vroom error message for corrupted file

[Joëlle Pasman]

Hello,

I've spent most of my day figuring out this error, and thought to share my experience, and perhaps to suggest the developers to add a more informative error message. 

Here's what happened: I updated my BiocManager, and immediately after the ldsc function stopped working. I got a vroom error, message: 

Error: The size of the connection buffer (131072) was not large enough
to fit a complete line:

  * Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`

 

Because I just updated BiocManager and there are known conflicts between vroom and that package, I obviously thought that the issue was in package conflicts. After a lot of trial and error, I found out that somehow one of the munged input files had become corrupted and had become unreadable. Nothing wrong with vroom or Biocmanager. I was completely put off track by the error message. If it's not too much work, perhaps the coming update from Genomic SEM could incorporate some read checks and corresponding error messages? 

[Michel Nivard]

Hi Joelle,

sounds frustrating! So I see 3 ways forward here.

1. if you have an idea for a read checks you can commit it as a pull request on github (I lack sufficient context to write one I feel, checks on what exactly, what file was corupted, what GenomicSEM function spit it out, were there any peculiarities in the log) 

2. If you have an idea but are not working with git, you can mail me the idea, or post it here and we can integrate.

3. We can put it on our to-do list and perhaps get to it, but without a specific issue its hard to do focused work to prevent (we don't know what caused the file to corrupt so its hard to put tests in place and with it warnings). 

I know this isn't why you are here but generally in my experience nothing good ever comes of updating anything, and I myself have even been experimenting with renv to fully insulate my projects from each-other: https://posit.co/blog/renv-project-environments-for-r/ 

Best,

Michel

[Joëlle Pasman]

Thanks for your answer and the options! I don't have much experience with reviewing and rewriting programmatic code, so I'll leave it at option 3, and suggest to incorporate an error message that just says 'fread error' when loading the files. I also have no clue why the file got corrupted but that probably doesn't have anything to do with the ldsc() command, so I wouldn't suggest to put effort into that. I think it's fine if this is not updated at all, at least now people can find this thread when they get a mysterious vroom error.

Op donderdag 3 augustus 2023 om 18:32:02 UTC+2 schreef m.g.n...@gmail.com: