cannot open URL 'http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip'

[danli349]

Hello Wubing Can you please fix this problem?

 Running KEGG+REACTOME+GOBP+Complex enrichment analysis
 Downloading genesets from CORUM ...
Error in download.file(base_url, locfname, quiet = TRUE) :
  cannot open URL 'http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip'
In addition: Warning messages:
1: ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
2: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
3: ggrepel: 16 unlabeled data points (too many overlaps). Consider increasing max.overlaps
4: In download.file(base_url, locfname, quiet = TRUE) :
  URL 'http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip': status was 'Couldn't connect to server'

Thanks

[nathanthorpe]

I fixed it in #16 but it looks like the provider updated the link to work on http again

[AnaSastrePerona]

Hello, i am getting also this error, do you know if it was fixed? If not, do you kwon an alternative?

Thanks!

[danli349]

I think you can try http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip, if it can't open then try https://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip

[nathanthorpe]

allComplexes.txt.zip

Here is a copy of the file if you want to host it locally, or I have a mirror set up if you want to replace the URL. http://mips.helmholtz-muenchen.de.s3.amazonaws.com/corum/download/allComplexes.txt.zip

[aastha-v]

Hello, the error now reads:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : cannot read from connection In addition: Warning message: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : URL 'https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/20234073/Achilles_gene_effect.csv?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20240623/eu-west-1/s3/aws4_request&X-Amz-Date=20240623T183401Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=207ac55ae3f5145ebbef4b6b178926a7c5b20d177b63b180e00a3efd07302a39': Timeout of 60 seconds was reached

Where in the code can I make modifications so that the locally downloaded allComplexes.txt.zip can be used instead?

I was able to download the file here, as suggested by @nathanthorpe above: https://github.com/WubingZhang/MAGeCKFlute/files/11398265/allComplexes.txt.zip