Open rdewald opened 3 years ago
mtopaz
commented
3 years ago Perfect- thanks so much for fixing this Richard! See if I can be of any help. Also, let me know if you are getting stuck with any specific packages- I can help find them and share with you.
rdewald
commented
3 years ago If we fix this by adding a local repo it would be helpful to hack up a VNSNY-specific version (we have it forked) of the installation R script so that it fetches the packages from our local repo instead of building them from devtools and github.
mtopaz
commented
3 years ago Sounds like a good solution to me Richard!
rdewald
commented
3 years ago In order to separate the RS Connect issue from #17 I went back another server and verified the app loads and runs as expected in R 3.6.3, which is where I originally deployed it, and what we were using during the demo to the VNSNY BIA group.
However, when I try to publish, I am met with this error, which is not related to the problems your are having in https://github.com/vnsny-bia/server-datasci.vnsny.org/issues/35 by the way. If you weren't having that problem, you would have had this one next:
This is what gets deployed. The read me from one of the github dependencies. You'll need to be behind the VPN to see that. Since this is a public repo, allow me:
Doh!
The problem is that rsconnect is looking for a deployable document, I think you might need to make an RMarkdown version of your app.
It works just fine in RStudio Pro, I will be communicating in a separate channel about the way forward with the research project.
rdewald
commented
3 years ago I have addressed the issues with package management for the shiny app with vnsny-bia/nimbleMine#1
rword2vec and wordVectors are loaded using
devtools::install_github("mukul13/rword2vec")
devtools::install_github("bmschmidt/wordVectors")The functions that used to be loaded into the local build of the NimbleMiner package now are available in a local repo on datasci. This repo is added via:
options(repos = c("https://cloud.r-project.org/", "https://datasci.vnsny.org/r-pkgs/"))Because of this success, our fork vnsny-bia/NimbleMiner has had the installer trimmed.
@mtopaz I haven't sent a PR because when I deploy in RStudio-connect, this error is generated:
Any ideas?
mtopaz
commented
3 years ago Thanks Richard! It looks to me like the issue is with a package called "NLP" and some issues with tensorflow. Would installing these packages help? https://cran.r-project.org/web/packages/tensorflow/index.html and https://cran.r-project.org/web/packages/NLP/index.html I don't believe that NimbleMiner uses either of these packages so it is a bit weird.
On Tue, Jan 26, 2021 at 7:25 PM Richard DeWald notifications@github.com wrote:
I have addressed the issues with package management for the shiny app with vnsny-bia/nimbleMine#1 https://github.com/vnsny-bia/nimbleMine/issues/1
rword2vec and wordVectors are loaded using
devtools::install_github("mukul13/rword2vec") devtools::install_github("bmschmidt/wordVectors")
The functions that used to be loaded into the local build of the NimbleMiner package now are available in a local repo on datasci https://datasci.vnsny.org/r-pkgs/. This repo is added via:
options(repos = c("https://cloud.r-project.org/", "https://datasci.vnsny.org/r-pkgs/"))
Because of this success, our fork vnsny-bia/NimbleMiner https://github.com/vnsny-bia/NimbleMiner has had the installer trimmed.
@mtopaz https://github.com/mtopaz I haven't sent a PR because when I deploy in RStudio-connect, this error is generated:
[image: nimbleMiner-RSConnect] https://user-images.githubusercontent.com/1530216/105923358-434d2200-600a-11eb-8bc8-388ce9f8215a.jpg
Any ideas?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mtopaz/NimbleMiner/issues/16#issuecomment-767918910, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI3EDCJ5ZFGESMGXQM43RG3S35MN3ANCNFSM4TRCVEFQ .
Maxim (Max) Topaz PhD, RN, MA Elizabeth Standish Gill Associate Professor of Nursing
Columbia University Medical Center
Columbia University Data Science Institute
Visiting Nurse Service of New York
Harvard Medical School & Brigham and Women's Hospital
Website: http://nursing.columbia.edu/profile/mtopaz http://nursing.columbia.edu/profile/mtopaz
rdewald
commented
3 years ago Thanks Richard! It looks to me like the issue is with a package called "NLP" and some issues with tensorflow. Would installing these packages help? https://cran.r-project.org/web/packages/tensorflow/index.html and https://cran.r-project.org/web/packages/NLP/index.html I don't believe that NimbleMiner uses either of these packages so it is a bit weird.
Right, I think the issues is related to a backend package called reticulate that mediates the integration with python, which is likely a dependency in almost any machine learning environment. Deeper than that, the issue is probably with our python install on that server, which has it's own issues.
We are working on a cloud instance of RStudio-connect. Once we start testing that I'll publish NimbleMiner to that location and report back with I learn. In the meantime, your researchers have something to use anyway.
mtopaz
commented
3 years ago Yes! Excellent- thanks
On Wed, Jan 27, 2021 at 11:09 AM Richard DeWald notifications@github.com wrote:
Thanks Richard! It looks to me like the issue is with a package called "NLP" and some issues with tensorflow. Would installing these packages help? https://cran.r-project.org/web/packages/tensorflow/index.html and https://cran.r-project.org/web/packages/NLP/index.html I don't believe that NimbleMiner uses either of these packages so it is a bit weird.
Right, I think the issues is related to a backend package called reticulate that mediates the integration with python, which is likely a dependency in almost any machine learning environment. Deeper than that, the issue is probably with our python install on that server, which has it's own issues.
We are working on a cloud instance of RStudio-connect. Once we start testing that I'll publish NimbleMiner to that location and report back with I learn. In the meantime, your researchers have something to use anyway.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mtopaz/NimbleMiner/issues/16#issuecomment-768392535, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI3EDCPN62MYSKKQRLW3I2DS4A3CZANCNFSM4TRCVEFQ .
Maxim (Max) Topaz PhD, RN, MA Elizabeth Standish Gill Associate Professor of Nursing
Columbia University Medical Center
Columbia University Data Science Institute
Visiting Nurse Service of New York
Harvard Medical School & Brigham and Women's Hospital
Website: http://nursing.columbia.edu/profile/mtopaz http://nursing.columbia.edu/profile/mtopaz
You have three packages as dependencies not on CRAN, rword2vec, wordVectors, and the package the installation routine builds, NimbleMiner.
After getting application to work in RStudio Pro, I tried to publish to RStudio Connect and most of it went okay until it came to installation of these three packages
We have RStudio Package Manager available, I will be investigating a fix by setting up a local repo that is accessible to RSConnect, but I thought you might want to know that it appears this will be an issue to address if you want to publish this app to RSConnect.
I will update when I make progress.