Error in all_dims[, 1L] : incorrect number of dimensions

[chenyangsu]

Hi MRCIEU team, Would it be possible to merge the pull request titled issue #27 convert to gwasglue2 summaryset inside gwasvcf package #28 at #28? I'm using your package for a project for finding LD proxies but this error still remains.

Error:
! The validate argument of as_tibble() was deprecated in tibble 2.0.0 and is now defunct.
ℹ Please use the .name_repair argument instead.

In addition, I was able to bypass the error by installing the branch with the new changes:

library(remotes)
install_github("MRCIEU/gwasvcf@27-convert-to-gwasglue2-summaryset-inside-gwasvcf-package")

However, after running
query_gwas(outcome_vcf, rsid=input_rsid, proxies="only", bfile=ld_file, build = "GRCh38", tag_kb = 1000, tag_r2=0.8) there's another error at the align step:

Determining searchspace...
Proxy lookup...
Finding proxies...
Taking input= as a system command ('gunzip -c /tmp/RtmpnitEtI/file3098e72a46191.targets.ld.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Found 24 proxies
Extrating proxies...
Identified proxies for 1 of 1 rsids
Aligning...
Error in all_dims[, 1L] : incorrect number of dimensions

It seems like others have also ran into trouble at the Aligning step: #25 (comment)
Would it be possible to solve this incorrect dimension issue? Thanks a lot!

[remlapmot]

Thanks - but there is no need to open a new issue - both of these already exist - please add your comments to the existing issues next time.

[chenyangsu]

No problem and thanks for your response! I'll make sure to do that next time.

[Ericzhu0524]

Hi,

I'm encountering the same error during the alignment step, with the following error message:

"Error in all_dims[, 1L] : incorrect number of dimensions."

Have you successfully solved this issue, and if so, how you went about doing so? I would greatly appreciate your assistance.

Best wishes,

Eric