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b2slab / FELLA

FELLA: an R package for Metabolomics data enrichment through diffusion
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buildGraphFromKEGGREST can't work #23

Closed wuzeming closed 1 year ago

wuzeming commented 2 years ago

@nturaga

Dear,

I appreciate your distinguished work published in BMC bioinformatics 2018. I can't agree with you more that metabolomics community must embrace new generation data mining philosophy for enrichment and get inslight about altered metabolic pathway.

but, i am facing trouble as shown below when i am trying your program. actually, I am a mass spectrometrist, and l know very limited about R programming. Could you help me to fix my problem, pls? image

nturaga commented 2 years ago

Hi,

Please send an email to bioc-devel@r-project.org if you have questions regarding Bioconductor.

SergiPicart commented 2 years ago

Dear Wuzeming,

Thank you for using FELLA. It looks like there are issues retrieving the files from the KEGG servers. Have you checked if a command like KEGGREST::keggLink("cpd", "pathway") works? (since FELLA uses KEGGREST under the hood). If it does not, you may check for general connectivity issues, like firewalls or proxies Best, Sergi

wuzeming commented 2 years ago

Dear Sergi,

thank your kindly reply. I tried your recommendation and the command KEGGREST::keggLink("cpd", "pathway") still can't work. anyway, i will go to my webmaster to check the general connectivity of my workstation. thanks again.

Best, zeming