title: How do I overcome issues with MetaboAnalyst in R when trying to run pathway analysis?
body: <p>I am using this code <a href="https://drive.google.com/file/d/1CXluzyYqNoPqu1DI3HwvDAmRVGMe825m/view" rel="nofollow noreferrer">https://drive.google.com/file/d/1CXluzyYqNoPqu1DI3HwvDAmRVGMe825m/view</a> in order to undertake a pathway analysis using <a href="https://github.com/jsychong/MetaboAnalystR/" rel="nofollow noreferrer"><code>MetaboAnalystR</code></a>. </p>
  
  <p>When I get to this stage</p>
  
  <pre><code> mSet&lt;-CalculateOraScore(mSet, "rbc", "hyperg")
  </code></pre>
  
  <p>I get this error</p>
  
  <pre><code>Loading files from server unsuccessful. Ensure curl is downloaded on your computer
  
  Error in if (is_http) { : argument is of length zero
  </code></pre>
  
  <p>I have gone through the FAQs and troubleshooting pages, and can't rectify this. I have gone through all of the installation steps on another computer ( Windows again unfortunately, and I get the same issue). </p>
  
  <p>This is likely to be a curl problem on Windows. ( It is already installed for me on Windows 10, please see other question <a href="https://stackoverflow.com/questions/62122313/what-else-can-i-do-to-make-sure-that-curl-is-working-when-i-am-using-r-metaboa">What else can I do to make sure that curl is working when I am using R ( MetaboAnalyst package) in Windows 10?</a>). </p>
  
  <p>The trouble shooting advice on <a href="https://github.com/xia-lab/MetaboAnalystR/blob/master/R/general_data_utils.R" rel="nofollow noreferrer">https://github.com/xia-lab/MetaboAnalystR/blob/master/R/general_data_utils.R</a> regarding curl issues also does not work for me. </p>
  
  <p>EDIT 2: larger list of compounds</p>
  
  <p>If possible, I would be very grateful if anybody would please be willing to run the below code, and get the graph of Pathway Impact vs -log(p), with a results output, so I can annotate the spots on the graph if neccessary. The code is as follows;</p>
  
  <pre><code>  library(MetaboAnalystR)
       tmp.vec &lt;- c(tmp.vec &lt;- c("Indole-3-carboxylic acid", "4-O-Methylgallic acid", "Hippuric acid", "Pyrocatechol", "Hydroquinone",
          "Aspartame", "trans-Ferulic acid", "2,6-Dimethoxyphenol", "2-Methylhippuric acid", "2-(Hydroxymethyl)benzoic acid", 
          "3-(2-Hydroxyphenyl)propanoic acid", "1-Methyluric acid", "Dehydroisoandrosterone 3-glucuronide", "Ascorbic acid",
          "D-Tartaric acid", "Kynurenic acid", "Xanthine", "Vanillic acid", "Glyceraldehyde", "D-Lactic acid", "Pregnanediol", 
          "7-Methylguanine", "Gluconic acid", "4-Aminophenol", "Caffeic acid", "Enterolactone", "Adipic acid", 
          "1H-Indole-3-carboxaldehyde", "4-Hydroxybenzoic acid", "Creatinine", "2-Aminobenzoic acid", "Uric acid")
  
   mSet&lt;-InitDataObjects("conc", "pathora", FALSE)
   mSet&lt;-Setup.MapData(mSet, tmp.vec);
   mSet&lt;-CrossReferencing(mSet, "name");
   mSet&lt;-CreateMappingResultTable(mSet);
  
   ##4-O-Methylgallic acid and 2-Methylhippuric acid need correct kegg ID format
  
   mSet$dataSet$map.table[2,5] &lt;- "C05616"
   mSet$dataSet$map.table[9,5] &lt;- "C01586"
  
  
   mSet&lt;-SetKEGG.PathLib(mSet, "hsa", "current")
   mSet&lt;-SetMetabolomeFilter(mSet, F)
   mSet&lt;-CalculateOraScore(mSet, "rbc", "hyperg")
   mSet&lt;-PlotPathSummary(mSet, "path_view_0_", "png", 72, width=NA)
  </code></pre>