Last updated on 2020-03-07 11:48:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.71 | 9.96 | 31.07 | 41.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.71 | 6.96 | 24.62 | 31.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.71 | 60.49 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.71 | 49.42 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.71 | 24.00 | 61.00 | 85.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.71 | 25.00 | 67.00 | 92.00 | OK | |
| r-patched-linux-x86_64 | 0.71 | 7.28 | 34.86 | 42.14 | OK | |
| r-patched-solaris-x86 | 0.71 | 117.00 | WARN | |||
| r-release-linux-x86_64 | 0.71 | 6.89 | 34.61 | 41.50 | OK | |
| r-release-windows-ix86+x86_64 | 0.71 | 22.00 | 58.00 | 80.00 | OK | |
| r-release-osx-x86_64 | 0.71 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.71 | 19.00 | 57.00 | 76.00 | OK | |
| r-oldrel-osx-x86_64 | 0.71 | OK |
Version: 0.71
Check: examples
Result: ERROR
Running examples in 'MetaSKAT-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MetaSKAT_wZ
> ### Title: Meta analysis SKAT with individual level genotype data
> ### Aliases: MetaSKAT_wZ
>
> ### ** Examples
>
>
>
> data(Example)
> attach(Example)
>
> #############################################################
> # Compute a p-value of the first gene
>
> obj<-Meta_Null_Model(y.list, x.list, n.cohort=3, out_type="D")
>
> # rho=0
> MetaSKAT_wZ(Z.list[[1]], obj)$p.value
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x3383568>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
Calls: MetaSKAT_wZ -> Meta_SKAT_SaveData -> Meta_SKAT_MAIN_Check_Z
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.71
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'MetaSKAT.Rnw' using Sweave
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
engine$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 22: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MetaSKAT.Rcheck/vign_test/MetaSKAT",
ser_elibs = "/tmp/RtmpdZj3vA/file4cd3562b616d.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0xcb9050>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'MetaSKAT.Rnw' failed with diagnostics:
chunk 2 (label = MetaSKAT1)
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
--- failed re-building 'MetaSKAT.Rnw'
SUMMARY: processing the following file failed:
'MetaSKAT.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.71
Check: examples
Result: ERROR
Running examples in ‘MetaSKAT-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MetaSKAT_wZ
> ### Title: Meta analysis SKAT with individual level genotype data
> ### Aliases: MetaSKAT_wZ
>
> ### ** Examples
>
>
>
> data(Example)
> attach(Example)
>
> #############################################################
> # Compute a p-value of the first gene
>
> obj<-Meta_Null_Model(y.list, x.list, n.cohort=3, out_type="D")
>
> # rho=0
> MetaSKAT_wZ(Z.list[[1]], obj)$p.value
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x556fbe6c1b60>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
Calls: MetaSKAT_wZ -> Meta_SKAT_SaveData -> Meta_SKAT_MAIN_Check_Z
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.71
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘MetaSKAT.Rnw’ using Sweave
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
engine$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 22: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MetaSKAT.Rcheck/vign_test/MetaSKAT",
ser_elibs = "/home/hornik/tmp/scratch/RtmpNb795m/fileb051d9270bb.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x560027eb95e0>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'MetaSKAT.Rnw' failed with diagnostics:
chunk 2 (label = MetaSKAT1)
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
--- failed re-building ‘MetaSKAT.Rnw’
SUMMARY: processing the following file failed:
‘MetaSKAT.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.71
Check: examples
Result: ERROR
Running examples in ‘MetaSKAT-Ex.R’ failed
The error most likely occurred in:
> ### Name: MetaSKAT_wZ
> ### Title: Meta analysis SKAT with individual level genotype data
> ### Aliases: MetaSKAT_wZ
>
> ### ** Examples
>
>
>
> data(Example)
> attach(Example)
>
> #############################################################
> # Compute a p-value of the first gene
>
> obj<-Meta_Null_Model(y.list, x.list, n.cohort=3, out_type="D")
>
> # rho=0
> MetaSKAT_wZ(Z.list[[1]], obj)$p.value
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x3248fb0>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
Calls: MetaSKAT_wZ -> Meta_SKAT_SaveData -> Meta_SKAT_MAIN_Check_Z
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.71
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘MetaSKAT.Rnw’ using Sweave
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
engine$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 22: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/MetaSKAT.Rcheck/vign_test/MetaSKAT",
ser_elibs = "/tmp/Rtmp0Xjjyq/filea8fc7a428d42.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x1fba650>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'MetaSKAT.Rnw' failed with diagnostics:
chunk 2 (label = MetaSKAT1)
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
--- failed re-building ‘MetaSKAT.Rnw’
SUMMARY: processing the following file failed:
‘MetaSKAT.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.71
Check: examples
Result: ERROR
Running examples in ‘MetaSKAT-Ex.R’ failed
The error most likely occurred in:
> ### Name: MetaSKAT_wZ
> ### Title: Meta analysis SKAT with individual level genotype data
> ### Aliases: MetaSKAT_wZ
>
> ### ** Examples
>
>
>
> data(Example)
> attach(Example)
>
> #############################################################
> # Compute a p-value of the first gene
>
> obj<-Meta_Null_Model(y.list, x.list, n.cohort=3, out_type="D")
>
> # rho=0
> MetaSKAT_wZ(Z.list[[1]], obj)$p.value
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x302dd58>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
Calls: MetaSKAT_wZ -> Meta_SKAT_SaveData -> Meta_SKAT_MAIN_Check_Z
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.71
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘MetaSKAT.Rnw’ using Sweave
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MetaSKAT
--- call from context ---
Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
--- call from argument ---
if (class(Z) != "matrix") stop("Z is not a matrix")
--- R stacktrace ---
where 1: Meta_SKAT_MAIN_Check_Z(Z, n, obj.res$id_include, SetID, impute.method = impute.method)
where 2: Meta_SKAT_SaveData(Z1, obj$out[[i]], SetID = NULL, impute.method = impute.method)
where 3: MetaSKAT_wZ(Z.list[[1]], obj)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
engine$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 22: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/MetaSKAT.Rcheck/vign_test/MetaSKAT",
ser_elibs = "/tmp/RtmpWQiiBj/filebe875e2d671d.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (Z, n, id_include, SetID, is_dosage = FALSE, impute.method = "fixed")
{
m = ncol(Z)
if (class(Z) != "matrix")
stop("Z is not a matrix")
if (nrow(Z) != n)
stop("Dimensions of y and Z do not match")
if (is_dosage == TRUE) {
impute.method = "fixed"
}
IDX_MISS <- union(which(is.na(Z)), which(Z == 9))
if (length(IDX_MISS) > 0) {
Z[IDX_MISS] <- NA
}
missing.ratio <- rep(0, m)
for (i in 1:m) {
missing.ratio[i] <- length(which(is.na(Z[, i])))/n
if (missing.ratio[i] > 0.9) {
Z[, i] <- 0
}
}
MAF <- colMeans(Z, na.rm = TRUE)/2
IDX.Err <- which(MAF > 0.5)
if (length(IDX.Err) > 0) {
msg <- sprintf("Genotypes of some variants are not the number of minor alleles!")
}
Z <- SKAT:::Impute(Z, impute.method)
Z <- cbind(Z)
Z.test <- as.matrix(Z[id_include, ])
return(list(Z.test = Z.test, missing_rate = missing.ratio,
MAF = MAF, return = 0))
}
<bytecode: 0x1c3ff28>
<environment: namespace:MetaSKAT>
--- function search by body ---
Function Meta_SKAT_MAIN_Check_Z in namespace MetaSKAT has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'MetaSKAT.Rnw' failed with diagnostics:
chunk 2 (label = MetaSKAT1)
Error in if (class(Z) != "matrix") stop("Z is not a matrix") :
the condition has length > 1
--- failed re-building ‘MetaSKAT.Rnw’
SUMMARY: processing the following file failed:
‘MetaSKAT.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.71
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘MetaSKAT.Rnw’ using Sweave
*** caught segfault ***
address 6e267eb8, cause 'memory not mapped'
Traceback:
1: Open_MSSD_File_2Read(File.Mat.vec, File.Info.vec)
2: eval(expr, .GlobalEnv)
3: eval(expr, .GlobalEnv)
4: withVisible(eval(expr, .GlobalEnv))
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: 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))})
9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
10: evalFunc(ce, options)
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
13: driver$runcode(drobj, chunk, chunkopts)
14: utils::Sweave(...)
15: engine$weave(file, quiet = quiet, encoding = enc)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: 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)))})
20: tools:::buildVignettes(dir = "/home/ripley/R/packages/tests32/MetaSKAT.Rcheck/vign_test/MetaSKAT", ser_elibs = "/tmp/RtmpmVaGU2/file6d74527b3c18.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86