gseKEGG()函数运行时出错

[ZhanshenWu]

老师 您好， 在运行gseKEGG的过程中，出现了报错，网上找到的修改clusterProfiler.download.method也没能解决 代码如下： gse <- gseKEGG(geneList = geneList, organism = 'hsa', nPerm = 10000, minGSSize = 10, maxGSSize = 200, pvalueCutoff = 0.05, pAdjustMethod = "fdr") 报错如下： Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"... Error in file(con, "r") : cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway' 此外: Warning message: In file(con, "r") : URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'SSL connect error'

[guidohooiveld]

This code is working for me. Be sure to use the latest version of clusterProfiler.

Also, to exclude networks problems, check that the URL above is work in your browser (i.e. https://rest.kegg.jp/link/hsa/pathway).

[PanSX-Dr]

兄弟，我也遇到同样的问题了，但是我是最新版本的，还是没解决。你的解决没？

[huerqiang]

我暂时没能复现你的这个问题，我建议你尝试下别的网路环境，有没有受VPN的影响？

[HayleyVoltri]

我也遇到一样的问题！不知道有没有朋友解决了的？我的clusterProfiler是4.10.0，R是4.3.2，用了VPN也是说连不上https://rest.kegg.jp/link/hsa/pathway，但是浏览器可以打开这个网页...谢谢各位大佬们！

[guidohooiveld]

In case your web traffic is monitored, I would like to point you to this post. The proposed solution may also work for you. https://stackoverflow.com/a/76684292/19054992

[HayleyVoltri]

Thanks so much for the advice! After trying many approaches in the past 1 week, the bug surprisingly disappeared last night, so I guess it was the web traffic problem (perhaps because of the Spring Festival). If this bug comes back again, I will firstly turn to the post you pointed to me. Many thanks again!

------------------ 原始邮件 ------------------ 发件人: "YuLab-SMU/clusterProfiler" @.>; 发送时间: 2024年2月12日(星期一) 下午4:40 @.>; @.@.>; 主题: Re: [YuLab-SMU/clusterProfiler] gseKEGG()函数运行时出错 (Issue #652)

In case your web traffic is monitored, I would like to point you to this post. The proposed solution may also work for you. https://stackoverflow.com/a/76684292/19054992

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