Error(s) in re-building vignettes:
--- re-building 'anintro.Rmd' using rmarkdown
Error: processing vignette 'anintro.Rmd' failed with diagnostics:
DLL 'Rcpp' not found: maybe not installed for this architecture?
--- failed re-building 'anintro.Rmd'

--- re-building 'eos-regress.Rmd' using rmarkdown
Error: processing vignette 'eos-regress.Rmd' failed with diagnostics:
DLL 'Rcpp' not found: maybe not installed for this architecture?
--- failed re-building 'eos-regress.Rmd'

--- re-building 'obigt.Rmd' using rmarkdown
Error: processing vignette 'obigt.Rmd' failed with diagnostics:
DLL 'Rcpp' not found: maybe not installed for this architecture?
--- failed re-building 'obigt.Rmd'

--- re-building 'equilibrium.Rnw' using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'AAsetup'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'AAfigures'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'AAnames'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'showtime'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 200 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 200 values from -20 to 10
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: from numeric argument value
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 80 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 80 values from -20 to 10
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: from numeric argument value
equilibrate: n.balance is 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
equilibrate: loga.balance is -1.69897000433602
equilibrate: using boltzmann method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 200 values from -71 to -66
affinity: variable 2 is log10(a_H2O) at 200 values from -8 to 4
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 80 values from -71 to -66
affinity: variable 2 is log10(a_H2O) at 80 values from -8 to 4
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -0.97061622231479
equilibrate: using reaction method
palply: equil.reaction running 6400 calculations on 2 cores
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 128 values from -8 to 4
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -0.97061622231479
equilibrate: using reaction method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 128 values from -8 to 4
subcrt: 25 species at 298.15 K and 1 bar (wet)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -1.97061622231479
equilibrate: using reaction method
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'PRsetup'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'PRfigures'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 80 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 80 values from -20 to 0
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using reaction method
palply: equil.reaction running 6400 calculations on 2 cores
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 200 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 200 values from -20 to 0
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 200 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 200 values from -20 to 0
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 128 values from -90 to -70
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using reaction method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 128 values from -90 to -70
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 128 values from -90 to -70
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'PRplot2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 200 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 200 values from -20 to 0
subcrt: 12 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'as.residue' in calculation of predominant species
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'Pourbaix'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 1.6 to 7.6
affinity: variable 2 is Eh at 400 values from -0.2 to 1 V
subcrt: 8 species at 298.15 K and 1 bar (wet)
balance: moles of Cu+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 1.6 to 7.6
affinity: variable 2 is Eh at 400 values from -0.2 to 1 V
subcrt: 8 species at 298.15 K and 1 bar (wet)
balance: moles of Cu+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 1.6 to 7.6
affinity: variable 2 is Eh at 400 values from -0.2 to 1 V
subcrt: 8 species at 298.15 K and 1 bar (wet)
balance: moles of Cu+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 1.6 to 7.6
affinity: variable 2 is Eh at 400 values from -0.2 to 1 V
subcrt: 8 species at 298.15 K and 1 bar (wet)
balance: moles of Cu+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'glutathione'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is Eh at 128 values from -0.3 to -0.1 V
subcrt: 8 species at 298.15 K and 1 bar (wet)
balance: moles of C10H17N3O6S in formation reactions
equilibrate: n.balance is 1 2
equilibrate: loga.balance is -2
equilibrate: using reaction method
balance: moles of C10H17N3O6S in formation reactions
equilibrate: n.balance is 1 2
equilibrate: loga.balance is -2.52287874528034
equilibrate: using reaction method
balance: moles of C10H17N3O6S in formation reactions
equilibrate: n.balance is 1 2
equilibrate: loga.balance is -3
equilibrate: using reaction method
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'AddObigt'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinFormation'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinAffinity'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinActivities'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinBasis'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinEquil'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ProteinSpeciation'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 128 values from -100 to -65
subcrt: 16 species at 298.15 K and 1 bar (wet)
subcrt: 18 species at 298.15 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 571 530 571 828 553 278 736 1198 844 481
equilibrate: loga.balance is 0.81888541459401
equilibrate: using reaction method
balance: from protein length
equilibrate: n.balance is 571 530 571 828 553 278 736 1198 844 481
equilibrate: loga.balance is 0.81888541459401
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'SulfurSpeciation'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

affinity: temperature is 325 C
affinity: pressure is 350 bar
affinity: variable 1 is log10(f_O2) at 128 values from -50 to -15
subcrt: 17 species at 598.15 K and 350 bar (wet)
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 2 3 2 2 3 5 2 1 1 1
equilibrate: loga.balance is -2
equilibrate: using reaction method
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 2 3 2 2 3 5 2 1 1 1
equilibrate: loga.balance is -2
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
--- finished re-building 'equilibrium.Rnw'

--- re-building 'hotspring.Rnw' using knitr
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 11 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 330.25 to 366.45 K
affinity: variable 2 is pH at 128 values from 7.35 to 8.257
affinity: variable 3 is log10(a_H2) at 128 values from -6.7175 to -4.0025
subcrt: 11 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
equilibrate: n.balance is 199.13 184.347 195.485 191.803 189.401
equilibrate: loga.balance is -0.0176536766982609
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 330.25 to 366.45 K
affinity: variable 2 is pH at 128 values from 7.35 to 8.257
affinity: variable 3 is log10(a_H2) at 128 values from -6.7175 to -4.0025
subcrt: 36 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 199.13 184.347 195.485 191.803 189.401
equilibrate: loga.balance is -0.0176536766982609
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 246.802 215.664 212.678 218.348 212.768
equilibrate: loga.balance is 0.0438572095139632
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 228.112 217.548 230.214 231.561 223.405
equilibrate: loga.balance is 0.0534011619257556
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 278.511 253.651 259.441 240.969 234.61
equilibrate: loga.balance is 0.102838995245895
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 251.726 232.591 245.652 240.172 236.252
equilibrate: loga.balance is 0.0814888085736157
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
balance: from protein length
equilibrate: using 5 of 30 species
equilibrate: n.balance is 228.73 222.955 234.511 231.369 225.382
equilibrate: loga.balance is 0.0580260920390162
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
reset: resetting "thermo" object
obigt: loading default database with 1841 aqueous, 3360 total species
add.obigt: read 2 rows; made 2 replacements, 0 additions, units = cal
add.obigt: use obigt() or reset() to restore default database
add.protein: added 105 new protein(s) to thermo$protein
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T and P (wet)
subcrt: 18 species at 128 values of T and P (wet)
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
add.protein: added 33 new protein(s) to thermo$protein
affinity: temperature is 93.3 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2) at 101 values from -11 to -1
subcrt: 27 species at 366.45 K and 1 bar (wet)
subcrt: 18 species at 366.45 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 245.95 195.69 211.71 177.2 167.09
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGtr in 1 dimensions
affinity: temperature is 79.4 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2) at 101 values from -11 to -1
subcrt: 27 species at 352.55 K and 1 bar (wet)
subcrt: 18 species at 352.55 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 227.81 207.97 197.37 199.88 210.45 181.82 170.96
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGtr in 1 dimensions
affinity: temperature is 67.5 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2) at 101 values from -11 to -1
subcrt: 27 species at 340.65 K and 1 bar (wet)
subcrt: 18 species at 340.65 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 194.35 220.39 216.78 236.97 229.93 206.83 201.52
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGtr in 1 dimensions
affinity: temperature is 65.3 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2) at 101 values from -11 to -1
subcrt: 27 species at 338.45 K and 1 bar (wet)
subcrt: 18 species at 338.45 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 271.12 210.79 213.12 212.4 209.98 204.53 197.72
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGtr in 1 dimensions
affinity: temperature is 57.1 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2) at 101 values from -11 to -1
subcrt: 27 species at 330.25 K and 1 bar (wet)
subcrt: 18 species at 330.25 K and 1 bar (wet)
balance: from protein length
equilibrate: n.balance is 213.59 212.57 216.98 201.97 220.72 199.31 176.6
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGtr in 1 dimensions
info.character: found H2(aq); other available state is gas
subcrt: 3 species at 6 values of T and P (wet)
info.character: found H2O(liq); other available states are cr, aq
info.character: found H2(aq); other available state is gas
subcrt: 5 species at 5 values of T and P (wet)
info.character: found O2(aq); other available state is gas
info.character: found H2(aq); other available state is gas
info.character: found H2O(liq); other available states are cr, aq
subcrt: 3 species at 5 values of T and P (wet)
--- finished re-building 'hotspring.Rnw'

SUMMARY: processing the following files failed:
  'anintro.Rmd' 'eos-regress.Rmd' 'obigt.Rmd'

Error: Vignette re-building failed.
Execution halted