Last updated on 2019-11-26 00:51:47 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.3 | 27.49 | 137.43 | 164.92 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.3 | 19.99 | 104.51 | 124.50 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.3 | 442.19 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.3 | 420.31 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.3.3 | 54.00 | 597.00 | 651.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.3.3 | 47.00 | 499.00 | 546.00 | OK | |
| r-patched-linux-x86_64 | 1.3.3 | 25.81 | 329.87 | 355.68 | OK | |
| r-patched-solaris-x86 | 1.3.3 | 512.40 | NOTE | |||
| r-release-linux-x86_64 | 1.3.3 | 25.44 | 334.71 | 360.15 | OK | |
| r-release-windows-ix86+x86_64 | 1.3.3 | 45.00 | 620.00 | 665.00 | OK | |
| r-release-osx-x86_64 | 1.3.3 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.3.3 | 31.00 | 458.00 | 489.00 | OK | |
| r-oldrel-osx-x86_64 | 1.3.3 | OK |
Version: 1.3.3
Check: examples
Result: ERROR
Running examples in 'CHNOSZ-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: affinity
> ### Title: Chemical Affinities of Formation Reactions
> ### Aliases: affinity
>
> ### ** Examples
>
> ## Don't show:
> reset()
reset: resetting "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
> ## End(Don't show)## set up a system and calculate
> ## chemical affinities of formation reactions
> basis(c("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
----------- 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("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
--- 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: 0x12739b0>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: tests
Result: ERROR
Running 'testthat.R' [7s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
----------- 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 at testthat/test-affinity.R#10: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#6: test_that("errors come as expected", {
expect_error(affinity(iprotein = 7), "basis species are not defined")
expect_error(affinity(iprotein = NA), "has some NA values")
expect_error(affinity(iprotein = 0), "are not rownumbers")
basis("CHNOS")
expect_error(affinity(), "species have not been defined")
species("CO2")
expect_error(affinity(pe = c(-10, 10), pH = c(0, 14)), "pe.*does not match any basis species")
expect_error(affinity(O2 = c(-80, -60), pH = c(0, 14)), "pH.*does not match any basis species")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- 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: 0x2d89920>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: re-building of vignette outputs
Result: WARN
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/RtmpCZNOE2/file72a2312851e8.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: 0x88b1400>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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/RtmpCZNOE2/file72a22e86afcf.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: 0x838f698>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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/RtmpCZNOE2/file72a21e08b515.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: 0x21a7cd8>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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/RtmpCZNOE2/file72a22bbf30cd.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: 0x3a71170>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
SUMMARY: processing the following files failed:
'anintro.Rmd' 'eos-regress.Rmd' 'equilibrium.Rnw' 'hotspring.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: examples
Result: ERROR
Running examples in ‘CHNOSZ-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: affinity
> ### Title: Chemical Affinities of Formation Reactions
> ### Aliases: affinity
>
> ### ** Examples
>
> ## Don't show:
> reset()
reset: resetting "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
> ## End(Don't show)## set up a system and calculate
> ## chemical affinities of formation reactions
> basis(c("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
----------- 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("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
--- 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: 0x55cfa1d33d78>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
----------- 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 at testthat/test-affinity.R#10: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#6: test_that("errors come as expected", {
expect_error(affinity(iprotein = 7), "basis species are not defined")
expect_error(affinity(iprotein = NA), "has some NA values")
expect_error(affinity(iprotein = 0), "are not rownumbers")
basis("CHNOS")
expect_error(affinity(), "species have not been defined")
species("CO2")
expect_error(affinity(pe = c(-10, 10), pH = c(0, 14)), "pe.*does not match any basis species")
expect_error(affinity(O2 = c(-80, -60), pH = c(0, 14)), "pH.*does not match any basis species")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- 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: 0x55e1cd33dbf0>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: re-building of vignette outputs
Result: WARN
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-gcc/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "anintro", "UTF-8", "/home/hornik/tmp/scratch/RtmpI2zjRs/file5dfb7cec5409.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: 0x5652124dfdc0>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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-gcc/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "eos-regress", "UTF-8", "/home/hornik/tmp/scratch/RtmpI2zjRs/file5dfb1dfff10f.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: 0x55d52db02648>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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-gcc/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "equilibrium", "latin-9", "/home/hornik/tmp/scratch/RtmpI2zjRs/file5dfb45409e1a.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: 0x562c687806f8>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
--- 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-gcc/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "hotspring", "latin-9", "/home/hornik/tmp/scratch/RtmpI2zjRs/file5dfb3f8b387.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: 0x55c211688760>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
SUMMARY: processing the following files failed:
‘anintro.Rmd’ ‘eos-regress.Rmd’ ‘equilibrium.Rnw’ ‘hotspring.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 2.5Mb
Flavor: r-patched-solaris-x86