Query_gwas raises defunct error with tibble v3

[jjmpal]

Running query_gwas raises following defunct error with tibble v.3.2.1. I believe that in proxy.r lines that pipe input to as_tibble(.data) are interpreted as as_tibble(., .data). Within tibble in the following steps tibble:::as_tibble.data.frame takes the second argument to flag validate as not null and causes the deprecate_stop. Replacing .data with . seems to fix the issue.

<error/lifecycle_error_deprecated>
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.
---
Backtrace:
    x
 1. +-df_outcome %>% as_tibble(.data)
 2. +-tibble::as_tibble(., .data)
 3. +-readr:::as_tibble.spec_tbl_df(., .data)
 4. +-base::NextMethod("as_tibble")
 5. \-tibble:::as_tibble.data.frame(., .data)
 6.   \-lifecycle::deprecate_stop(...)
 7.     \-lifecycle:::deprecate_stop0(msg)
Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.
```

[jtnedoctor]

I met the same error when using the get_ld_proxies function:
"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.

Backtrace:
▆

1. ├─gwasvcf::get_ld_proxies(...)
2. │ └─cbind(ld, temp) %>% dplyr::as_tibble(.data, .name_repair = "minimal")
3. ├─dplyr::as_tibble(., .data, .name_repair = "minimal")
4. └─tibble:::as_tibble.data.frame(., .data, .name_repair = "minimal")
5. └─lifecycle::deprecate_stop(...)

6. └─lifecycle:::deprecate_stop0(msg)
   

Run rlang::last_trace(drop = FALSE) to see 1 hidden frame."

Does anyone know how to fix this issue? Thank you!

[nadineparker]

I am having the same issue when using query_gwas for identifying proxy SNPs. Would be great to have a fix or work around.

[nadineparker]

Thanks for the fix. I see that proxies are now being generated but there is an error after "Aligning".

The error says:
"Error in validObject(assays) : invalid class “SimpleAssays” object:
'dim(x)' must return a numeric vector"

I am running the following command
query_gwas(
vcf=outcome_vcf, rsid="rs1034858", proxies="yes",
bfile="/path/to/ref/data/1kg_v3/EUR",
tag_kb = 5000, tag_nsnp = 5000, tag_r2 = 0.6
)

the full console output is below:
Initial search...
Extracted 0 out of 1 rsids
Searching for proxies for 1 rsids
Determining searchspace...
Proxy lookup...
Finding proxies...
Taking input= as a system command ('gunzip -c /var/folders/4t/_d7c3w_d1n9d_1z9pg7g02mh0000gn/T//RtmppExvWt/file1378a60b0231b.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 3 proxies
Extrating proxies...
Identified proxies for 1 of 1 rsids
Aligning...
Error in validObject(assays) : invalid class “SimpleAssays” object:
'dim(x)' must return a numeric vector