Last updated on 2020-02-19 10:48:59 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 59.10 | 35.03 | 94.13 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 42.32 | 28.26 | 70.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 135.51 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 128.56 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.1.0 | 107.00 | 75.00 | 182.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.1.0 | 166.00 | 104.00 | 270.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.0 | 50.08 | 38.65 | 88.73 | OK | |
| r-patched-solaris-x86 | 0.1.0 | 133.20 | OK | |||
| r-release-linux-x86_64 | 0.1.0 | 51.53 | 38.31 | 89.84 | OK | |
| r-release-windows-ix86+x86_64 | 0.1.0 | 107.00 | 77.00 | 184.00 | OK | |
| r-release-osx-x86_64 | 0.1.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.0 | 90.00 | 70.00 | 160.00 | OK | |
| r-oldrel-osx-x86_64 | 0.1.0 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in 'memnet-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alc
> ### Title: Average local clustering (alc) coefficient
> ### Aliases: alc
>
> ### ** Examples
>
>
> # get fluency data
> data(animal_fluency)
>
> # edge lists of fluency graphs
> edge_list = threshold_graph(animal_fluency)
>
> # get adjacency matrices
> adj = edg_to_adj(edge_list)
>
> # get local average clustering coefficient
> alc(adj)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
alc(adj)
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: alc(adj)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, types = "uncorrected", weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
res = c()
cc = igraph::transitivity(g, type = "localaverage")
for (type in types) {
if (type == "uncorrected") {
res = c(res, cc)
names(res)[length(res)] = "cc"
}
else if (type == "corrected") {
nv = igraph::vcount(g)
ne = igraph::ecount(g)
k = ne/nv
res = c(res, cc/(k/nv))
names(res)[length(res)] = "cc_c"
}
}
res
}
<bytecode: 0x2a24df0>
<environment: namespace:memnet>
--- function search by body ---
Function alc in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(adj) != "igraph") { : the condition has length > 1
Calls: alc
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: package vignettes
Result: NOTE
Package vignette with placeholder title 'Vignette Title':
'memnet.Rmd'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'memnet.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
network_stats(edg_to_adj(net_comunity))
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: network_stats(edg_to_adj(net_comunity))
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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 9: evaluate::evaluate(...)
where 10: 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$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$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 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: 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$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/memnet.Rcheck/vign_test/memnet",
ser_elibs = "/tmp/Rtmpyj2beg/file1c02381120eb.rds")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, giant = FALSE, weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
comp = l_comp(g, igraph = TRUE)
comp_p = comp[[2]]
if (giant == TRUE) {
g = comp[[1]]
}
n_v = igraph::vcount(g)
n_e = igraph::ecount(g)
k = n_e/n_v
cc = igraph::transitivity(g, type = "localaverage")
cc_c = cc/(k/n_v)
aspl = igraph::mean_distance(g, directed = mode == "directed")
aspl_c = aspl/(log(n_v)/log(n_e))
smallw = cc_c/aspl_c
assor = igraph::assortativity_degree(g, directed = mode ==
"directed")
res = c(n_v, n_e, k, cc, cc_c, aspl, aspl_c, smallw, assor,
comp_p)
names(res) = c("|V|", "|E|", "k", "C", "Cc", "L", "Lc", "S",
"A", "p")
res
}
<bytecode: 0x41cc068>
<environment: namespace:memnet>
--- function search by body ---
Function network_stats in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 33-59 (memnet.Rmd)
Error: processing vignette 'memnet.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'memnet.Rmd'
SUMMARY: processing the following file failed:
'memnet.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘memnet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alc
> ### Title: Average local clustering (alc) coefficient
> ### Aliases: alc
>
> ### ** Examples
>
>
> # get fluency data
> data(animal_fluency)
>
> # edge lists of fluency graphs
> edge_list = threshold_graph(animal_fluency)
>
> # get adjacency matrices
> adj = edg_to_adj(edge_list)
>
> # get local average clustering coefficient
> alc(adj)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
alc(adj)
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: alc(adj)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, types = "uncorrected", weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
res = c()
cc = igraph::transitivity(g, type = "localaverage")
for (type in types) {
if (type == "uncorrected") {
res = c(res, cc)
names(res)[length(res)] = "cc"
}
else if (type == "corrected") {
nv = igraph::vcount(g)
ne = igraph::ecount(g)
k = ne/nv
res = c(res, cc/(k/nv))
names(res)[length(res)] = "cc_c"
}
}
res
}
<bytecode: 0x55983ec082b8>
<environment: namespace:memnet>
--- function search by body ---
Function alc in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(adj) != "igraph") { : the condition has length > 1
Calls: alc
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘memnet.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
network_stats(edg_to_adj(net_comunity))
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: network_stats(edg_to_adj(net_comunity))
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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 9: evaluate::evaluate(...)
where 10: 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$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$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 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: 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$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/memnet.Rcheck/vign_test/memnet",
ser_elibs = "/home/hornik/tmp/scratch/RtmppFvVYI/file4c3839883b97.rds")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, giant = FALSE, weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
comp = l_comp(g, igraph = TRUE)
comp_p = comp[[2]]
if (giant == TRUE) {
g = comp[[1]]
}
n_v = igraph::vcount(g)
n_e = igraph::ecount(g)
k = n_e/n_v
cc = igraph::transitivity(g, type = "localaverage")
cc_c = cc/(k/n_v)
aspl = igraph::mean_distance(g, directed = mode == "directed")
aspl_c = aspl/(log(n_v)/log(n_e))
smallw = cc_c/aspl_c
assor = igraph::assortativity_degree(g, directed = mode ==
"directed")
res = c(n_v, n_e, k, cc, cc_c, aspl, aspl_c, smallw, assor,
comp_p)
names(res) = c("|V|", "|E|", "k", "C", "Cc", "L", "Lc", "S",
"A", "p")
res
}
<bytecode: 0x56307acc9de8>
<environment: namespace:memnet>
--- function search by body ---
Function network_stats in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 33-59 (memnet.Rmd)
Error: processing vignette 'memnet.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘memnet.Rmd’
SUMMARY: processing the following file failed:
‘memnet.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
doc 1.6Mb
libs 3.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘memnet-Ex.R’ failed
The error most likely occurred in:
> ### Name: alc
> ### Title: Average local clustering (alc) coefficient
> ### Aliases: alc
>
> ### ** Examples
>
>
> # get fluency data
> data(animal_fluency)
>
> # edge lists of fluency graphs
> edge_list = threshold_graph(animal_fluency)
>
> # get adjacency matrices
> adj = edg_to_adj(edge_list)
>
> # get local average clustering coefficient
> alc(adj)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
alc(adj)
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: alc(adj)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, types = "uncorrected", weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
res = c()
cc = igraph::transitivity(g, type = "localaverage")
for (type in types) {
if (type == "uncorrected") {
res = c(res, cc)
names(res)[length(res)] = "cc"
}
else if (type == "corrected") {
nv = igraph::vcount(g)
ne = igraph::ecount(g)
k = ne/nv
res = c(res, cc/(k/nv))
names(res)[length(res)] = "cc_c"
}
}
res
}
<bytecode: 0x3a8d6d0>
<environment: namespace:memnet>
--- function search by body ---
Function alc in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(adj) != "igraph") { : the condition has length > 1
Calls: alc
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘memnet.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
network_stats(edg_to_adj(net_comunity))
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: network_stats(edg_to_adj(net_comunity))
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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 9: evaluate::evaluate(...)
where 10: 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$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$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 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: 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$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/memnet.Rcheck/vign_test/memnet",
ser_elibs = "/tmp/RtmpH85e8a/fileb67476688b0.rds")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, giant = FALSE, weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
comp = l_comp(g, igraph = TRUE)
comp_p = comp[[2]]
if (giant == TRUE) {
g = comp[[1]]
}
n_v = igraph::vcount(g)
n_e = igraph::ecount(g)
k = n_e/n_v
cc = igraph::transitivity(g, type = "localaverage")
cc_c = cc/(k/n_v)
aspl = igraph::mean_distance(g, directed = mode == "directed")
aspl_c = aspl/(log(n_v)/log(n_e))
smallw = cc_c/aspl_c
assor = igraph::assortativity_degree(g, directed = mode ==
"directed")
res = c(n_v, n_e, k, cc, cc_c, aspl, aspl_c, smallw, assor,
comp_p)
names(res) = c("|V|", "|E|", "k", "C", "Cc", "L", "Lc", "S",
"A", "p")
res
}
<bytecode: 0x39a1f38>
<environment: namespace:memnet>
--- function search by body ---
Function network_stats in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 33-59 (memnet.Rmd)
Error: processing vignette 'memnet.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘memnet.Rmd’
SUMMARY: processing the following file failed:
‘memnet.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘memnet-Ex.R’ failed
The error most likely occurred in:
> ### Name: alc
> ### Title: Average local clustering (alc) coefficient
> ### Aliases: alc
>
> ### ** Examples
>
>
> # get fluency data
> data(animal_fluency)
>
> # edge lists of fluency graphs
> edge_list = threshold_graph(animal_fluency)
>
> # get adjacency matrices
> adj = edg_to_adj(edge_list)
>
> # get local average clustering coefficient
> alc(adj)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
alc(adj)
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: alc(adj)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, types = "uncorrected", weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
res = c()
cc = igraph::transitivity(g, type = "localaverage")
for (type in types) {
if (type == "uncorrected") {
res = c(res, cc)
names(res)[length(res)] = "cc"
}
else if (type == "corrected") {
nv = igraph::vcount(g)
ne = igraph::ecount(g)
k = ne/nv
res = c(res, cc/(k/nv))
names(res)[length(res)] = "cc_c"
}
}
res
}
<bytecode: 0x3345138>
<environment: namespace:memnet>
--- function search by body ---
Function alc in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(adj) != "igraph") { : the condition has length > 1
Calls: alc
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘memnet.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
memnet
--- call from context ---
network_stats(edg_to_adj(net_comunity))
--- call from argument ---
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
} else {
g = adj
}
--- R stacktrace ---
where 1: network_stats(edg_to_adj(net_comunity))
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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 9: evaluate::evaluate(...)
where 10: 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$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$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 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: 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$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/memnet.Rcheck/vign_test/memnet",
ser_elibs = "/tmp/RtmpXhN3uc/filea5e43db1ec1b.rds")
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (adj, giant = FALSE, weights = NULL, mode = "undirected")
{
if (class(adj) != "igraph") {
g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
if (!is.null(weights))
igraph::E(g)$weight = weights
}
else {
g = adj
}
comp = l_comp(g, igraph = TRUE)
comp_p = comp[[2]]
if (giant == TRUE) {
g = comp[[1]]
}
n_v = igraph::vcount(g)
n_e = igraph::ecount(g)
k = n_e/n_v
cc = igraph::transitivity(g, type = "localaverage")
cc_c = cc/(k/n_v)
aspl = igraph::mean_distance(g, directed = mode == "directed")
aspl_c = aspl/(log(n_v)/log(n_e))
smallw = cc_c/aspl_c
assor = igraph::assortativity_degree(g, directed = mode ==
"directed")
res = c(n_v, n_e, k, cc, cc_c, aspl, aspl_c, smallw, assor,
comp_p)
names(res) = c("|V|", "|E|", "k", "C", "Cc", "L", "Lc", "S",
"A", "p")
res
}
<bytecode: 0x3b5ce58>
<environment: namespace:memnet>
--- function search by body ---
Function network_stats in namespace memnet has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 33-59 (memnet.Rmd)
Error: processing vignette 'memnet.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘memnet.Rmd’
SUMMARY: processing the following file failed:
‘memnet.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc