############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data immunotation ### ############################################################################## ############################################################################## * checking for file ‘immunotation/DESCRIPTION’ ... OK * preparing ‘immunotation’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘immunotation_vignette.Rmd’ using rmarkdown Quitting from immunotation_vignette.Rmd:342-348 [unnamed-chunk-18] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `getURL()`: ! 'getURL()' failed: URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci= error: cannot open the connection --- Backtrace: ▆ 1. └─immunotation::query_haplotype_frequencies(...) 2. └─immunotation:::read_complete_freq_table(queryurl, type = "haplotype") 3. └─immunotation:::getURL(url, read_method = "html") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'immunotation_vignette.Rmd' failed with diagnostics: 'getURL()' failed: URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci= error: cannot open the connection --- failed re-building ‘immunotation_vignette.Rmd’ SUMMARY: processing the following file failed: ‘immunotation_vignette.Rmd’ Error: Vignette re-building failed. Execution halted