object 'LD' not found in installation (build_vignettes=TRUE)

[bbb801]

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]

I'll take a look at this next week. Meantime you could install from CRAN which is pretty up to date.

-- https://chr1swallace.github.io

---

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?

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/125, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2BKG7NRSMFL5RLKWH3XQIWLRANCNFSM6AAAAAA2LCX3PY. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[bbb801]

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]

Thanks. You can view the vignette here till I fix the issue.

https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html

-- https://chr1swallace.github.io

---

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

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/125#issuecomment-1636799647, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2H4YUAM5FUR6MZRXFDXQKYOXANCNFSM6AAAAAA2LCX3PY. You are receiving this because you commented.Message ID: @.***>

[bbb801]

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

-- https://chr1swallace.github.io

---

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

― Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/125#issuecomment-1636799647, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2H4YUAM5FUR6MZRXFDXQKYOXANCNFSM6AAAAAA2LCX3PY. You are receiving this because you commented.Message ID: @.***>

― Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/125#issuecomment-1636812074, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMPCDZNPO7RKLBY33YV6PFLXQK6H5ANCNFSM6AAAAAA2LCX3PY. You are receiving this because you authored the thread.Message ID: @.***>