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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Error in download.file(url, quiet = quiet, method = "libcurl"), libcurl cannot be change #648

Open Junyan1996 opened 10 months ago

Junyan1996 commented 10 months ago

I use the following command library(clusterProfiler) data("geneList",package = "DOSE") de=names(geneList)[1:100] enrichKEGG(de)

result

Reading KEGG annotation online:

fail to download KEGG data...
Error in download.KEGG.Path(species) :
'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...
In addition: Warning message:
In utils::download.file(url, quiet = quiet, method = "libcurl", :
URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer

I try to fix it by

options(clusterProfiler.download.method = "curl")
options(download.file.extra = "-k")
R.utils::setOption("clusterProfiler.download.method","auto")

and the out put of getOption("clusterProfiler.download.method") is [1] "auto"

but when I do enrichKEGG(de) again， get the same result as above

Junyan1996 commented 10 months ago

R version 4.0.3 (2020-10-10) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 19044)

BiocManager_1.30.22
clusterProfiler_3.18.1

guidohooiveld commented 9 months ago

Please use the latest version of R (=R-4.3.x) and Bioconductor (=3.18)! Development of packages goes on continuously, and you are using a very old version of R (and corresponding Bioconductor packages); these are more than 3 years old!

For example, I know that the API of the KEGG website has changed several times after June 2020, so this will never work in R-4.0.3!