Last updated on 2020-02-26 18:47:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.81 | 43.16 | 389.46 | 432.62 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.81 | WARN | ||||
| r-devel-linux-x86_64-fedora-clang | 1.81 | 551.57 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.81 | 440.63 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.81 | 72.00 | 323.00 | 395.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.81 | 76.00 | 325.00 | 401.00 | OK | |
| r-patched-linux-x86_64 | 1.81 | 38.46 | 325.86 | 364.32 | OK | |
| r-patched-solaris-x86 | 1.81 | 687.60 | OK | |||
| r-release-linux-x86_64 | 1.81 | 35.49 | 325.66 | 361.15 | OK | |
| r-release-windows-ix86+x86_64 | 1.81 | 65.00 | 310.00 | 375.00 | OK | |
| r-release-osx-x86_64 | 1.81 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.81 | 51.00 | 307.00 | 358.00 | OK | |
| r-oldrel-osx-x86_64 | 1.81 | ERROR |
Version: 1.81
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'mvgraphnorm-intro.Rnw' using Sweave
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: mvtnorm
Loading required package: qpgraph
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Attaching package: 'qpgraph'
The following object is masked from 'package:mvtnorm':
rmvnorm
The following object is masked from 'package:igraph':
graph
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
mvgraphnorm
--- call from context ---
.GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
--- call from argument ---
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
--- R stacktrace ---
where 1: .GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
where 2: .gensample(n = n.samples + nrow(net.str), bin.mat = net.str,
method = method[1], cor = cor, mean.vector = mean.vector,
m.var = m.var)
where 3: rmvggm(20, net.str = g, method = "htf", cor = m)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$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/mvgraphnorm.Rcheck/vign_test/mvgraphnorm",
ser_elibs = "/tmp/RtmpaYLDNp/filec964f84b6a1.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (diag_, rho = 0, method = "IPF")
{
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
w <- as.matrix(qpG2Sigma(diag_, rho = rho, matrix.completion = method))
d_d <- diag(diag(w)^(-1/2), nrow(diag_))
dg <- d_d %*% w %*% d_d
retval <- list(sigcov = w, sigcor = dg)
return(retval)
}
<bytecode: 0x2a474e40>
<environment: namespace:mvgraphnorm>
--- function search by body ---
Function .GRCM_n in namespace mvgraphnorm has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'mvgraphnorm-intro.Rnw' failed with diagnostics:
chunk 4 (label = plotunif)
Error in if (class(rho) == "matrix") { : the condition has length > 1
--- failed re-building 'mvgraphnorm-intro.Rnw'
SUMMARY: processing the following file failed:
'mvgraphnorm-intro.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.81
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘mvgraphnorm-intro.Rnw’ using Sweave
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: mvtnorm
Loading required package: qpgraph
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
Attaching package: ‘qpgraph’
The following object is masked from ‘package:mvtnorm’:
rmvnorm
The following object is masked from ‘package:igraph’:
graph
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
mvgraphnorm
--- call from context ---
.GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
--- call from argument ---
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
--- R stacktrace ---
where 1: .GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
where 2: .gensample(n = n.samples + nrow(net.str), bin.mat = net.str,
method = method[1], cor = cor, mean.vector = mean.vector,
m.var = m.var)
where 3: rmvggm(20, net.str = g, method = "htf", cor = m)
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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 22: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvgraphnorm.Rcheck/vign_test/mvgraphnorm",
ser_elibs = "/home/hornik/tmp/scratch/RtmpiJ4NNd/file17007e42d75a.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (diag_, rho = 0, method = "IPF")
{
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
w <- as.matrix(qpG2Sigma(diag_, rho = rho, matrix.completion = method))
d_d <- diag(diag(w)^(-1/2), nrow(diag_))
dg <- d_d %*% w %*% d_d
retval <- list(sigcov = w, sigcor = dg)
return(retval)
}
<bytecode: 0x55a6de46f468>
<environment: namespace:mvgraphnorm>
--- function search by body ---
Function .GRCM_n in namespace mvgraphnorm has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'mvgraphnorm-intro.Rnw' failed with diagnostics:
chunk 4 (label = plotunif)
Error in if (class(rho) == "matrix") { : the condition has length > 1
--- failed re-building ‘mvgraphnorm-intro.Rnw’
SUMMARY: processing the following file failed:
‘mvgraphnorm-intro.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.81
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘mvgraphnorm-intro.Rnw’ using Sweave
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: mvtnorm
Loading required package: qpgraph
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
Attaching package: ‘qpgraph’
The following object is masked from ‘package:mvtnorm’:
rmvnorm
The following object is masked from ‘package:igraph’:
graph
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
mvgraphnorm
--- call from context ---
.GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
--- call from argument ---
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
--- R stacktrace ---
where 1: .GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
where 2: .gensample(n = n.samples + nrow(net.str), bin.mat = net.str,
method = method[1], cor = cor, mean.vector = mean.vector,
m.var = m.var)
where 3: rmvggm(20, net.str = g, method = "htf", cor = m)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 15: driver$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/mvgraphnorm.Rcheck/vign_test/mvgraphnorm",
ser_elibs = "/tmp/RtmpbGZzn7/file2ac779db9bb.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (diag_, rho = 0, method = "IPF")
{
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
w <- as.matrix(qpG2Sigma(diag_, rho = rho, matrix.completion = method))
d_d <- diag(diag(w)^(-1/2), nrow(diag_))
dg <- d_d %*% w %*% d_d
retval <- list(sigcov = w, sigcor = dg)
return(retval)
}
<bytecode: 0x269683e0>
<environment: namespace:mvgraphnorm>
--- function search by body ---
Function .GRCM_n in namespace mvgraphnorm has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'mvgraphnorm-intro.Rnw' failed with diagnostics:
chunk 4 (label = plotunif)
Error in if (class(rho) == "matrix") { : the condition has length > 1
--- failed re-building ‘mvgraphnorm-intro.Rnw’
SUMMARY: processing the following file failed:
‘mvgraphnorm-intro.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.81
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘mvgraphnorm-intro.Rnw’ using Sweave
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: mvtnorm
Loading required package: qpgraph
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
Attaching package: ‘qpgraph’
The following object is masked from ‘package:mvtnorm’:
rmvnorm
The following object is masked from ‘package:igraph’:
graph
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
mvgraphnorm
--- call from context ---
.GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
--- call from argument ---
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
--- R stacktrace ---
where 1: .GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
where 2: .gensample(n = n.samples + nrow(net.str), bin.mat = net.str,
method = method[1], cor = cor, mean.vector = mean.vector,
m.var = m.var)
where 3: rmvggm(20, net.str = g, method = "htf", cor = m)
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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 22: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/mvgraphnorm.Rcheck/vign_test/mvgraphnorm",
ser_elibs = "/tmp/Rtmp6486YX/filea5373946d91.rds")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (diag_, rho = 0, method = "IPF")
{
if (class(rho) == "matrix") {
diag(rho) <- 1
if (!is.positive.definite(rho)) {
rho <- as.matrix(nearPD(rho, corr = T)$mat)
}
}
w <- as.matrix(qpG2Sigma(diag_, rho = rho, matrix.completion = method))
d_d <- diag(diag(w)^(-1/2), nrow(diag_))
dg <- d_d %*% w %*% d_d
retval <- list(sigcov = w, sigcor = dg)
return(retval)
}
<bytecode: 0x26de31f0>
<environment: namespace:mvgraphnorm>
--- function search by body ---
Function .GRCM_n in namespace mvgraphnorm has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'mvgraphnorm-intro.Rnw' failed with diagnostics:
chunk 4 (label = plotunif)
Error in if (class(rho) == "matrix") { : the condition has length > 1
--- failed re-building ‘mvgraphnorm-intro.Rnw’
SUMMARY: processing the following file failed:
‘mvgraphnorm-intro.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.81
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-release-osx-x86_64
Version: 1.81
Check: package dependencies
Result: ERROR
Package required but not available: ‘qpgraph’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-osx-x86_64