error for netAnalysis_contribution

[QiangShiPKU]

Error in `levels<-`(`*tmp*`, value = as.character(levels)) : factor level [3] is duplicated

It seems to result from duplicate L-R pairs of certain pathways in CellChatDB.
The same error: https://www.jianshu.com/p/ffe99c3028da

[sqjin]

@QiangShiPKU Are you using the zebrafish database or others?

[QiangShiPKU]

@sqjin Thanks for your quick response. I am using the human database.
cellchat@DB <- CellChatDB.human

[lisch7]

Same issue when using CellChatDB.human. I countered this issue when I ran netAnalysis_contribution(cellchat,signaling = "SIRP")

[lisch7]

It seems that RA, SIRP, PARS, LAIR1 might have duplicated pair according to the code offered in https://www.jianshu.com/p/ffe99c3028da

@sqjin

[hualihushaoaaaaa]

ERROR: dependency 'presto' is not available for package 'CellChat'

• removing 'C:/Users/juwai/AppData/Local/R/win-library/4.3/CellChat'
  Warning message:
  In i.p(...) :
  安装程序包‘C:/Users/juwai/AppData/Local/Temp/RtmpusRCDH/file456c30a93d66/CellChat_2.1.2.tar.gz’时退出狀態的值不是0

[chenfengQAQ]

I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue!

[hualihushaoaaaaa]

| | juwairenjiamiao | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 2/25/2024 19:03 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[chenfengQAQ]

| | juwairenjiamiao | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 2/25/2024 19:03 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

Sorry,but I couldn't understand well.Could you please provide a more specific description?Thanks!

[sqjin]

@hualihushaoaaaaa devtools::install_github('immunogenomics/presto')

[hwbdhuidhcoi]

| | juwairenjiamiao | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 2/25/2024 19:03 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

@hualihushaoaaaaa devtools::install_github('immunogenomics/presto')

if presto can not be installed,make sure you have the correct version Rtools

[chenfengQAQ]

Thanks your response,I've known how to solve it! At 2024-03-08 09:38:28, "hwbdhuidhcoi" ***@***.***> wrote: | | juwairenjiamiao | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 2/25/2024 19:03 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***> @hualihushaoaaaaadevtools::install_github('immunogenomics/presto') if presto can not be installed,make sure you have the correct version Rtools — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[hualihushaoaaaaa]

可能是每个人电脑的问题，我只是按照发给你的图片上面的操作来的，就直接安装了。 | | juwairenjiamiao | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 3/8/2024 11:30 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | Thanks your response,I've known how to solve it! At 2024-03-08 09:38:28, "hwbdhuidhcoi" ***@***.***> wrote: | | juwairenjiamiao | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 2/25/2024 19:03 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***> @hualihushaoaaaaadevtools::install_github('immunogenomics/presto') if presto can not be installed,make sure you have the correct version Rtools — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[chenfengQAQ]

感谢回复！我已按照作者提供的方案解决了！ At 2024-03-09 10:06:39, "hualihushaoaaaaa" ***@***.***> wrote: 可能是每个人电脑的问题，我只是按照发给你的图片上面的操作来的，就直接安装了。 | | juwairenjiamiao | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 3/8/2024 11:30 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | Thanks your response,I've known how to solve it! At 2024-03-08 09:38:28, "hwbdhuidhcoi" ***@***.***> wrote: | | juwairenjiamiao | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 2/25/2024 19:03 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [jinworks/CellChat] error for netAnalysis_contribution (Issue #5) | I recently encountered the following issue while installing CellChat: "dependency 'presto' is not available for package 'CellChat'". I ensured that my three packages, NMF (v0.27), circlize (v0.4.15), and ComplexHeatmap (v2.18.0), were installed correctly. I searched for 'presto' on the R official website and Bioconductor, but did not get any results. The version of R I am using is 4.3.2. I am looking forward to your response regarding this issue! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***> @hualihushaoaaaaadevtools::install_github('immunogenomics/presto') if presto can not be installed,make sure you have the correct version Rtools — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>