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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "patient_id"
NOTE: Auto-guessing columns suitable for analysis...OK.
NOTE: Reliability will 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 (roxithromycin), 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                          I10
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.
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.
NOTE: Using column `bacteria` as input for `col_mo`.
NOTE: Using column `date` as input for `col_date`.
NOTE: Using column `patient_id` as input for `col_patient_id`.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'AMR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘AMR.Rmd’

--- re-building ‘EUCAST.Rmd’ using rmarkdown
NOTE: Using column `mo` as input for `col_mo`.
NOTE: Auto-guessing columns suitable for analysis...OK.
NOTE: Reliability will be improved if these antimicrobial results would be available too: AMK (amikacin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), 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), CIP (ciprofloxacin), CLR (clarithromycin), CLI (clindamycin), COL (colistin), DAP (daptomycin), DOX (doxycycline), ETP (ertapenem), ERY (erythromycin), FLC (flucloxacillin), FOS (fosfomycin), FUS (fusidic acid), GEN (gentamicin), 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 (roxithromycin), SIS (sisomicin), TEC (teicoplanin), TCY (tetracycline), TIC (ticarcillin), TGC (tigecycline), TOB (tobramycin), TMP (trimethoprim), SXT (trimethoprim/sulfamethoxazole), VAN (vancomycin)
NOTE: Using column `mo` as input for `col_mo`.
NOTE: Auto-guessing columns suitable for analysis...OK.
NOTE: Reliability will be improved if these antimicrobial results would be available too: AMK (amikacin), AMC (amoxicillin/clavulanic acid), AMP (ampicillin), AZM (azithromycin), AZL (azlocillin), ATM (aztreonam), RID (cefaloridine), CZO (cefazolin), FEP (cefepime), CTX (cefotaxime), CRO (ceftriaxone), CED (cephradine), CHL (chloramphenicol), CIP (ciprofloxacin), CLR (clarithromycin), CLI (clindamycin), DAP (daptomycin), DOX (doxycycline), ETP (ertapenem), ERY (erythromycin), FLC (flucloxacillin), FOS (fosfomycin), FUS (fusidic acid), GEN (gentamicin), 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), PIP (piperacillin), TZP (piperacillin/tazobactam), PLB (polymyxin B), PRI (pristinamycin), QDA (quinupristin/dalfopristin), RIF (rifampicin), RXT (roxithromycin), SIS (sisomicin), TEC (teicoplanin), TCY (tetracycline), TIC (ticarcillin), TGC (tigecycline), TOB (tobramycin), TMP (trimethoprim), SXT (trimethoprim/sulfamethoxazole)
NOTE: Using column `AMX` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'EUCAST.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘EUCAST.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

NOTE: Using column `mo` as input for `col_mo`.
NOTE: Auto-guessing columns suitable for analysis...OK.
NOTE: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)
Warning in mdro(., info = FALSE) :
  NA introduced for isolates where the available percentage of antimicrobial classes was below 50% (set with `pct_required_classes`)
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'MDR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘MDR.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'WHONET.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘WHONET.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'resistance_predict.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘resistance_predict.Rmd’

SUMMARY: processing the following files failed:
  ‘AMR.Rmd’ ‘EUCAST.Rmd’ ‘MDR.Rmd’ ‘WHONET.Rmd’
  ‘resistance_predict.Rmd’

Error: Vignette re-building failed.
Execution halted