Error(s) in re-building vignettes:
  ...
--- re-building 'anintro.Rmd' using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CHNOSZ
 --- call from context --- 
put.basis(ispecies, logact)
 --- call from argument --- 
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
 --- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4: basis("CHNOSe")
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 14: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 29: tools:::.buildOneVignette("anintro.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ", 
    TRUE, FALSE, "anintro", "UTF-8", "/tmp/RtmprDz9bN/file103e5923b0b1.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (ispecies, logact = rep(NA, length(ispecies))) 
{
    thermo <- get("thermo", CHNOSZ)
    state <- thermo$obigt$state[ispecies]
    comp <- makeup(ispecies, count.zero = TRUE)
    comp <- sapply(comp, c)
    comp <- t(comp)
    rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
    if ("(Z-1)" %in% rownames(comp)) 
        rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
    if (nrow(comp) > ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is greater than the number of elements and charge")
        else stop("the number of basis species is greater than the number of elements")
    }
    if (nrow(comp) < ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is less than the number of elements and charge")
        else stop("the number of basis species is less than the number of elements")
    }
    if (class(try(solve(comp), silent = TRUE)) == "try-error") 
        stop("singular stoichiometric matrix")
    comp <- cbind(as.data.frame(comp), ispecies, logact, state, 
        stringsAsFactors = FALSE)
    thermo$basis <- comp
    assign("thermo", thermo, CHNOSZ)
    species(delete = TRUE)
    return(thermo$basis)
}
<bytecode: 0x8874090>
<environment: namespace:CHNOSZ>
 --- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 212-216 (anintro.Rmd) 
Error: processing vignette 'anintro.Rmd' failed with diagnostics:
the condition has length > 1
--- 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]
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CHNOSZ
 --- call from context --- 
put.basis(ispecies, logact)
 --- call from argument --- 
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
 --- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 27: tools:::.buildOneVignette("eos-regress.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ", 
    TRUE, FALSE, "eos-regress", "UTF-8", "/tmp/RtmprDz9bN/file103e87ba310.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (ispecies, logact = rep(NA, length(ispecies))) 
{
    thermo <- get("thermo", CHNOSZ)
    state <- thermo$obigt$state[ispecies]
    comp <- makeup(ispecies, count.zero = TRUE)
    comp <- sapply(comp, c)
    comp <- t(comp)
    rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
    if ("(Z-1)" %in% rownames(comp)) 
        rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
    if (nrow(comp) > ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is greater than the number of elements and charge")
        else stop("the number of basis species is greater than the number of elements")
    }
    if (nrow(comp) < ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is less than the number of elements and charge")
        else stop("the number of basis species is less than the number of elements")
    }
    if (class(try(solve(comp), silent = TRUE)) == "try-error") 
        stop("singular stoichiometric matrix")
    comp <- cbind(as.data.frame(comp), ispecies, logact, state, 
        stringsAsFactors = FALSE)
    thermo$basis <- comp
    assign("thermo", thermo, CHNOSZ)
    species(delete = TRUE)
    return(thermo$basis)
}
<bytecode: 0x8a53130>
<environment: namespace:CHNOSZ>
 --- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 435-440 (eos-regress.Rmd) 
Error: processing vignette 'eos-regress.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'eos-regress.Rmd'

--- re-building 'obigt.Rmd' using rmarkdown
--- finished re-building 'obigt.Rmd'

--- re-building 'equilibrium.Rnw' using knitr
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CHNOSZ
 --- call from context --- 
put.basis(ispecies, logact)
 --- call from argument --- 
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
 --- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4: basis("CHNOS")
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 14: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", 
    file)) knit2pandoc else knit)(file, encoding = encoding, 
    quiet = quiet, envir = globalenv(), ...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 27: tools:::.buildOneVignette("equilibrium.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ", 
    TRUE, FALSE, "equilibrium", "latin-9", "/tmp/RtmprDz9bN/file103e2ae30589.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (ispecies, logact = rep(NA, length(ispecies))) 
{
    thermo <- get("thermo", CHNOSZ)
    state <- thermo$obigt$state[ispecies]
    comp <- makeup(ispecies, count.zero = TRUE)
    comp <- sapply(comp, c)
    comp <- t(comp)
    rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
    if ("(Z-1)" %in% rownames(comp)) 
        rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
    if (nrow(comp) > ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is greater than the number of elements and charge")
        else stop("the number of basis species is greater than the number of elements")
    }
    if (nrow(comp) < ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is less than the number of elements and charge")
        else stop("the number of basis species is less than the number of elements")
    }
    if (class(try(solve(comp), silent = TRUE)) == "try-error") 
        stop("singular stoichiometric matrix")
    comp <- cbind(as.data.frame(comp), ispecies, logact, state, 
        stringsAsFactors = FALSE)
    thermo$basis <- comp
    assign("thermo", thermo, CHNOSZ)
    species(delete = TRUE)
    return(thermo$basis)
}
<bytecode: 0x2875210>
<environment: namespace:CHNOSZ>
 --- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 225-229 (equilibrium.Rnw) 
Error: processing vignette 'equilibrium.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building 'equilibrium.Rnw'

--- re-building 'hotspring.Rnw' using knitr
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CHNOSZ
 --- call from context --- 
put.basis(ispecies, logact)
 --- call from argument --- 
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
 --- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at <text>#2: basis(c("HCO3-", "H2O", "NH3", "HS-", "H2", "H+"))
where 3: setup.basis()
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 19: process_file(text, output)
where 20: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", 
    file)) knit2pandoc else knit)(file, encoding = encoding, 
    quiet = quiet, envir = globalenv(), ...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("hotspring.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ", 
    TRUE, FALSE, "hotspring", "latin-9", "/tmp/RtmprDz9bN/file103e5231dd83.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (ispecies, logact = rep(NA, length(ispecies))) 
{
    thermo <- get("thermo", CHNOSZ)
    state <- thermo$obigt$state[ispecies]
    comp <- makeup(ispecies, count.zero = TRUE)
    comp <- sapply(comp, c)
    comp <- t(comp)
    rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
    if ("(Z-1)" %in% rownames(comp)) 
        rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
    if (nrow(comp) > ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is greater than the number of elements and charge")
        else stop("the number of basis species is greater than the number of elements")
    }
    if (nrow(comp) < ncol(comp)) {
        if ("Z" %in% colnames(comp)) 
            stop("the number of basis species is less than the number of elements and charge")
        else stop("the number of basis species is less than the number of elements")
    }
    if (class(try(solve(comp), silent = TRUE)) == "try-error") 
        stop("singular stoichiometric matrix")
    comp <- cbind(as.data.frame(comp), ispecies, logact, state, 
        stringsAsFactors = FALSE)
    thermo$basis <- comp
    assign("thermo", thermo, CHNOSZ)
    species(delete = TRUE)
    return(thermo$basis)
}
<bytecode: 0x3cd3778>
<environment: namespace:CHNOSZ>
 --- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 247-250 (hotspring.Rnw) 
Error: processing vignette 'hotspring.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building 'hotspring.Rnw'

SUMMARY: processing the following files failed:
  'anintro.Rmd' 'eos-regress.Rmd' 'equilibrium.Rnw' 'hotspring.Rnw'

Error: Vignette re-building failed.
Execution halted