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nolanlab / citrus

Citrus Development Code
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Citrus GUI not recognizing commands #61

Closed horowitzamir closed 10 years ago

horowitzamir commented 10 years ago

I have a dataset that I am analyzing in Citrus. In the GUI, there are multiple areas where upon clicking to highlight/activate, the field is not checked. For example, I wanted to analyze medians. I could click on that feature but was unable to select any of the markers that appear below. This is happening in other areas as well. Thanks for looking into this.

rbruggner commented 10 years ago

Could you upload a screen shot just to help me get a better idea of what to look for? Also, which version of R, citrus, and browser are you using?

Thanks!

horowitzamir commented 10 years ago

Hi Rob,

Thanks. I am using R version 3.1.0 browser: Google chrome Citrus: I think version 0.7 but the GUI may have read v0.8

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 18, 2014, at 10:41 AM, Robert Bruggner notifications@github.com wrote:

Could you upload a screen shot just to help me get a better idea of what to look for? Also, which version of R, citrus, and browser are you using?

Thanks!

— Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

Can you take a look at the runCitrus.R file? It should tell you which version of Citrus that you're using. I'm just curious because I recently updated the codebase a bit and am trying to figure out if that's related.

horowitzamir commented 10 years ago

The runCitrusR file reads v0.7

Thanks Rob A

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 18, 2014, at 12:24 PM, Robert Bruggner notifications@github.com wrote:

Can you take a look at the runCitrus.R file? It should tell you which version of Citrus that you're using. I'm just curious because I recently updated the codebase a bit and am trying to figure out if that's related.

— Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

Thanks - can you post or send a screenshot of the things that are failing?

On Jun 18, 2014, at 12:29 PM, horowitzamir notifications@github.com wrote:

The runCitrusR file reads v0.7

Thanks Rob A

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 18, 2014, at 12:24 PM, Robert Bruggner notifications@github.com wrote:

Can you take a look at the runCitrus.R file? It should tell you which version of Citrus that you're using. I'm just curious because I recently updated the codebase a bit and am trying to figure out if that's related.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

horowitzamir commented 10 years ago

Well, unfortunately, it’s an interactive feature that is failing, Rob. Don’t know how to capture that in a screenshot. Essentially, I am trying to check off boxes in the GUI and they won’t activate.

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 18, 2014, at 12:46 PM, Robert Bruggner notifications@github.com wrote:

Thanks - can you post or send a screenshot of the things that are failing?

On Jun 18, 2014, at 12:29 PM, horowitzamir notifications@github.com wrote:

The runCitrusR file reads v0.7

Thanks Rob A

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 18, 2014, at 12:24 PM, Robert Bruggner notifications@github.com wrote:

Can you take a look at the runCitrus.R file? It should tell you which version of Citrus that you're using. I'm just curious because I recently updated the codebase a bit and am trying to figure out if that's related.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

I have managed to replicate this problem on my computer. It appears as though an update to web UI package (probably the shiny package) has changed the behavior / is causing problems. I will get started on a fix.

rbruggner commented 10 years ago

This is definitely related to the shiny package. While I'm working on a fix, you can get around the problem by installing an older version of the shiny package. In R, run the following commands:

library("devtools")
install_url("http://cran.r-project.org/src/contrib/Archive/shiny/shiny_0.9.1.tar.gz")

Let me know if that fixes things.

horowitzamir commented 10 years ago

Hey Rob,

I installed the older version, but the problem still exists

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 19, 2014, at 12:21 PM, Robert Bruggner notifications@github.com wrote:

This is definitely related to the shiny package. While I'm working on a fix, you can get around the problem by installing an older version of the shiny package. In R, run the following commands:

library("devtools") install_url("http://cran.r-project.org/src/contrib/Archive/shiny/shiny_0.9.1.tar.gz") Let me know if that fixes things.

— Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

Did you restart R after installing?

On Jun 19, 2014, at 12:37 PM, horowitzamir notifications@github.com wrote:

Hey Rob,

I installed the older version, but the problem still exists

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 19, 2014, at 12:21 PM, Robert Bruggner notifications@github.com wrote:

This is definitely related to the shiny package. While I'm working on a fix, you can get around the problem by installing an older version of the shiny package. In R, run the following commands:

library("devtools") install_url("http://cran.r-project.org/src/contrib/Archive/shiny/shiny_0.9.1.tar.gz") Let me know if that fixes things.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

horowitzamir commented 10 years ago

I have indeed restarted R. I then wrote: library(citrus) and finally launched it using your synthetic dataset. Still not functioning.

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 19, 2014, at 12:50 PM, Robert Bruggner notifications@github.com wrote:

Did you restart R after installing?

On Jun 19, 2014, at 12:37 PM, horowitzamir notifications@github.com wrote:

Hey Rob,

I installed the older version, but the problem still exists

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 19, 2014, at 12:21 PM, Robert Bruggner notifications@github.com wrote:

This is definitely related to the shiny package. While I'm working on a fix, you can get around the problem by installing an older version of the shiny package. In R, run the following commands:

library("devtools") install_url("http://cran.r-project.org/src/contrib/Archive/shiny/shiny_0.9.1.tar.gz") Let me know if that fixes things.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

I have tried to updated the UI code to fix the problem but have not yet pushed the changes to the master branch. Give this a try in R:

update.packages()
library("devtools")
install_github("citrus","nolanlab",ref="uiUpdate")

After that, restart R and reload the citrus package. Please let me know if that works.

horowitzamir commented 10 years ago

Hi Rob,

Thanks very much for getting back to me. I just followed the instructions. Everything seemed to install. I restarted a new R session, but it is still behaving the same way. I am feeling like this suggests that it’s something wrong with my computer. I am acquiring CyTOF data today at the FACS facility until tonight. I am around tomorrow though. Any reason you would find trouble shooting directly on my computer helpful? If so, I would be very happy to bring over to you for all/part of the day.

Really appreciate the help.

Thanks again

best Amir

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 30, 2014, at 1:51 PM, Robert Bruggner notifications@github.com wrote:

I have tried to updated the UI code to fix the problem but have not yet pushed the changes to the master branch. Give this a try in R:

update.packages() library("devtools") install_github("citrus","nolanlab",ref="uiUpdate") After that, restart R and reload the citrus package. Please let me know if that works.

— Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

Hmmm... Now that I look at it again, I guess that did not fix things. I will take another crack at it tomorrow.

On Jun 30, 2014, at 2:56 PM, horowitzamir notifications@github.com wrote:

Hi Rob,

Thanks very much for getting back to me. I just followed the instructions. Everything seemed to install. I restarted a new R session, but it is still behaving the same way. I am feeling like this suggests that it’s something wrong with my computer. I am acquiring CyTOF data today at the FACS facility until tonight. I am around tomorrow though. Any reason you would find trouble shooting directly on my computer helpful? If so, I would be very happy to bring over to you for all/part of the day.

Really appreciate the help.

Thanks again

best Amir

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 30, 2014, at 1:51 PM, Robert Bruggner notifications@github.com wrote:

I have tried to updated the UI code to fix the problem but have not yet pushed the changes to the master branch. Give this a try in R:

update.packages() library("devtools") install_github("citrus","nolanlab",ref="uiUpdate") After that, restart R and reload the citrus package. Please let me know if that works.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

horowitzamir commented 10 years ago

Thanks for not giving up on this, Rob. Appreciate the help

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 30, 2014, at 11:19 PM, Robert Bruggner notifications@github.com wrote:

Hmmm... Now that I look at it again, I guess that did not fix things. I will take another crack at it tomorrow.

On Jun 30, 2014, at 2:56 PM, horowitzamir notifications@github.com wrote:

Hi Rob,

Thanks very much for getting back to me. I just followed the instructions. Everything seemed to install. I restarted a new R session, but it is still behaving the same way. I am feeling like this suggests that it’s something wrong with my computer. I am acquiring CyTOF data today at the FACS facility until tonight. I am around tomorrow though. Any reason you would find trouble shooting directly on my computer helpful? If so, I would be very happy to bring over to you for all/part of the day.

Really appreciate the help.

Thanks again

best Amir

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jun 30, 2014, at 1:51 PM, Robert Bruggner notifications@github.com wrote:

I have tried to updated the UI code to fix the problem but have not yet pushed the changes to the master branch. Give this a try in R:

update.packages() library("devtools") install_github("citrus","nolanlab",ref="uiUpdate") After that, restart R and reload the citrus package. Please let me know if that works.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

I've tried to push another fix - reinstall as described here: https://github.com/nolanlab/citrus/issues/61#issuecomment-47585313 ... and let me know if that's better?

horowitzamir commented 10 years ago

Rob, citrus is suddenly working now. Thanks very much for your effort in helping me. I'll let you know how it goes. Thanks again

rbruggner commented 10 years ago

Of course. Just to clarify, did the most recent update fix the problem or did an older version just start working for some unexplained reason?

horowitzamir commented 10 years ago

specifically, this most current update you sent, i.e. ?re-do #61? did the fix.

Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Building / Room D100 / 299 Campus Drive West, Stanford CA 94305-5126 / http://www.stanford.edu/group/parhamlab

On Jul 1, 2014, at 11:02 AM, Robert Bruggner notifications@github.com wrote:

Of course. Just to clarify, did the most recent update fix the problem or did an older version just start working for some unexplained reason?

? Reply to this email directly or view it on GitHub.

rbruggner commented 10 years ago

Great - will merge in those changes to the master branch.

Fixed in 6bb09170acd925f25c704fc9dff699e6ca6ee2ff.