Error(s) in re-building vignettes:
  ...
--- re-building ‘anintro.Rmd’ using rmarkdown
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 128 values from -12 to 0
affinity: variable 2 is Eh at 128 values from -0.4 to -0.2 V
subcrt: 11 species at 100 C and 1.01 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 128 values from -12 to 0
subcrt: 11 species at 100 C and 1.01 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 5 4 5 5 4
equilibrate: loga.balance is -1.63827216398241
equilibrate: using reaction method
info.character: found methane(aq); other available states are liq, gas
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
subcrt: 1 species at 5511 values of T (C) and P (bar) (wet) [energy units: cal]
changed temperature units to K
changed pressure units to MPa
changed energy units to J
info.character: found methane(aq); other available states are liq, gas
subcrt: 1 species at 298.15 K and 0.1 MPa (wet) [energy units: J]
info.character: found methane(aq); other available states are liq, gas
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
subcrt: 2 species at 36 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 2 species at 36 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 2 species at 36 values of T (C) and P (bar) (wet) [energy units: cal]
info.character: found methane(aq); other available states are liq, gas
subcrt: 2 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 1 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 2  3  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
info.character: found methane(aq); other available states are liq, gas
subcrt: 1 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
info.character: found methane(aq); other available states are liq, gas
subcrt: 2 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
changed energy units to J
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 1 species at 55 C and 50 bar [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 2  3  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 6 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 2  3  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 6 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 C and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 55 C and 50 bar (wet) [energy units: J]
reset: resetting "thermo" object
obigt: loading default database with 1849 aqueous, 3374 total species
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 0 to 12
affinity: variable 2 is Eh at 128 values from -0.5 to 1 V
subcrt: 10 species at 25 C and 1 bar (wet) [energy units: cal]
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr2) is NA; set by EOS parameters to 24.59 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr3) is NA; set by EOS parameters to 20.32 cal K-1 mol-1
info.character: found H2S(aq); other available state is gas
affinity: temperature is 200 C
affinity: pressure is Psat
affinity: variable 1 is pH at 300 values from 0 to 12
affinity: variable 2 is Eh at 300 values from -1.2 to 0.75 V
subcrt: 21 species at 200 C and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -6
equilibrate: using boltzmann method
balance: moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
info.character: found H2S(aq); other available state is gas
affinity: temperature is 200 C
affinity: pressure is Psat
affinity: variable 1 is pH at 300 values from -2 to 12
affinity: variable 2 is Eh at 300 values from -1 to 1 V
subcrt: 21 species at 200 C and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -6
equilibrate: using boltzmann method
balance: moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
info.character: found H2S(aq); other available state is gas
affinity: temperature is 200 C
affinity: pressure is Psat
affinity: variable 1 is pH at 300 values from -2 to 12
affinity: variable 2 is log10(a_H2) at 300 values from -30 to 10
subcrt: 21 species at 200 C and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -6
equilibrate: using boltzmann method
balance: moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
info.character: found H2S(aq); other available state is gas
affinity: temperature is 200 C
affinity: pressure is Psat
affinity: variable 1 is pH at 300 values from -2 to 12
affinity: variable 2 is log10(f_O2) at 300 values from -70 to 5
subcrt: 21 species at 200 C and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -6
equilibrate: using boltzmann method
balance: moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: pressure is Psat
affinity: variable 1 is T at 18 values from 278.596 to 622.8 K
affinity: variable 2 is log10(a_CO2) at 18 values from -3.6506 to -1.8288
affinity: variable 3 is log10(a_H2) at 18 values from -47.4549 to -1.8288
affinity: variable 4 is log10(a_NH4+) at 18 values from -6.2165 to -4.5641
affinity: variable 5 is log10(a_H2S) at 18 values from -5.2891 to -2.9213
affinity: variable 6 is pH at 18 values from 3.0312 to 7.1784
subcrt: 14 species at 18 values of T (C) and P (bar) (wet) [energy units: cal]
balance: from numeric argument value
diagram: plotting A/(2.303RT) / n.balance
affinity: temperature is 300 C
affinity: pressure is 100 bar
subcrt: 7 species at 300 C and 100 bar (wet) [energy units: cal]
affinity: temperature is 300 C
affinity: pressure is 100 bar
affinity: loading buffer species
subcrt: 7 species at 300 C and 100 bar (wet) [energy units: cal]
buffer: ( PPM ) for activity of H2S O2 (active), FeS2 (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 9 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phases 2,1 are stable
subcrt: 4 phases for iron ... phases 2,1 are stable
buffer: ( FeFeO ) for activity of H2 (active), Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 10 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phases 2,1 are stable
buffer: ( QFM ) for activity of H2 (active), SiO2, Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 10 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: temperature(s) of 598.346850393701 K and above exceed limit for pyrrhotite cr2 (extrapolating G)
subcrt: 4 phases for iron ... phases 2,1 are stable
buffer: ( PPM ) for activity of H2 (active), H2S, Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 9 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phases 2,1 are stable
buffer: ( HM ) for activity of H2 (active), Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
subcrt: 9 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
subcrt: 9 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
affinity: pressure is 300 bar
affinity: variable 1 is T at 128 values from 273.15 to 623.15 K
subcrt: 9 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 4 to 13
subcrt: 9 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: temperature is 150 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 4 to 13
subcrt: 9 species at 150 C and 4.76 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
diagram: plotting A/(2.303RT) / n.balance
balance: moles of CO2 in formation reactions
diagram: plotting A/(2.303RT) / n.balance
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 1 1 1
equilibrate: loga.balance is -3
equilibrate: using boltzmann method
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 1 1 1
equilibrate: loga.balance is -3
equilibrate: using boltzmann method
add.obigt: read 169 rows; made 41 replacements, 128 additions [energy units: cal]
add.obigt: use obigt() or reset() to restore default database
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 0 to 10
subcrt: 9 species at 25 C and 1 bar (wet) [energy units: cal]
solubility: test for dissociation reaction returns FALSE
balance: moles of Al2O3 in formation reactions
reset: resetting "thermo" object
obigt: loading default database with 1849 aqueous, 3374 total species
info.character: found methanol(aq); other available states are liq, gas
info.character: found acetone(aq); other available states are liq, gas
info.character: found acetic acid(aq); other available state is liq
info.character: found n-dodecanoic acid(aq); other available state is liq
info.character: found ethylene(aq); other available state is gas
affinity: pressure is Psat
affinity: variable 1 is T at 343 values from 281.15 to 623.15 K
affinity: variable 2 is log10(f_O2) at 343 values from -79.68124673285 to -33.0210103059345
affinity: variable 3 is pH at 343 values from 4.30780425406988 to 6.99186808462121
subcrt: 51 species at 343 values of T (C) and P (bar) (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 1 1 1 2 3 4 5 6 7 8 3 4 5 6 7 8 2 3 4 5 6 7 8 9 10 11 12 2 3 4 5 6 7 8 9 10 11 12 2 3 4 5 6 7 8
equilibrate: loga.balance is -2.5
equilibrate: using reaction method
subcrt: 5 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 5 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: temperature is 250 C
affinity: pressure is 265 bar
affinity: variable 1 is log10(f_O2) at 200 values from -50 to -25
affinity: variable 2 is log10(f_CO2) at 200 values from -10 to 15
subcrt: 25 species at 250 C and 265 bar (wet) [energy units: cal]
info.character: found alanine(aq); other available state is cr
info.character: found cysteine(aq); other available state is cr
info.character: found aspartic acid(aq); other available state is cr
info.character: found glutamic acid(aq); other available state is cr
info.character: found phenylalanine(aq); other available state is cr
info.character: found glycine(aq); other available state is cr
info.character: found histidine(aq); other available state is cr
info.character: found isoleucine(aq); other available state is cr
info.character: found lysine(aq); other available state is cr
info.character: found leucine(aq); other available state is cr
info.character: found methionine(aq); other available state is cr
info.character: found asparagine(aq); other available state is cr
info.character: found proline(aq); other available state is cr
info.character: found glutamine(aq); other available state is cr
info.character: found arginine(aq); other available state is cr
info.character: found serine(aq); other available state is cr
info.character: found threonine(aq); other available state is cr
info.character: found valine(aq); other available state is cr
info.character: found tryptophan(aq); other available state is cr
info.character: found tyrosine(aq); other available state is cr
balance: from numeric argument value
diagram: using maximum affinity method for 2-D diagram
balance: moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of H2O in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: moles of N2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: from volume
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 13 species at 100 C and 1.01 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10
equilibrate: loga.balance is -1.30102999566398
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 13 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10
equilibrate: loga.balance is -1.30102999566398
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 128 values from 3 to 9
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 C
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 128 values from -2 to -7
subcrt: 17 species at 100 C and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
protein.obigt: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
subcrt: 1 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
protein.obigt: found CYC_BOVIN (C517H825N143O150S4, 104 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) (wet) [energy units: cal]
protein.obigt: found CYC_BOVIN (C517H825N143O150S4, 104 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) [energy units: cal]
subcrt: 1 species at 151 values of T (C) and P (bar) (wet) [energy units: cal]
protein.obigt: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) [energy units: cal]
protein.obigt: found MYG_PHYCA (C783H1240N216O216S2, 153 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) (wet) [energy units: cal]
protein.obigt: found MYG_PHYCA (C783H1240N216O216S2, 153 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) [energy units: cal]
protein.obigt: found RNAS1_BOVIN (C575H909N171O193S12, 124 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) (wet) [energy units: cal]
protein.obigt: found RNAS1_BOVIN (C575H909N171O193S12, 124 residues)
subcrt: 1 species at 151 values of T (C) and P (bar) [energy units: cal]
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 0 to 14
subcrt: 27 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: temperature is 25 C
affinity: pressure is Psat
subcrt: 26 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: temperature is 25 C
affinity: pressure is Psat
subcrt: 9 species at 25 C and 1 bar (wet) [energy units: cal]
read.fasta: reading rubisco.fasta ... 239 lines ... 27 sequences
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 128 values from -80 to -73
subcrt: 27 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
balance: from protein length
equilibrate: n.balance is 1273 929 297 876 2195
equilibrate: loga.balance is 0
equilibrate: using reaction method
balance: from protein length
equilibrate: n.balance is 1273 929 297 876 2195
equilibrate: loga.balance is 0
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGinf in 1 dimensions
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 50 values from -5.5 to 0.5
affinity: variable 2 is log10(f_O2) at 50 values from -106 to -70
subcrt: 26 species at 25 C and 1 bar (wet) [energy units: cal]
balance: from numeric argument value
diagram: plotting A/(2.303RT) / n.balance
read.fasta: reading EF-Tu.aln ... 64 lines ... 8 sequences
protein.obigt: found PRIO_HUMAN (C1227H1834N352O352S16, 253 residues)
subcrt: 1 species at 25 C and 1 bar (wet) [energy units: cal]
affinity: temperature is 25 C
affinity: pressure is Psat
subcrt: 6 species at 25 C and 1 bar (wet) [energy units: cal]
add.protein: added 1 new protein(s) to thermo$protein
add.protein: replaced 1 existing protein(s) in thermo$protein
affinity: temperature is 25 C
affinity: pressure is Psat
subcrt: 27 species at 25 C and 1 bar (wet) [energy units: cal]
add.protein: added 5 new protein(s) to thermo$protein
affinity: pressure is Psat
affinity: variable 1 is T at 300 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 300 values from -8 to -3
subcrt: 27 species at 300 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 300 values of T (C) and P (bar) (wet) [energy units: cal]
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
info.character: found aspartic acid(aq); other available state is cr
info.character: found threonine(aq); other available state is cr
info.character: found serine(aq); other available state is cr
info.character: found glutamic acid(aq); other available state is cr
info.character: found glycine(aq); other available state is cr
info.character: found alanine(aq); other available state is cr
info.character: found lysine(aq); other available state is cr
info.character: found histidine(aq); other available state is cr
affinity: temperature is 270 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 64 values from -50 to -25
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 1 dimensions
affinity: temperature is 270 C
affinity: pressure is Psat
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 0 dimensions
affinity: temperature is 270 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 64 values from -50 to -25
affinity: variable 2 is log10(a_NH3) at 64 values from -15 to 10
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
palply: equil.reaction running 4096 calculations on 2 cores
revisit: calculating RMSD in 2 dimensions
affinity: temperature is 270 C
affinity: pressure is Psat
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 0 dimensions

###### findit: iteration 1 of 3
### O2 new limits: -50 -25
### NH3 new limits: -15 10
### H2O new limits: -15 10
affinity: temperature is 270 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 8 values from -50 to -25
affinity: variable 2 is log10(a_NH3) at 8 values from -15 to 10
affinity: variable 3 is log10(a_H2O) at 8 values from -15 to 10
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 3 dimensions
revisit: calculating RMSD in 2 dimensions

###### findit: iteration 2 of 3
### O2 optimal: -35.7143  new limits: -43.2143 -28.2143
### NH3 optimal: -0.7143  new limits: -8.2143 6.7857
### H2O optimal: -0.7143  new limits: -8.2143 6.7857
affinity: temperature is 270 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 8 values from -43.2142857142857 to -28.2142857142857
affinity: variable 2 is log10(a_NH3) at 8 values from -8.21428571428571 to 6.78571428571429
affinity: variable 3 is log10(a_H2O) at 8 values from -8.21428571428571 to 6.78571428571429
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 3 dimensions
revisit: calculating RMSD in 2 dimensions

###### findit: iteration 3 of 3
### O2 optimal: -36.7857  new limits: -41.2857 -32.2857
### NH3 optimal: -1.7857  new limits: -6.2857 2.7143
### H2O optimal: -1.7857  new limits: -6.2857 2.7143
affinity: temperature is 270 C
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 8 values from -41.2857142857143 to -32.2857142857143
affinity: variable 2 is log10(a_NH3) at 8 values from -6.28571428571428 to 2.71428571428572
affinity: variable 3 is log10(a_H2O) at 8 values from -6.28571428571428 to 2.71428571428572
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 3 dimensions
revisit: calculating RMSD in 2 dimensions
affinity: temperature is 270 C
affinity: pressure is Psat
subcrt: 13 species at 270 C and 55 bar (wet) [energy units: cal]
balance: moles of CO2 in formation reactions
equilibrate: n.balance is 4 4 3 5 2 3 6 6
equilibrate: loga.balance is -4.45854557125241
equilibrate: using reaction method
revisit: calculating RMSD in 0 dimensions
info.character: found C2H5OH(aq); other available states are liq, gas
info.character: found O2(aq); other available state is gas
info.character: found CO2(aq); other available state is gas
info.character: found H2O(liq); other available states are cr, aq
subcrt: 4 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 3 species at 8 values of T (C) and P (bar) (wet) [energy units: cal]
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 31 values from -80 to -50
affinity: variable 2 is T at 101 values from 273.15 to 373.15 K
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'anintro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘anintro.Rmd’

--- re-building ‘eos-regress.Rmd’ using rmarkdown
EOSplot: plotting line for P=279.96 bar
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=1000 bar
EOSplot: plotting line for P=1000 bar
add.obigt: read 3 rows; made 2 replacements, 1 additions [energy units: cal]
add.obigt: use obigt() or reset() to restore default database
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 50 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found H4SiO4(aq); other available state is aq
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 3 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
info.character: found H4SiO4(aq); other available state is aq
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 3 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
affinity: temperature is 25 C
affinity: pressure is Psat
affinity: variable 1 is log10(a_H4SiO4) at 300 values from -8 to 0
affinity: variable 2 is log10(a_K+) at 300 values from -1 to 8
subcrt: 11 species at 25 C and 1 bar (wet) [energy units: cal]
balance: moles of Al+3 in formation reactions
diagram: using maximum affinity method for 2-D diagram
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'eos-regress.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘eos-regress.Rmd’

--- re-building ‘obigt.Rmd’ using rmarkdown
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'obigt.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- 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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
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 25 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 C and 1 bar (wet) [energy units: cal]
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 325 C and 350 bar (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
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 1849 aqueous, 3374 total species
add.obigt: read 2 rows; made 2 replacements, 0 additions [energy units: cal]
add.obigt: use obigt() or reset() to restore default database
add.protein: added 105 new protein(s) to thermo$protein
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: pressure is Psat
affinity: variable 1 is T at 128 values from 323.15 to 373.15 K
affinity: variable 2 is log10(a_H2) at 128 values from -7 to -4
subcrt: 27 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: 18 species at 128 values of T (C) and P (bar) (wet) [energy units: cal]
balance: from protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
add.protein: added 33 new protein(s) to thermo$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 93.3 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 93.3 C and 1 bar (wet) [energy units: cal]
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 79.4 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 79.4 C and 1 bar (wet) [energy units: cal]
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 67.5 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 67.5 C and 1 bar (wet) [energy units: cal]
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 65.3 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 65.3 C and 1 bar (wet) [energy units: cal]
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 57.1 C and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 57.1 C and 1 bar (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
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 (C) and P (bar) (wet) [energy units: cal]
--- 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