949fd47a1
adduser: Please enter a username matching the regular expression configured
via the NAME_REGEX[_SYSTEM] configuration variable. Use the `--force-badname'
option to relax this check or reconfigure NAME_REGEX. ""
Tim Head
@betatim
what does whoami print when you runn it inn the terminal you ran repo2docker?
rschmaelzle
@rschmaelzle
thanks, I had done that and found out there can be issues with "Ralf" (my old name), so i changed it to lowercase. I did, however, not properly restart and thus the error stayed. but now with lowercase name and restart, i can run repo2docker locally, which is an advance. i am , however, still digging into dependecies of bootnet, which i don't yet understand. I am listing a ton in the install.R file, but so far i couldn't get to the root of the problem.
Tim Head
@betatim
@rschmaelzle it might be a system dependency, so something like gfortran or some such? if you want to install a ubuntu package add a apt.txt file where you have your install.R
and on each lien in napt.txt list a package you want to install
a bit annoying that https://cran.r-project.org/web/packages/bootnet/index.html doesn't list what system dependencies you need :-/
if you have a moment could you file an issue in https://github.com/jupyter/repo2docker about your username containing uppercase letters, what operating system you use and the error message you got? then we have a record and someone could start working on fixing it
rschmaelzle
@rschmaelzle
will do, thank you, and will try the apt. All very helpful!
rschmaelzle
@rschmaelzle
i tried to work with apt, but I am getting deeper into the dependency-jungle. For instance, a prerequisite of bootnet is networktools, which needs heplots, which needs cars. So i trie to do install.packages("car"), but it tells me that “package ‘car’ is not available (for R version 3.4.4)”, which is curious since I had in the runtime.txt asked for the very latest version ("r-2019-07-05" ), which should be 3.6.5 (according to https://cran.r-project.org/doc/manuals/r-release/NEWS.pdf). So perhaps it could be that somehow repo2docker is installing a wrong R? In the updates during installations, the packages are being loaded from the r-2019-07-05-snapshots on "mran", but I couldn't find the part where the core R gets installted.
Sarah Gibson
@sgibson91
runtime.txt for R tells repo2docker which snapshot of MRAN to download the packages from, not the core R version. Unfortunately, it's not yet possible to pin the version of R that's installed 😔 You can follow this issue jupyter/repo2docker#661 on the topic
rschmaelzle
@rschmaelzle
thank you. that make sense - although it doesn't get the problem solved. Specifically, I've been trying to "install.packages("car")", and i get the response that it isn't available for R3.4.4. Is there any workaround that (the two options being: i) upgrade R to higher version- see link to issue on this ii) make "car" work with 3.4.4. Ideas still welcome .