Last updated on 2019-11-26 00:52:14 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.68 | 4.65 | 32.86 | 37.51 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.0.68 | 3.50 | 25.92 | 29.42 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 1.0.68 | 76.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.68 | 72.01 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.0.68 | 17.00 | 304.00 | 321.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.68 | 16.00 | 251.00 | 267.00 | OK | |
| r-patched-linux-x86_64 | 1.0.68 | 4.24 | 54.41 | 58.65 | OK | |
| r-patched-solaris-x86 | 1.0.68 | 688.50 | OK | |||
| r-release-linux-x86_64 | 1.0.68 | 4.20 | 55.16 | 59.36 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.68 | 13.00 | 230.00 | 243.00 | OK | |
| r-release-osx-x86_64 | 1.0.68 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.68 | 7.00 | 300.00 | 307.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.68 | OK |
Version: 1.0.68
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'stockR.Rnw' using knitr
Removing any SNP with no variation amongst *any* fish (there are 87 of them)
Finding starting values using K-means on rotated data (using specified number of PCAs)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
stockR
--- call from context ---
calcCondMeans(all.data, taus, K)
--- call from argument ---
if (class(FishPerSNP) == "matrix") FishPerSNP <- as.list(as.data.frame(FishPerSNP))
--- R stacktrace ---
where 1: calcCondMeans(all.data, taus, K)
where 2: stockSTRUCTURE(myData, K = 3)
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: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
file)) knit2pandoc else knit)(file, encoding = encoding,
quiet = quiet, envir = globalenv(), ...)
where 20: engine$weave(file, quiet = quiet, encoding = enc)
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch({
engine$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 25: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stockR.Rcheck/vign_test/stockR",
ser_elibs = "/tmp/RtmpAhlCHI/file46dd14876d52.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (all.data, taus, K)
{
taus.fish <- taus[all.data$sample.grps.num, , drop = FALSE]
weights.fish <- all.data$weights[all.data$sample.grps.num]
wted.taus.fish <- taus.fish * rep(weights.fish, times = K)
means <- totWtsPerSNP <- matrix(NA, nrow = nrow(all.data$SNPdata),
ncol = K)
FishPerSNP <- apply(all.data$SNPdata, 1, function(x) which(!is.na(x)))
if (class(FishPerSNP) == "matrix")
FishPerSNP <- as.list(as.data.frame(FishPerSNP))
for (kk in 1:K) {
tmp <- all.data$SNPdata * rep(wted.taus.fish[, kk], each = nrow(all.data$SNPdata))
means[, kk] <- rowSums(tmp, na.rm = TRUE)
totWtsPerSNP[, kk] <- sapply(FishPerSNP, function(x) sum(wted.taus.fish[x,
kk]))
}
means <- means/totWtsPerSNP
means <- means/2
means[means > 1] <- 1
means[means < 0] <- 0
return(means)
}
<bytecode: 0x12e1358>
<environment: namespace:stockR>
--- function search by body ---
Function calcCondMeans in namespace stockR has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.68
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘stockR.Rnw’ using knitr
Removing any SNP with no variation amongst *any* fish (there are 87 of them)
Finding starting values using K-means on rotated data (using specified number of PCAs)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
stockR
--- call from context ---
calcCondMeans(all.data, taus, K)
--- call from argument ---
if (class(FishPerSNP) == "matrix") FishPerSNP <- as.list(as.data.frame(FishPerSNP))
--- R stacktrace ---
where 1: calcCondMeans(all.data, taus, K)
where 2: stockSTRUCTURE(myData, K = 3)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$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$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
file)) knit2pandoc else knit)(file, encoding = encoding,
quiet = quiet, envir = globalenv(), ...)
where 20: engine$weave(file, quiet = quiet, encoding = enc)
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 25: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stockR.Rcheck/vign_test/stockR",
ser_elibs = "/home/hornik/tmp/scratch/RtmpGAmOMI/file61535bd6dbea.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (all.data, taus, K)
{
taus.fish <- taus[all.data$sample.grps.num, , drop = FALSE]
weights.fish <- all.data$weights[all.data$sample.grps.num]
wted.taus.fish <- taus.fish * rep(weights.fish, times = K)
means <- totWtsPerSNP <- matrix(NA, nrow = nrow(all.data$SNPdata),
ncol = K)
FishPerSNP <- apply(all.data$SNPdata, 1, function(x) which(!is.na(x)))
if (class(FishPerSNP) == "matrix")
FishPerSNP <- as.list(as.data.frame(FishPerSNP))
for (kk in 1:K) {
tmp <- all.data$SNPdata * rep(wted.taus.fish[, kk], each = nrow(all.data$SNPdata))
means[, kk] <- rowSums(tmp, na.rm = TRUE)
totWtsPerSNP[, kk] <- sapply(FishPerSNP, function(x) sum(wted.taus.fish[x,
kk]))
}
means <- means/totWtsPerSNP
means <- means/2
means[means > 1] <- 1
means[means < 0] <- 0
return(means)
}
<bytecode: 0x55ccfed76cc0>
<environment: namespace:stockR>
--- function search by body ---
Function calcCondMeans in namespace stockR has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc