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diyabc / diyabcGUI

User interface to DIYABC/AbcRanger
https://diyabc.github.io/
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Maximum upload size exceeded #100

Open selasphoruskershaw opened 3 years ago

selasphoruskershaw commented 3 years ago

Hello,

I am launching the GUI on a Mac using R Studio. When I try to import my .snp data file (generated by the vcf2DIYabc script), I get the following message: "Maximum upload size exceeded." When I navigate to preferences and change the "Maximum upload file size (in Mb)" to "1000" (my data file is about 625 Mb) I still get the same error when I try to import it. Is there something I'm missing here? Is there an alternative? I'm using whole-genome SNP data. Thanks for your help.

fradav commented 3 years ago

Hi,

You closed the issue, did you solve it ? Otherwise I'll transfer it to the right repo : https://github.com/diyabc/diyabcGUI/issues

selasphoruskershaw commented 3 years ago

Hi there,

I was able to upload my data, however, it has now been on the "loading and checking the data file may take some time" message for about 16 hours now, and I have not been able to set up my analysis any further. I'd appreciate any help I can get. Thanks.

On Mon, May 17, 2021 at 11:59 PM fradav @.***> wrote:

Hi,

You closed the issue, did you solve it ? Otherwise I'll transfer it to the right repo : https://github.com/diyabc/diyabcGUI/issues

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/diyabc/diyabc/issues/49#issuecomment-842906378, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARZ3FXD6SN57IZQZ55NUWVTTOIF6JANCNFSM45A2UW4Q .

gdurif commented 3 years ago

Hi, Increasing the "Maximum upload file size" should do the trick. I will check if there is some issue with it.

Regarding your second problem with the data checking, we are currently working on a major release that should robustify the whole data processing framework. It should be available in the next few days. Would that be possible for you to wait for it ?

Thanks in advance, I'll keep you updated here

selasphoruskershaw commented 3 years ago

Thank you! Yes, I can wait for the new release. Looking forward to it!

On Wed, May 19, 2021 at 7:14 AM gdurif @.***> wrote:

Hi, Increasing the "Maximum upload file size" should do the trick. I will check if there is some issue with it.

Regarding your second problem with the data checking, we are currently working on a major release that should robustify the whole data processing framework. It should be available in the next few days. Would that be possible for you to wait for it ?

Thanks in advance, I'll keep you updated here

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gdurif commented 3 years ago

Hi, I am really sorry, the next release was delayed to the end of June. I hope this will be ok. All apologies for the trouble.

selasphoruskershaw commented 3 years ago

Hello,

Just wondering if you have a target date for when the fix for diyabc-Rf Wil be finished.

Thanks,

Brian Myers On Mon, Jun 14, 2021 at 6:38 AM gdurif @.***> wrote:

Hi, I am really sorry, the next release was delayed to the end of June. I hope this will be ok. All apologies for the trouble.

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gdurif commented 3 years ago

Hi, Sorry again for the delay. The new release should be available next week. Best

gdurif commented 3 years ago

Hi, I am again really sorry for the delay, but the new version of the GUI is at least available on branch refactor_app, see PR #96

If you want to try it first hand, you can install the R package and run the app with:

devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app", subdir = "R-pkg")
library(diyabcGUI)
dl_all_latest_bin()
diyabc()

It will be merged tomorrow in master and a new version of the beta release will be published.

selasphoruskershaw commented 3 years ago

Hello,

Thanks for your email. I tried using the code you provided to install the updated version of DIYABC-RF, and received this message:

devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app") Downloading GitHub repo @.***_app Error: Failed to install 'diyabcGUI' from GitHub: Does not appear to be an R package (no DESCRIPTION)

What should I do?

Thanks, Brian

On Mon, Aug 23, 2021 at 9:24 AM gdurif @.***> wrote:

Hi @ALL https://github.com/ALL, I am again really sorry for the delay, but the new version of the GUI is at least available on branch refactor_app, see PR #96 https://github.com/diyabc/diyabcGUI/pull/96

If you want to try it first hand, you can install the R package and run the app with:

devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app") dl_all_latest_bin() diyabc()

It will be merged tomorrow in master and a new version of the beta release will be published.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/diyabc/diyabcGUI/issues/100#issuecomment-903924515, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARZ3FXH5JFC2745DUECR3UDT6JY4HANCNFSM45CZ5QQA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

gdurif commented 3 years ago

I am really sorry, I fixed the code snippet, it was missing some stuff.

selasphoruskershaw commented 3 years ago

Hello,

Unfortunately I'm still getting the same error. Should I just wait until the beta release is updated tomorrow?

Thanks for your help, Brian

On Mon, Aug 23, 2021 at 2:16 PM gdurif @.***> wrote:

I am really sorry, I fixed the code snippet, it was missing some stuff.

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gdurif commented 3 years ago

Hi, I am encountering a network issue delaying the release build (always the final step...), hopefully it will be fixed in a few hours.

In the mean time, could tell more information about your system (OS, R version). I tested the command devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app", subdir = "R-pkg") and it worked for me, so I don't understand what could be the problem.

Thanks,

selasphoruskershaw commented 3 years ago

Hi,

I was able to get that above command to run, but I now get the following error message when trying to run the GUI when running the diyabcGUI::diyabc() command:

"Warning in get0(oNam, envir = ns) : restarting interrupted promise evaluation Warning in get0(oNam, envir = ns) : internal error -3 in R_decompress1 Error in get0(oNam, envir = ns) : lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cachem/R/cachem.rdb' is corrupt

"

Here is all of the code:

library(devtools) devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app", subdir = "R-pkg") devtools::install_github( "diyabc/diyabcGUI", subdir = "R-pkg" ) diyabcGUI::dl_all_latest_bin() diyabc() library(diyabcGUI) diyabcGUI::diyabc()

I have MacOS Big Sur 11.2.3. RStudio 1.4.1106, R 4.0.5.

Thanks for your help, Brian

On Tue, Aug 24, 2021 at 6:13 AM gdurif @.***> wrote:

Hi, I am encountering a network issue delaying the release build (always the final step...), hopefully it will be fixed in a few hours.

In the mean time, could tell more information about your system (OS, R version). I tested the command devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app", subdir = "R-pkg") and it worked for me, so I don't understand what could be the problem.

Thanks,

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/diyabc/diyabcGUI/issues/100#issuecomment-904630297, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARZ3FXHSNRPC76L3Q33OSSLT6OLG3ANCNFSM45CZ5QQA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

gdurif commented 3 years ago

The new code is now merged into the main branch, so devtools::install_github("diyabc/diyabcGUI", subdir = "R-pkg") will now work.

Regarding your issue, I think you could try to reinstall the cachem package with install.packages("cachem") before trying to run library(diyabc) and diyabc().

At the moment, I am not able to do some checks on a MacOS machine. In addition, I use R 4.1.0, maybe there is also a retro-compatibility issue. I will try to test an older version of R.

gdurif commented 3 years ago

The new beta release is available (but only for Windows at the moment, on MacOS you will have to continue installing the R package).

selasphoruskershaw commented 3 years ago

Hi there,

After waiting for the update and increasing the maximum upload size, when I try to upload my data file (~650 Mb), it continuously loads, and will do so for several days, without ever being loaded. Thus, I can't get the software to run because I can't get my dataset uploaded. Can you please help?

I am using a Mac and am up to date with the software.

On Fri, Aug 27, 2021 at 2:11 AM gdurif @.***> wrote:

The new beta release is available (but only for Windows at the moment, on MacOS you will have to continue installing the R package).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/diyabc/diyabcGUI/issues/100#issuecomment-907052815, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARZ3FXEFPWYNN57253VAZM3T65JE7ANCNFSM45CZ5QQA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

selasphoruskershaw commented 3 years ago

Hi, I was able to work through the issue above, but I'm having a similar issue as others: I keep having an issue in which I validate all of my parameters, but upon hitting "simulate", I receive the issue: Project is not ready. Check settings above. Do you know when a fix will be ready? Thanks!

gdurif commented 2 years ago

Hi, there is a new release v1.1.1-beta. Could you tell me if it works for you?