Error in r$status_code : $ operator is invalid for atomic vectors OR Error in tophits_query(id = id, pval = pval, clump = clump, r2 = r2, kb = kb, : There was an error, please contact the developers[BUG]:

[cainiaomengxin]

Describe the bug (required)

The code I run is as follows:
"> library(TwoSampleMR) #Load R package
TwoSampleMR version 0.5.11
[>] New: Option to use non-European LD reference panels for clumping etc
[>] Some studies temporarily quarantined to verify effect allele
[>] See news(package = 'TwoSampleMR') and https://gwas.mrcieu.ac.uk for further details

options(ieugwasr_api = 'gwas-api.mrcieu.ac.uk/')
library(ieugwasr)
OpenGWAS updates:
Date: 2024-03-07
[>] There is exceptional load on the OpenGWAS servers.
[>] Urgent infrastructure development being performed.
[>] See local options for analysis: https://mrcieu.github.io/gwasvcf/.

Loading the program package: ‘ieugwasr’

The following object is masked from ‘package:TwoSampleMR’:

 ld_matrix

exposure_dat <- extract_instruments(outcomes='eqtl-a-ENSG00000077809',p1 = 5e-06,clump = FALSE)
Error in r$status_code : $ operator is invalid for atomic vectors
OR
Error in tophits_query(id = id, pval = pval, clump = clump, r2 = r2, kb = kb, : There was an error, please contact the developers"

Describe the current behaviour you observe (required)

exposure_dat <- extract_instruments(outcomes='GWAS ID',p1 = 5e-06,clump = FALSE)
OR
exposure_clump <- clump_data(exposure_dat,clump_kb = 10000,clump_r2 = 0.001,clump_p1 = 1,clump_p2 = 1, pop = "EUR")

Describe the behaviour you expect (required)

Hope it can be back up and running.

R code to reproduce the issue (required)

exposure_dat <- extract_instruments(outcomes='GWAS ID',p1 = 5e-06,clump = FALSE)
OR
exposure_clump <- clump_data(exposure_dat,clump_kb = 10000,clump_r2 = 0.001,clump_p1 = 1,clump_p2 = 1, pop = "EUR")

System information

windows

[docZ9]

I met the same problems like you. did you solve this?

[cainiaomengxin]

I met the same problems like you. did you solve this?

I think it may be that non-local data acquisition is unstable. You can choose local data acquisition.

[docZ9]

I met the same problems like you. did you solve this?

I think it may be that non-local data acquisition is unstable. You can choose local data acquisition.

but my classmate's computer can do it smoothly, i don't know why

[Jiang337]

I met the same problems like you. did you solve this?

[zjralkc]

try remove the package TwoSampleMR and reinstall it.

[dzhaobio]

I also ran into this problem. Is this bug newly introduced? Does any release work without this problem? If any, I would like to try. Thanks!