Last updated on 2020-02-19 10:49:01 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.25 | 14.39 | 144.18 | 158.57 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.25 | 12.34 | 107.26 | 119.60 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.25 | 198.67 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.25 | 188.80 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.25 | 29.00 | 200.00 | 229.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.25 | 43.00 | 266.00 | 309.00 | NOTE | |
| r-patched-linux-x86_64 | 0.25 | 13.36 | 166.81 | 180.17 | OK | |
| r-patched-solaris-x86 | 0.25 | 189.10 | WARN | |||
| r-release-linux-x86_64 | 0.25 | 11.05 | 164.02 | 175.07 | OK | |
| r-release-windows-ix86+x86_64 | 0.25 | 23.00 | 187.00 | 210.00 | NOTE | |
| r-release-osx-x86_64 | 0.25 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 0.25 | 19.00 | 201.00 | 220.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.25 | WARN |
Version: 0.25
Check: examples
Result: ERROR
Running examples in 'NormalizeMets-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ComparePvalHist
> ### Title: p-value Histogram
> ### Aliases: ComparePvalHist
>
> ### ** Examples
>
> data("alldata_eg")
> featuredata_eg<-alldata_eg$featuredata
> dataview(featuredata_eg)
- The data consists of 150 rows by 128 columns
m_1 m_2 m_3 m_4 m_5 m_6 m_7
s_1 10485.867 33220.562 1112.9795 1408.6396 455.7529 1100.4023 122.36316
s_2 8960.469 29995.516 926.2891 529.0449 873.6094 2201.2461 173.08020
s_3 10160.445 28559.641 1230.3330 1306.3203 1027.5078 2066.5918 269.79980
s_4 8794.477 27593.750 901.7622 1800.0830 675.0396 1675.8496 287.99927
s_5 8956.922 28161.766 979.1724 818.0366 904.0254 1245.9912 167.41333
s_6 9092.258 31685.312 634.6899 478.3811 980.4233 1259.5635 97.56250
s_7 2271.045 7692.176 143.1688 109.8399 730.6172 1387.7920 149.09668
s_8 7850.402 26462.797 822.5991 1341.2158 583.5830 2164.1270 227.76965
s_9 10969.062 21605.141 408.0005 1499.4795 452.2375 916.5283 234.49756
s_10 1743.933 7647.645 218.4199 127.4294 408.2913 999.5718 74.82697
m_8 ...
s_1 3855.805 ...
s_2 5090.637 ...
s_3 4483.906 ...
s_4 4949.262 ...
s_5 4302.934 ...
s_6 4406.344 ...
s_7 1543.406 ...
s_8 5030.688 ...
s_9 4657.254 ...
s_10 1510.012 ...
> sampledata_eg<-alldata_eg$sampledata
> dataview(sampledata_eg)
- The data consists of 150 rows by 4 columns
batch gender Age bmi
s_1 Batch 2 code_1 58.66 22.22
s_2 Batch 2 code_0 76.70 23.74
s_3 Batch 2 code_0 56.15 28.19
s_4 Batch 2 code_0 77.22 26.18
s_5 Batch 2 code_0 74.29 26.37
s_6 Batch 2 code_1 66.82 26.39
s_7 Batch 1 code_0 65.00 29.00
s_8 Batch 2 code_1 66.51 26.13
s_9 Batch 2 code_0 70.23 27.26
s_10 Batch 1 code_1 55.00 25.00
> metabolitedata_eg<-alldata_eg$metabolitedata
> dataview(metabolitedata_eg)
- The data consists of 128 rows by 4 columns
names IS neg_controls pos_controls_gender
1 m_1 0 1 0
2 m_2 0 1 0
3 m_3 0 1 0
4 m_4 0 0 0
5 m_5 0 0 0
6 m_6 0 0 0
7 m_7 0 0 0
8 m_8 0 1 0
9 m_9 0 1 0
10 m_10 0 1 0
>
> logdata <- LogTransform(featuredata_eg)
> dataview(logdata$featuredata)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(logdata$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(logdata$featuredata)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x6a9d2c0>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe") :
the condition has length > 1
Calls: dataview
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'NormalizeMets_vignette.Rmd' using rmarkdown
Warning: Zero sample variances detected, have been offset away from zero
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(uv_ruvrandclust$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(uv_ruvrandclust$featuredata)
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/NormalizeMets.Rcheck/vign_test/NormalizeMets",
ser_elibs = "/tmp/Rtmp21Lv9p/file258e1760eaf0.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x90bb578>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 458-472 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'NormalizeMets_vignette.Rmd'
SUMMARY: processing the following file failed:
'NormalizeMets_vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.25
Check: examples
Result: ERROR
Running examples in ‘NormalizeMets-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ComparePvalHist
> ### Title: p-value Histogram
> ### Aliases: ComparePvalHist
>
> ### ** Examples
>
> data("alldata_eg")
> featuredata_eg<-alldata_eg$featuredata
> dataview(featuredata_eg)
- The data consists of 150 rows by 128 columns
m_1 m_2 m_3 m_4 m_5 m_6 m_7
s_1 10485.867 33220.562 1112.9795 1408.6396 455.7529 1100.4023 122.36316
s_2 8960.469 29995.516 926.2891 529.0449 873.6094 2201.2461 173.08020
s_3 10160.445 28559.641 1230.3330 1306.3203 1027.5078 2066.5918 269.79980
s_4 8794.477 27593.750 901.7622 1800.0830 675.0396 1675.8496 287.99927
s_5 8956.922 28161.766 979.1724 818.0366 904.0254 1245.9912 167.41333
s_6 9092.258 31685.312 634.6899 478.3811 980.4233 1259.5635 97.56250
s_7 2271.045 7692.176 143.1688 109.8399 730.6172 1387.7920 149.09668
s_8 7850.402 26462.797 822.5991 1341.2158 583.5830 2164.1270 227.76965
s_9 10969.062 21605.141 408.0005 1499.4795 452.2375 916.5283 234.49756
s_10 1743.933 7647.645 218.4199 127.4294 408.2913 999.5718 74.82697
m_8 ...
s_1 3855.805 ...
s_2 5090.637 ...
s_3 4483.906 ...
s_4 4949.262 ...
s_5 4302.934 ...
s_6 4406.344 ...
s_7 1543.406 ...
s_8 5030.688 ...
s_9 4657.254 ...
s_10 1510.012 ...
> sampledata_eg<-alldata_eg$sampledata
> dataview(sampledata_eg)
- The data consists of 150 rows by 4 columns
batch gender Age bmi
s_1 Batch 2 code_1 58.66 22.22
s_2 Batch 2 code_0 76.70 23.74
s_3 Batch 2 code_0 56.15 28.19
s_4 Batch 2 code_0 77.22 26.18
s_5 Batch 2 code_0 74.29 26.37
s_6 Batch 2 code_1 66.82 26.39
s_7 Batch 1 code_0 65.00 29.00
s_8 Batch 2 code_1 66.51 26.13
s_9 Batch 2 code_0 70.23 27.26
s_10 Batch 1 code_1 55.00 25.00
> metabolitedata_eg<-alldata_eg$metabolitedata
> dataview(metabolitedata_eg)
- The data consists of 128 rows by 4 columns
names IS neg_controls pos_controls_gender
1 m_1 0 1 0
2 m_2 0 1 0
3 m_3 0 1 0
4 m_4 0 0 0
5 m_5 0 0 0
6 m_6 0 0 0
7 m_7 0 0 0
8 m_8 0 1 0
9 m_9 0 1 0
10 m_10 0 1 0
>
> logdata <- LogTransform(featuredata_eg)
> dataview(logdata$featuredata)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(logdata$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(logdata$featuredata)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x561e3b2b2038>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe") :
the condition has length > 1
Calls: dataview
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning: Zero sample variances detected, have been offset away from zero
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(uv_ruvrandclust$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(uv_ruvrandclust$featuredata)
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/NormalizeMets.Rcheck/vign_test/NormalizeMets",
ser_elibs = "/home/hornik/tmp/scratch/Rtmpu5mxXb/file7ce249fa42f3.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x56146173d2c8>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 458-472 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NormalizeMets_vignette.Rmd’
SUMMARY: processing the following file failed:
‘NormalizeMets_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.25
Check: installed package size
Result: NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
doc 8.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 0.25
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.25
Check: examples
Result: ERROR
Running examples in ‘NormalizeMets-Ex.R’ failed
The error most likely occurred in:
> ### Name: ComparePvalHist
> ### Title: p-value Histogram
> ### Aliases: ComparePvalHist
>
> ### ** Examples
>
> data("alldata_eg")
> featuredata_eg<-alldata_eg$featuredata
> dataview(featuredata_eg)
- The data consists of 150 rows by 128 columns
m_1 m_2 m_3 m_4 m_5 m_6 m_7
s_1 10485.867 33220.562 1112.9795 1408.6396 455.7529 1100.4023 122.36316
s_2 8960.469 29995.516 926.2891 529.0449 873.6094 2201.2461 173.08020
s_3 10160.445 28559.641 1230.3330 1306.3203 1027.5078 2066.5918 269.79980
s_4 8794.477 27593.750 901.7622 1800.0830 675.0396 1675.8496 287.99927
s_5 8956.922 28161.766 979.1724 818.0366 904.0254 1245.9912 167.41333
s_6 9092.258 31685.312 634.6899 478.3811 980.4233 1259.5635 97.56250
s_7 2271.045 7692.176 143.1688 109.8399 730.6172 1387.7920 149.09668
s_8 7850.402 26462.797 822.5991 1341.2158 583.5830 2164.1270 227.76965
s_9 10969.062 21605.141 408.0005 1499.4795 452.2375 916.5283 234.49756
s_10 1743.933 7647.645 218.4199 127.4294 408.2913 999.5718 74.82697
m_8 ...
s_1 3855.805 ...
s_2 5090.637 ...
s_3 4483.906 ...
s_4 4949.262 ...
s_5 4302.934 ...
s_6 4406.344 ...
s_7 1543.406 ...
s_8 5030.688 ...
s_9 4657.254 ...
s_10 1510.012 ...
> sampledata_eg<-alldata_eg$sampledata
> dataview(sampledata_eg)
- The data consists of 150 rows by 4 columns
batch gender Age bmi
s_1 Batch 2 code_1 58.66 22.22
s_2 Batch 2 code_0 76.70 23.74
s_3 Batch 2 code_0 56.15 28.19
s_4 Batch 2 code_0 77.22 26.18
s_5 Batch 2 code_0 74.29 26.37
s_6 Batch 2 code_1 66.82 26.39
s_7 Batch 1 code_0 65.00 29.00
s_8 Batch 2 code_1 66.51 26.13
s_9 Batch 2 code_0 70.23 27.26
s_10 Batch 1 code_1 55.00 25.00
> metabolitedata_eg<-alldata_eg$metabolitedata
> dataview(metabolitedata_eg)
- The data consists of 128 rows by 4 columns
names IS neg_controls pos_controls_gender
1 m_1 0 1 0
2 m_2 0 1 0
3 m_3 0 1 0
4 m_4 0 0 0
5 m_5 0 0 0
6 m_6 0 0 0
7 m_7 0 0 0
8 m_8 0 1 0
9 m_9 0 1 0
10 m_10 0 1 0
>
> logdata <- LogTransform(featuredata_eg)
> dataview(logdata$featuredata)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(logdata$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(logdata$featuredata)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x555d238>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe") :
the condition has length > 1
Calls: dataview
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning: Zero sample variances detected, have been offset away from zero
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(uv_ruvrandclust$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(uv_ruvrandclust$featuredata)
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/NormalizeMets.Rcheck/vign_test/NormalizeMets",
ser_elibs = "/tmp/RtmpDxcRpX/file81cc228d90e5.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x91829e8>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 458-472 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NormalizeMets_vignette.Rmd’
SUMMARY: processing the following file failed:
‘NormalizeMets_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.25
Check: examples
Result: ERROR
Running examples in ‘NormalizeMets-Ex.R’ failed
The error most likely occurred in:
> ### Name: ComparePvalHist
> ### Title: p-value Histogram
> ### Aliases: ComparePvalHist
>
> ### ** Examples
>
> data("alldata_eg")
> featuredata_eg<-alldata_eg$featuredata
> dataview(featuredata_eg)
- The data consists of 150 rows by 128 columns
m_1 m_2 m_3 m_4 m_5 m_6 m_7
s_1 10485.867 33220.562 1112.9795 1408.6396 455.7529 1100.4023 122.36316
s_2 8960.469 29995.516 926.2891 529.0449 873.6094 2201.2461 173.08020
s_3 10160.445 28559.641 1230.3330 1306.3203 1027.5078 2066.5918 269.79980
s_4 8794.477 27593.750 901.7622 1800.0830 675.0396 1675.8496 287.99927
s_5 8956.922 28161.766 979.1724 818.0366 904.0254 1245.9912 167.41333
s_6 9092.258 31685.312 634.6899 478.3811 980.4233 1259.5635 97.56250
s_7 2271.045 7692.176 143.1688 109.8399 730.6172 1387.7920 149.09668
s_8 7850.402 26462.797 822.5991 1341.2158 583.5830 2164.1270 227.76965
s_9 10969.062 21605.141 408.0005 1499.4795 452.2375 916.5283 234.49756
s_10 1743.933 7647.645 218.4199 127.4294 408.2913 999.5718 74.82697
m_8 ...
s_1 3855.805 ...
s_2 5090.637 ...
s_3 4483.906 ...
s_4 4949.262 ...
s_5 4302.934 ...
s_6 4406.344 ...
s_7 1543.406 ...
s_8 5030.688 ...
s_9 4657.254 ...
s_10 1510.012 ...
> sampledata_eg<-alldata_eg$sampledata
> dataview(sampledata_eg)
- The data consists of 150 rows by 4 columns
batch gender Age bmi
s_1 Batch 2 code_1 58.66 22.22
s_2 Batch 2 code_0 76.70 23.74
s_3 Batch 2 code_0 56.15 28.19
s_4 Batch 2 code_0 77.22 26.18
s_5 Batch 2 code_0 74.29 26.37
s_6 Batch 2 code_1 66.82 26.39
s_7 Batch 1 code_0 65.00 29.00
s_8 Batch 2 code_1 66.51 26.13
s_9 Batch 2 code_0 70.23 27.26
s_10 Batch 1 code_1 55.00 25.00
> metabolitedata_eg<-alldata_eg$metabolitedata
> dataview(metabolitedata_eg)
- The data consists of 128 rows by 4 columns
names IS neg_controls pos_controls_gender
1 m_1 0 1 0
2 m_2 0 1 0
3 m_3 0 1 0
4 m_4 0 0 0
5 m_5 0 0 0
6 m_6 0 0 0
7 m_7 0 0 0
8 m_8 0 1 0
9 m_9 0 1 0
10 m_10 0 1 0
>
> logdata <- LogTransform(featuredata_eg)
> dataview(logdata$featuredata)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(logdata$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(logdata$featuredata)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x5103e00>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe") :
the condition has length > 1
Calls: dataview
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning: Zero sample variances detected, have been offset away from zero
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NormalizeMets
--- call from context ---
dataview(uv_ruvrandclust$featuredata)
--- call from argument ---
if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
--- R stacktrace ---
where 1: dataview(uv_ruvrandclust$featuredata)
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/NormalizeMets.Rcheck/vign_test/NormalizeMets",
ser_elibs = "/tmp/Rtmphe7s7q/file83b97ab9da4.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (data)
{
if (class(data) %in% c("list"))
stop("Input data must be a vector, a matrix, or a dataframe")
data <- as.data.frame(data)
hdata <- data
dsize <- dim(hdata)
if (dsize[1] > 10) {
hdata <- hdata[1:10, ]
}
if (dsize[2] > 8) {
hdata <- hdata[, 1:9]
hdata[, 9] <- rep("...", nrow(hdata))
colnames(hdata)[9] <- "..."
}
write(paste("\n - The data consists of ", dsize[1], " rows by ",
dsize[2], " columns \n", sep = ""), "")
return(hdata)
}
<bytecode: 0x8f15e70>
<environment: namespace:NormalizeMets>
--- function search by body ---
Function dataview in namespace NormalizeMets has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 458-472 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NormalizeMets_vignette.Rmd’
SUMMARY: processing the following file failed:
‘NormalizeMets_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘NormalizeMets_vignette.Rmd’
SUMMARY: processing the following file failed:
‘NormalizeMets_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-patched-solaris-x86, r-release-osx-x86_64
Version: 0.25
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd)
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Flavor: r-oldrel-osx-x86_64