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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Error with creating ArrowFile #1527

Closed jshi7 closed 2 years ago

jshi7 commented 2 years ago

ArchR-createArrows-74357945f688-Date-2022-07-27_Time-16-27-19.log

Hello, I'm trying to create an ArrowFile and I keep getting this error:

<simpleError in validObject(r): invalid class “dgTMatrix” object: lengths of slots i and j must match> I followed all the default tutorial parameters and only used one thread. I am using 10x fragments data.

The tutorial dataset works fine but I'm not sure why I'm getting this error for my dataset.

I saw this issue thread but already have v. 1.0.2 https://github.com/GreenleafLab/ArchR/issues/1145

rcorces commented 2 years ago

Hi @jshi7! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
Before we help you, you must respond to the following questions unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

rcorces commented 2 years ago

I think this may be a bug. I'm not sure if this patch will fix it but could you try installing the dev_matchID branch and re-running?

Make sure to unload and reload ArchR like so:

devtools::install_github("GreenleafLab/ArchR", ref="dev_matchID", repos = BiocManager::repositories())
detach("package:ArchR", unload=TRUE)
library(ArchR)

Please report back on whether or not this works.

jshi7 commented 2 years ago

Creating the arrowfile works now :) Thank you so much for your help!

tanlongzhi commented 2 years ago

Thank you @rcorces for the prompt fix! We really appreciated your kind help!

rcorces commented 2 years ago

This has been merged into the dev branch and will be incorporated into the next stable release_1.0.3

jiangpuxuan commented 2 years ago

I think this may be a bug. I'm not sure if this patch will fix it but could you try installing the dev_matchID branch and re-running?

Make sure to unload and reload ArchR like so:

devtools::install_github("GreenleafLab/ArchR", ref="dev_matchID", repos = BiocManager::repositories())
detach("package:ArchR", unload=TRUE)
library(ArchR)

Please report back on whether or not this works.

Hi, I am very glad to find this update, but installing dev_match_ID got error :

> devtools::install_github("GreenleafLab/ArchR", ref="dev_matchID", repos = BiocManager::repositories())
Downloading GitHub repo GreenleafLab/ArchR@dev_matchID
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  cannot open URL 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/dev_matchID'
rcorces commented 2 years ago

As stated in https://github.com/GreenleafLab/ArchR/issues/1527#issuecomment-1199567614 these changes were merged into the dev branch. dev_matchID was deleted after merge so it no longer exists