object 'LD' not found in installation (build_vignettes=TRUE)
bbb801 opened this issue · 4 comments
bbb801 commented
Dear Sir/Madam,
When I install th package using:
if(!require("remotes"))
-
install.packages("remotes") # if necessary
library(remotes)
install_github("chr1swallace/coloc@main",build_vignettes=TRUE,force=TRUE)
I got:
Quitting from lines 57-61 [unnamed-chunk-3] (a06_SuSiE.Rmd)
Error: processing vignette 'a06_SuSiE.Rmd' failed with diagnostics:
object 'LD' not found
--- failed re-building 'a06_SuSiE.Rmd'
SUMMARY: processing the following file failed:
'a06_SuSiE.Rmd'
Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'coloc' from GitHub:
! System command 'Rcmd.exe' failed
I know I can set 'build_vignettes=FALSE'. But what and why object 'LD' is no found? Which package is it in? How to solve this problem?
chr1swallace commented
I'll take a look at this next week. Meantime you could install from CRAN which is pretty up to date.
…________________________________
From: Jundong LIU ***@***.***>
Sent: Saturday, July 15, 2023 6:57:12 AM
To: chr1swallace/coloc ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [chr1swallace/coloc] object 'LD' not found in installation (build_vignettes=TRUE) (Issue #125)
Dear Sir/Madam,
When I install th package using:
if(!require("remotes"))
*
install.packages("remotes") # if necessary
library(remotes)
***@***.***",build_vignettes=TRUE,force=TRUE)
I got:
Quitting from lines 57-61 [unnamed-chunk-3] (a06_SuSiE.Rmd)
Error: processing vignette 'a06_SuSiE.Rmd' failed with diagnostics:
object 'LD' not found
--- failed re-building 'a06_SuSiE.Rmd'
SUMMARY: processing the following file failed:
'a06_SuSiE.Rmd'
Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'coloc' from GitHub:
! System command 'Rcmd.exe' failed
[1689400367087]<https://user-images.githubusercontent.com/52306405/253721685-042a49af-a783-47e9-89cf-bbccb50dcd95.png>
I know I can set 'build_vignettes=FALSE'. But what and why object 'LD' is no found? Which package is it in? How to solve this problem?
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bbb801 commented
Thank you.
By the way, I run 'a06_SuSiE.Rmd', and I have a similar issue. It seems 'LD' is not set for D3 but not for D4. I check they have an 'LD' matrix.
chr1swallace commented
Thanks. You can view the vignette here till I fix the issue.
https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html
…________________________________
From: Jundong LIU ***@***.***>
Sent: Saturday, July 15, 2023 4:21:15 PM
To: chr1swallace/coloc ***@***.***>
Cc: Chris Wallace ***@***.***>; Comment ***@***.***>
Subject: Re: [chr1swallace/coloc] object 'LD' not found in installation (build_vignettes=TRUE) (Issue #125)
Thank you.
By the way, I run 'a06_SuSiE.Rmd', and I have a similar issue. It seems 'LD' is not set for D3 but not for D4. I check they have an 'LD' matrix.
[1689434302638]<https://user-images.githubusercontent.com/52306405/253749140-22a4441f-ef3f-428a-99dc-1f2fcc6cfc7c.png>
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bbb801 commented
Thank you very much
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…________________________________
From: Chris Wallace ***@***.***>
Sent: Sunday, July 16, 2023 12:10:38 AM
To: chr1swallace/coloc ***@***.***>
Cc: LIU Jundong ***@***.***>; Author ***@***.***>
Subject: [Ext] Re: [chr1swallace/coloc] object 'LD' not found in installation (build_vignettes=TRUE) (Issue #125)
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Thanks. You can view the vignette here till I fix the issue.
https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html
________________________________
From: Jundong LIU ***@***.***>
Sent: Saturday, July 15, 2023 4:21:15 PM
To: chr1swallace/coloc ***@***.***>
Cc: Chris Wallace ***@***.***>; Comment ***@***.***>
Subject: Re: [chr1swallace/coloc] object 'LD' not found in installation (build_vignettes=TRUE) (Issue #125)
Thank you.
By the way, I run 'a06_SuSiE.Rmd', and I have a similar issue. It seems 'LD' is not set for D3 but not for D4. I check they have an 'LD' matrix.
[1689434302638]<https://user-images.githubusercontent.com/52306405/253749140-22a4441f-ef3f-428a-99dc-1f2fcc6cfc7c.png>
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Reply to this email directly, view it on GitHub<#125 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAQWR2H4YUAM5FUR6MZRXFDXQKYOXANCNFSM6AAAAAA2LCX3PY>.
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