Last updated on 2020-02-19 10:49:10 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3 | 7.06 | 69.59 | 76.65 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3 | 5.82 | 54.33 | 60.15 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3 | 93.75 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3 | 82.08 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.3 | 13.00 | 85.00 | 98.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.3 | 19.00 | 113.00 | 132.00 | NOTE | |
| r-patched-linux-x86_64 | 1.3 | 7.18 | 75.33 | 82.51 | NOTE | |
| r-release-linux-x86_64 | 1.3 | 5.72 | 75.54 | 81.26 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.3 | 11.00 | 78.00 | 89.00 | NOTE | |
| r-release-osx-x86_64 | 1.3 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.3 | 7.00 | 76.00 | 83.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.3 | NOTE |
Version: 1.3
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 1.3
Check: examples
Result: ERROR
Running examples in 'SimuChemPC-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ### character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ### expected potency improvement, gaussian process
>
> ### ** Examples
>
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x2c91988>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'SimuChemPC_vignette.Rnw' using Sweave
Loading required package: rcdklibs
Loading required package: rJava
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
WARNING: Please consider reporting this to the maintainers of RJavaTools
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: trainChemPC(xTrain, yTrain)
where 3: eval(expr, .GlobalEnv)
where 4: eval(expr, .GlobalEnv)
where 5: withVisible(eval(expr, .GlobalEnv))
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 11: evalFunc(ce, options)
where 12: tryCatchList(expr, classes, parentenv, handlers)
where 13: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 14: driver$runcode(drobj, chunk, chunkopts)
where 15: utils::Sweave(...)
where 16: engine$weave(file, quiet = quiet, encoding = enc)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: tryCatch({
engine$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 21: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SimuChemPC.Rcheck/vign_test/SimuChemPC",
ser_elibs = "/tmp/RtmpwRTe9v/file59b83f43a884.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x7e16a70>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
chunk 9
Error in if (class(x) == "data.frame") { : the condition has length > 1
--- failed re-building 'SimuChemPC_vignette.Rnw'
SUMMARY: processing the following file failed:
'SimuChemPC_vignette.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘SimuChemPC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ### character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ### expected potency improvement, gaussian process
>
> ### ** Examples
>
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x56221070b1f0>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘SimuChemPC_vignette.Rnw’ using Sweave
Loading required package: rcdklibs
Loading required package: rJava
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
WARNING: Please consider reporting this to the maintainers of RJavaTools
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: trainChemPC(xTrain, yTrain)
where 3: eval(expr, .GlobalEnv)
where 4: eval(expr, .GlobalEnv)
where 5: withVisible(eval(expr, .GlobalEnv))
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 11: evalFunc(ce, options)
where 12: tryCatchList(expr, classes, parentenv, handlers)
where 13: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 14: driver$runcode(drobj, chunk, chunkopts)
where 15: utils::Sweave(...)
where 16: engine$weave(file, quiet = quiet, encoding = enc)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: tryCatch({
engine$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 21: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SimuChemPC.Rcheck/vign_test/SimuChemPC",
ser_elibs = "/home/hornik/tmp/scratch/RtmpEQk03u/file8fc45e21a9a.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x55ee62a4c268>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
chunk 9
Error in if (class(x) == "data.frame") { : the condition has length > 1
--- failed re-building ‘SimuChemPC_vignette.Rnw’
SUMMARY: processing the following file failed:
‘SimuChemPC_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3
Check: package dependencies
Result: WARN
Requires orphaned package: ‘rcdk’
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘SimuChemPC-Ex.R’ failed
The error most likely occurred in:
> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ### character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ### expected potency improvement, gaussian process
>
> ### ** Examples
>
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x2c1d530>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘SimuChemPC_vignette.Rnw’ using Sweave
Loading required package: rcdklibs
Loading required package: rJava
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
WARNING: Please consider reporting this to the maintainers of RJavaTools
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: trainChemPC(xTrain, yTrain)
where 3: eval(expr, .GlobalEnv)
where 4: eval(expr, .GlobalEnv)
where 5: withVisible(eval(expr, .GlobalEnv))
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 11: evalFunc(ce, options)
where 12: tryCatchList(expr, classes, parentenv, handlers)
where 13: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 14: driver$runcode(drobj, chunk, chunkopts)
where 15: utils::Sweave(...)
where 16: engine$weave(file, quiet = quiet, encoding = enc)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: tryCatch({
engine$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 21: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/SimuChemPC.Rcheck/vign_test/SimuChemPC",
ser_elibs = "/tmp/RtmpwlLXP8/file919037ef84ed.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x8fd74a8>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
chunk 9
Error in if (class(x) == "data.frame") { : the condition has length > 1
--- failed re-building ‘SimuChemPC_vignette.Rnw’
SUMMARY: processing the following file failed:
‘SimuChemPC_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘SimuChemPC-Ex.R’ failed
The error most likely occurred in:
> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ### character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ### expected potency improvement, gaussian process
>
> ### ** Examples
>
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x33ec680>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘SimuChemPC_vignette.Rnw’ using Sweave
Loading required package: rcdklibs
Loading required package: rJava
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SimuChemPC
--- call from context ---
normalize(yTrain)
--- call from argument ---
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
} else {
sigma = sd(x_norm)
}
--- R stacktrace ---
where 1: normalize(yTrain)
where 2: trainChemPC(xTrain, yTrain)
where 3: eval(expr, .GlobalEnv)
where 4: eval(expr, .GlobalEnv)
where 5: withVisible(eval(expr, .GlobalEnv))
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 11: evalFunc(ce, options)
where 12: tryCatchList(expr, classes, parentenv, handlers)
where 13: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 14: driver$runcode(drobj, chunk, chunkopts)
where 15: utils::Sweave(...)
where 16: engine$weave(file, quiet = quiet, encoding = enc)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: 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 21: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/SimuChemPC.Rcheck/vign_test/SimuChemPC",
ser_elibs = "/tmp/RtmpyVt2D4/fileb1657bc9a0f6.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
mu = colMeans(x)
x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
if (class(x) == "data.frame") {
sigma = sapply(x_norm, sd)
}
else {
sigma = sd(x_norm)
}
sigma[sigma == 0] = 1
norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
return(list(norm, mu, sigma))
}
<bytecode: 0x9655360>
<environment: namespace:SimuChemPC>
--- function search by body ---
Function normalize in namespace SimuChemPC has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
chunk 9
Error in if (class(x) == "data.frame") { : the condition has length > 1
--- failed re-building ‘SimuChemPC_vignette.Rnw’
SUMMARY: processing the following file failed:
‘SimuChemPC_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc