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I tried to get proxies for variants but encountered an error below. This is similar to a previous issue (#13), which hasn't been responded. So I opened this one here.
bmi_proxy <- query_gwas(bmi, rsid=bmi_snps$snp, proxies = "only", bfile = ldfile, tag_r2=0.6)
Determining searchspace...
Proxy lookup...
Finding proxies...
Taking input= as a system command ('gunzip -c C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c5b7c431a.targets.ld.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
'gunzip' is not recognized as an internal or external command,
operable program or batch file.
Warning in (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(gunzip -c C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c5b7c431a.targets.ld.gz) > C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c3b995ac2' execution failed with error code 1
Warning in data.table::fread(paste0("gunzip -c ", outname), header = TRUE) :
File 'C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c3b995ac2' has size 0. Returning a NULL data.table.
Error:
! Problem with filter() input ..1.
i Input ..1 is .data[["R"]]^2 > tag_r2.
x Column R not found in .data.
Backtrace:
gwasvcf::query_gwas(...)
dplyr <fn>(<rln_____>)
Was this because the query makes changes to the environment and I don't have admin rights?
Many thanks,
patrick
The text was updated successfully, but these errors were encountered:
Hi gwasvcf developer(s) and users,
I tried to get proxies for variants but encountered an error below. This is similar to a previous issue (#13), which hasn't been responded. So I opened this one here.
bmi_proxy <- query_gwas(bmi, rsid=bmi_snps$snp, proxies = "only", bfile = ldfile, tag_r2=0.6)
Determining searchspace...
Proxy lookup...
Finding proxies...
Taking input= as a system command ('gunzip -c C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c5b7c431a.targets.ld.gz') and a variable has been used in the expression passed to
input=
. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.'gunzip' is not recognized as an internal or external command,
operable program or batch file.
Warning in (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(gunzip -c C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c5b7c431a.targets.ld.gz) > C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c3b995ac2' execution failed with error code 1
Warning in data.table::fread(paste0("gunzip -c ", outname), header = TRUE) :
File 'C:\Users\xueminW\AppData\Local\Temp\RtmpwvwlJ4\file2d1c3b995ac2' has size 0. Returning a NULL data.table.
Error:
! Problem with
filter()
input..1
.i Input
..1
is.data[["R"]]^2 > tag_r2
.x Column
R
not found in.data
.Backtrace:
<fn>
(<rln_____>
)Was this because the query makes changes to the environment and I don't have admin rights?
Many thanks,
patrick
The text was updated successfully, but these errors were encountered: