Last updated on 2019-12-01 07:55:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.1 | 32.56 | 81.37 | 113.93 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 3.0.1 | 28.52 | 62.80 | 91.32 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.0.1 | 142.42 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0.1 | 142.40 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 3.0.1 | 73.00 | 125.00 | 198.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 3.0.1 | 76.00 | 129.00 | 205.00 | OK | |
| r-patched-linux-x86_64 | 3.0.1 | 30.66 | 77.13 | 107.79 | OK | |
| r-patched-solaris-x86 | 3.0.1 | 186.80 | OK | |||
| r-release-linux-x86_64 | 3.0.1 | 33.14 | 77.28 | 110.42 | OK | |
| r-release-windows-ix86+x86_64 | 3.0.1 | 68.00 | 123.00 | 191.00 | OK | |
| r-release-osx-x86_64 | 3.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 3.0.1 | 89.00 | 165.00 | 254.00 | OK | |
| r-oldrel-osx-x86_64 | 3.0.1 | OK |
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in 'JAGUAR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jaguar_process
> ### Title: Obtain significant gene-SNP pairs based on a predetermined
> ### threshold value
> ### Aliases: jaguar_process
> ### Keywords: score test GWAS eQTL
>
> ### ** Examples
>
> ## Example
> #
> # Load the example data
> data(jaguar_example);
>
> # Genome-wide analysis
> Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
> Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
> jag.out = jaguar_gwa(Gene_Mat,Geno_Mat);
Running Genome-Wide eQTL analysis on 10 genes and 1036 SNPs
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> dim(jag.out);
[1] 10 1036
>
> # Process results based on a predetermined threshold
> result = jaguar_process(jag.out,0.05);
Processing JAGUAR results
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
JAGUAR
--- call from context ---
jaguar_process(jag.out, 0.05)
--- call from argument ---
if (class(jaguar.out) != "matrix") stop("Wrong data type passed!")
--- R stacktrace ---
where 1: jaguar_process(jag.out, 0.05)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (jaguar.out, threshold, plot = FALSE)
{
cat("\nProcessing JAGUAR results\n\n")
if (class(jaguar.out) != "matrix")
stop("Wrong data type passed!")
if (plot) {
U.vec = as.vector(jaguar.out)
if (length(U.vec) > 50000) {
U.vec.temp = U.vec[sample(1:length(U.vec), 50000,
replace = F)]
}
else {
U.vec.temp = U.vec[sample(1:length(U.vec), length(U.vec),
replace = F)]
}
theoretical.quantiles = (1:length(U.vec.temp))/(1 + length(U.vec.temp))
data.quantiles = sort(U.vec.temp)
plot(-log10(theoretical.quantiles), -log10(data.quantiles),
main = "QQ-plot of the score test pvals", xlab = "Theoritical Quantiles",
ylab = "Data Quantiles")
abline(0, 1, col = "red")
}
w = which(jaguar.out < threshold, arr.ind = T)
val = jaguar.out[jaguar.out < threshold]
genes = rownames(jaguar.out)[w[, 1]]
snps = colnames(jaguar.out)[w[, 2]]
eQTL = data.frame(Gene = genes, SNP = snps, pvalue = val)
return(eQTL)
}
<bytecode: 0xcf4a650>
<environment: namespace:JAGUAR>
--- function search by body ---
Function jaguar_process in namespace JAGUAR has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘JAGUAR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jaguar_process
> ### Title: Obtain significant gene-SNP pairs based on a predetermined
> ### threshold value
> ### Aliases: jaguar_process
> ### Keywords: score test GWAS eQTL
>
> ### ** Examples
>
> ## Example
> #
> # Load the example data
> data(jaguar_example);
>
> # Genome-wide analysis
> Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
> Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
> jag.out = jaguar_gwa(Gene_Mat,Geno_Mat);
Running Genome-Wide eQTL analysis on 10 genes and 1036 SNPs
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> dim(jag.out);
[1] 10 1036
>
> # Process results based on a predetermined threshold
> result = jaguar_process(jag.out,0.05);
Processing JAGUAR results
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
JAGUAR
--- call from context ---
jaguar_process(jag.out, 0.05)
--- call from argument ---
if (class(jaguar.out) != "matrix") stop("Wrong data type passed!")
--- R stacktrace ---
where 1: jaguar_process(jag.out, 0.05)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (jaguar.out, threshold, plot = FALSE)
{
cat("\nProcessing JAGUAR results\n\n")
if (class(jaguar.out) != "matrix")
stop("Wrong data type passed!")
if (plot) {
U.vec = as.vector(jaguar.out)
if (length(U.vec) > 50000) {
U.vec.temp = U.vec[sample(1:length(U.vec), 50000,
replace = F)]
}
else {
U.vec.temp = U.vec[sample(1:length(U.vec), length(U.vec),
replace = F)]
}
theoretical.quantiles = (1:length(U.vec.temp))/(1 + length(U.vec.temp))
data.quantiles = sort(U.vec.temp)
plot(-log10(theoretical.quantiles), -log10(data.quantiles),
main = "QQ-plot of the score test pvals", xlab = "Theoritical Quantiles",
ylab = "Data Quantiles")
abline(0, 1, col = "red")
}
w = which(jaguar.out < threshold, arr.ind = T)
val = jaguar.out[jaguar.out < threshold]
genes = rownames(jaguar.out)[w[, 1]]
snps = colnames(jaguar.out)[w[, 2]]
eQTL = data.frame(Gene = genes, SNP = snps, pvalue = val)
return(eQTL)
}
<bytecode: 0x55b30f1bbf00>
<environment: namespace:JAGUAR>
--- function search by body ---
Function jaguar_process in namespace JAGUAR has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
jaguar.cpp:352:84: warning: 'bind2nd<std::__1::less<double>, double>' is deprecated [-Wdeprecated-declarations]
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.0.1
Check: compiled code
Result: NOTE
File ‘JAGUAR/libs/JAGUAR.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc