no html

[ypmjx123]

Hello.
FIREVAT software is great, and I have installed it on my computer too, but I'm not sure if it's because of compatibility issues, there are no HTML files in the output. Do you know what could be the possible reasons?
Thank you!

code:
library(FIREVAT)

Output directory

output.dir <- "E:/R/TCGA/FIREVAT/" # assign this path

VCF file

sample.vcf.file <- system.file("extdata", "DCC_PCAWG_Cell_Lines_HCC1954.vcf", package = "FIREVAT")

Configuration file

config.file <- system.file("config", "PCAWG_DKFZ_Cell_Line_Filtering_Params.json", package = "FIREVAT")

Run FIREVAT

results <- RunFIREVAT(vcf.file = sample.vcf.file,
vcf.file.genome = 'hg19', # for mouse variants: 'mm10'
config.file = config.file,
df.ref.mut.sigs = GetPCAWGMutSigs(),
target.mut.sigs = GetPCAWGMutSigsNames(),
sequencing.artifact.mut.sigs = PCAWG.All.Sequencing.Artifact.Signatures,
output.dir = output.dir,
objective.fn = Default.Obj.Fn,
num.cores = 2,
ga.pop.size = 100,
ga.max.iter = 5,
ga.run = 5,
perform.strand.bias.analysis = TRUE,
ref.forward.strand.var = "TumorDPRefForward",
ref.reverse.strand.var = "TumorDPRefReverse",
alt.forward.strand.var = "TumorDPAltForward",
alt.reverse.strand.var = "TumorDPAltReverse",
annotate = FALSE)

[khb7840]

It's hard to find out what is the problem in your environment just from command.

However, mainly, issues in HTML report come from R Markdown or pandoc dependency problems.

Please check if pandoc or R Markdown is working well in your machine.

[ypmjx123]

Warning message:
1: In melt(df.temp, id.vars = x.axis.var) :
The melt generic function in data.table is being passed a data.frame, which will soon be redirected to the corresponding method in reshape2; please note that reshape2 has been deprecated, and this redirection has also been deprecated. If you want to continue using the melt method from reshape2 while both data.table and reshape2 are attached (e.g., melt.list), you can prefix the namespace before the function name, such as reshape2::melt(df.temp). In the next version, this warning will become an error.
2: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
3: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
4: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
5: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
6: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
7: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
8: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
9: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
10: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
11: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
12: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
13: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
14: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
15: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
16: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
17: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
18: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
19: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
20: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
21: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
22: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
23: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
24: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
25: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
26: In melt(df.temp, id.vars = x.axis.var) :
The melt generic function in data.table is being passed a data.frame, which will soon be redirected to the corresponding method in reshape2; please note that reshape2 has been deprecated, and this redirection has also been deprecated. If you want to continue using the melt method from reshape2 while both data.table and reshape2 are attached (e.g., melt.list), you can prefix the namespace before the function name, such as reshape2::melt(df.temp). In the next version, this warning will become an error.
27: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
28: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
29: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
30: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
31: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
32: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
33: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
34: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
35: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
36: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
37: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
38: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
39: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
40: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
41: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
42: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
43: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
44: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
45: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
46: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
47: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
48: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
49: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)
50: In grid.Call(C_textBounds, as.graphicsAnnot(x$label), ... :
Unable to calculate text width/height (using zero)

[ypmjx123]

Hello, what is the problem?
In melt(df.temp, id.vars = x.axis.var):
The melt generic function in data.table has been passed a data.frame, which is about to be redirected to the corresponding method in reshape2. Please note that reshape2 has been deprecated, and this redirection is also deprecated. If you want to continue using the melt function from reshape2 while both data.table and reshape2 are attached (e.g., melt.list), you can prefix the namespace before the function name, such as reshape2::melt(df.temp). In the next version, this warning will become an error.

[ypmjx123]

And FIREVAT cannot analysis the insdel SNVs?