Error(s) in re-building vignettes:
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--- re-building ‘AMR.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

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Joining, by = "patient_id"
NOTE: Auto-guessing columns suitable for analysis...
NOTE: Reliability might be improved if these antimicrobial results would be available too: AMK (amikacin), AMP (ampicillin), AZM (azithromycin), AZL (azlocillin), ATM (aztreonam), RID (cefaloridine), CZO (cefazolin), FEP (cefepime), CTX (cefotaxime), FOX (cefoxitin), CAZ (ceftazidime), CRO (ceftriaxone), CXM (cefuroxime), CED (cephradine), CHL (chloramphenicol), CLR (clarithromycin), CLI (clindamycin), COL (colistin), DAP (daptomycin), DOX (doxycycline), ETP (ertapenem), ERY (erythromycin), FLC (flucloxacillin), FOS (fosfomycin), FUS (fusidic acid), IPM (imipenem), KAN (kanamycin), LVX (levofloxacin), LIN (lincomycin), LNZ (linezolid), MEM (meropenem), MEZ (mezlocillin), MNO (minocycline), MFX (moxifloxacin), NAL (nalidixic acid), NEO (neomycin), NET (netilmicin), NIT (nitrofurantoin), NOR (norfloxacin), NOV (novobiocin), OFX (ofloxacin), OXA (oxacillin), PEN (penicillin G), PIP (piperacillin), TZP (piperacillin/tazobactam), PLB (polymyxin B), PRI (pristinamycin), QDA (quinupristin/dalfopristin), RIF (rifampicin), RXT (roxithromicin), SIS (sisomicin), TEC (teicoplanin), TCY (tetracycline), TIC (ticarcillin), TGC (tigecycline), TOB (tobramycin), TMP (trimethoprim), SXT (trimethoprim/sulfamethoxazole), VAN (vancomycin)
NOTE: Using column `AMX` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.
  weighted_df[1, "patient_id"]
1                           D3
Warning: only using 3 different antibiotics as key antibiotics for Gram-positives. See ?key_antibiotics.
Warning: only using 4 different antibiotics as key antibiotics for Gram-negatives. See ?key_antibiotics.
Terminated
--- re-building ‘EUCAST.Rmd’ using rmarkdown
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--- re-building ‘MDR.Rmd’ using rmarkdown
--- finished re-building ‘MDR.Rmd’

--- re-building ‘WHONET.Rmd’ using rmarkdown

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--- re-building ‘resistance_predict.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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--- finished re-building ‘resistance_predict.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted