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umich-cphds / createUKBphenome

Create a PheWAS code based phenome using ICD9 and ICD10 data from baskets of the UK biobank
GNU General Public License v3.0
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Error: failed to load external entity "http://biobank.ndph.ox.ac.uk/showcase/list.cgi?it=0&vt=11" #3

Closed mbyrska closed 4 years ago

mbyrska commented 4 years ago

Hello, I'm running into the error below when trying to run the function.createUKBphenome.r script. It seems to be caused by line 24 in the function.collectFields.r script. Any advice how to fix this? Thanks so much!

Rscript ./scripts/function.createUKBphenome.r [1] "Mapping ICD9 codes to PheCodes" There were 19 warnings (use warnings() to see them) [1] "Rollup of phewas codes (ICD9 code)"

         original rolled up PheWAS code 
            18689                  2973

[1] "Mapping ICD10 codes to PheCodes" [1] "Rollup of phewas codes (ICD10 code)"

         original rolled up PheWAS code 
            15908                  7030

[1] "Mapping tables created and stored in ./results/UKB_PHENOME_ICD*_PHECODE_MAP_20201103.txt" [1] "Collecting UKB fields and data" Error: failed to load external entity "http://biobank.ndph.ox.ac.uk/showcase/list.cgi?it=0&vt=11" Execution halted

ilarsf commented 4 years ago

Hello, I rewrote function.collectFields.r to use a different R library. Also updated URL from http to https.

mbyrska commented 4 years ago

Perfect, it works fine now! Thanks a lot for your help!