kegg parameter change

[kkleinoros]

correction to download kegg.db

[GuangchuangYu]

@huerqiang pls check whether these changes are necessary.

[huerqiang]

@kkleinoros I don't know the reason for your amendment. Please explain it in detail.

[kkleinoros]

Hi there , As you can see by the number of issues people are reporting there is a problem in the kegg download of the database. There must have been a change in the parameters for the ‘get_data_from_KEGG_db’ function it now needs ‘hsa’ as an input and no need for the mapping from organism to species. In addition you have one more function from DOSE that was not declared ‘enricher_internal’. With these changes, I was able to get output for the ‘enrichKegg’ function. kathleen From: Erqiang Hu ***@***.***> Sent: Monday, March 20, 2023 11:48 PM To: YuLab-SMU/clusterProfiler ***@***.***> Cc: Kathleen Oros Klein ***@***.***>; Mention ***@***.***> Subject: Re: [YuLab-SMU/clusterProfiler] kegg parameter change (PR #565) @kkleinoros<https://github.com/kkleinoros> I don't know the reason for your amendment. Please explain it in detail. — Reply to this email directly, view it on GitHub<#565 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB4Y56PS6KYLOPXBVKTDZ5LW5EQH7ANCNFSM6AAAAAAWBRSRWE>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[huerqiang]

(1) As far as I know, it is necessory to use species <- organismMapper(organism). It will report error without using organismMapper() function. In addition, the current version should not have the KEGG download problem.
(2) We have delcared enricher_internal and GSEA_internal in utilities.R. Of course, using getFromNamespace in DOSE.R is a better choice, and we will change it in the next version.

[kkleinoros]

Look at the number of issues reported on your github page, I suggest you check it out. kathleen From: Erqiang Hu ***@***.***> Sent: Tuesday, March 21, 2023 9:53 AM To: YuLab-SMU/clusterProfiler ***@***.***> Cc: Kathleen Oros Klein ***@***.***>; Mention ***@***.***> Subject: Re: [YuLab-SMU/clusterProfiler] kegg parameter change (PR #565) (1) As far as I know, it is necessory to use species <- organismMapper(organism). It will report error without using organismMapper() function. In addition, the current version should not have the KEGG download problem. (2) We have delcared enricher_internal and GSEA_internal in utilities.R. Of course, using getFromNamespace in DOSE.R is a better choice, and we will change it in the next version. — Reply to this email directly, view it on GitHub<#565 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB4Y56JH3Q4HUVISBMB22ITW5GXFPANCNFSM6AAAAAAWBRSRWE>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[huerqiang]

DO you still have this issue using the latest version?

[kkleinoros]

I can’t load the latest version because of the DOSE dependency. kathleen From: Erqiang Hu ***@***.***> Sent: Tuesday, March 21, 2023 10:02 AM To: YuLab-SMU/clusterProfiler ***@***.***> Cc: Kathleen Oros Klein ***@***.***>; Mention ***@***.***> Subject: Re: [YuLab-SMU/clusterProfiler] kegg parameter change (PR #565) DO you still have this issue using the latest version? — Reply to this email directly, view it on GitHub<#565 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB4Y56JCOWQIK5UD3YLHW3LW5GYFTANCNFSM6AAAAAAWBRSRWE>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[huerqiang]

@kkleinoros Please update your packages.
@GuangchuangYu I think we should reject this PR. There is no such problem in the latest version, and the PR will cause errors.

[kkleinoros]

Confirming no issues with latest version on Windows platform, unfortunately I can not test it on our cluster as there are version conflicts. kathleen From: Erqiang Hu ***@***.***> Sent: Tuesday, March 21, 2023 10:13 AM To: YuLab-SMU/clusterProfiler ***@***.***> Cc: Kathleen Oros Klein ***@***.***>; Mention ***@***.***> Subject: Re: [YuLab-SMU/clusterProfiler] kegg parameter change (PR #565) @kkleinoros<https://github.com/kkleinoros> Please update your packages. @GuangchuangYu<https://github.com/GuangchuangYu> I think we should reject this PR. There is no such problem in the latest version, and the PR will cause errors. — Reply to this email directly, view it on GitHub<#565 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB4Y56LFI6TBDTFSF6KVNYLW5GZOTANCNFSM6AAAAAAWBRSRWE>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>