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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
15 stars 7 forks source link

First time use of PhenoptrReports errors #23

Closed michaelmooreny closed 5 years ago

michaelmooreny commented 5 years ago

Hi,

I recently installed phenoptr reports in RStudio and began trying to work through the tutorials for its use. When I tried to consolidate and analyze two merged cell seg data files I received the following error:

phenoptrReports:::addin_20_consolidate()

Listening on http://127.0.0.1:3680 Reading "Merge_cell_seg_data". Warning: Error in : 'field_column' is not an exported object from 'namespace:phenoptr' 79: stop 78: getExportedValue 77: :: 76: process_one_file 75: phenoptrReports::consolidate_and_summarize_cell_seg_data 74: observeEventHandler 3: shiny::runApp 2: shiny::runGadget 1: phenoptrReports:::addin_20_consolidate

I'm not really sure how to approach fixing these errors. Please let me know what files I should attach to this thread to allow you to help me solve this problem. Thanks!

AB-Kent commented 5 years ago

Please install the latest phenoptr and phenoptrReports. See instructions here: https://www.akoyabio.com/application/files/7915/6210/3607/PhenoptrRerports_Install_Instructions.v5.pdf

michaelmooreny commented 5 years ago

Hi,

Thanks for the quick reply! It is my understanding that I did install the latest phenoptr and phenoptrReports. Is there something in the error statement that is making you think the latest versions of phenoptr and phenoptrReports were not installed?

AB-Kent commented 5 years ago

Yes, the error you show was present in phenoptr earlier this year, it should be fixed now.

You can check the version you have installed: in RStudio, select the Packages tab, click on phenoptr, then "DESCRIPTION file". It should show version 0.2.3 dated 2019-08-07.

michaelmooreny commented 5 years ago

I think I understand why I might not have the most updated versions of phenoptr- I didn't use install_github from the devtools package in RStudio but rather downloaded phenoptr manually from github and then used install_local. I had to do this because I am downloading phenoptr from a computer in a research lab that is working behind a proxy. Do you think I will have to use install_github to download phenoptr?

AB-Kent commented 5 years ago

I don't think that sequence works, the zip file you get from GitHub is not in the correct format.

You may be able to configure install_github to use your proxy. See for example https://en.it1352.com/article/1fc9a9e6df984bb39106dde273d9c51f.html and https://anhhoangduc.com/blog/install-r-packages-from-github-through-proxy/.

If you unzip the downloaded file and open the project in RStudio, you should be able to install it from the Build tab by clicking "Install and Restart". Unfortunately this will not install any of the (many) dependencies; if you have an older version installed that may be OK, otherwise you will have to go through a similar process for them.

On Thu, Aug 29, 2019 at 9:22 AM michaelmooreny notifications@github.com wrote:

I think I understand why I might not have the most updated versions of phenoptr- I didn't use install_github from the devtools package in RStudio but rather downloaded phenoptr manually from github and then used install_local. I had to do this because I am downloading phenoptr from a computer in a research lab that is working behind a proxy. Do you think I will have to use install_github to download phenoptr?

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