Last updated on 2024-10-05 08:48:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 12.75 | 104.59 | 117.34 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 7.68 | 74.80 | 82.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 198.08 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 537.59 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 14.00 | 115.00 | 129.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 11.34 | 99.82 | 111.16 | ERROR | |
| r-release-linux-x86_64 | 0.1.0 | 11.91 | 99.87 | 111.78 | ERROR | |
| r-release-macos-arm64 | 0.1.0 | 226.00 | OK | |||
| r-release-macos-x86_64 | 0.1.0 | 499.00 | OK | |||
| r-release-windows-x86_64 | 0.1.0 | 13.00 | 117.00 | 130.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 237.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 453.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.0 | 18.00 | 145.00 | 163.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 2.163s elapsed (1.761s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MRWR 5.635 1.791 9.522
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 2.386s elapsed (2.395s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 5.022s elapsed (3.729s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 5.056s elapsed (3.331s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ssMutPA.Rmd’ using knitr
** Processing: figure/unnamed-chunk-6-1.png
576x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 85437 bytes
Input file size = 85635 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 58350
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 58350
Output IDAT size = 58350 bytes (27087 bytes decrease)
Output file size = 58428 bytes (27207 bytes = 31.77% decrease)
** Processing: figure/unnamed-chunk-7-1.png
576x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56192 bytes
Input file size = 56342 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47534
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47534
Output IDAT size = 47534 bytes (8658 bytes decrease)
Output file size = 47612 bytes (8730 bytes = 15.49% decrease)
** Processing: figure/unnamed-chunk-8-1.png
576x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81670 bytes
Input file size = 81856 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56645
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56645
Output IDAT size = 56645 bytes (25025 bytes decrease)
Output file size = 56723 bytes (25133 bytes = 30.70% decrease)
Quitting from lines 162-170 [unnamed-chunk-9] (ssMutPA.Rmd)
Error: processing vignette 'ssMutPA.Rmd' failed with diagnostics:
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
--- failed re-building ‘ssMutPA.Rmd’
SUMMARY: processing the following file failed:
‘ssMutPA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 3.181s elapsed (2.432s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssMutPA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Oncoplot
> ### Title: Drawing a waterfall plot of a particular pathway.
> ### Aliases: Oncoplot
>
> ### ** Examples
>
> #load the data
> mut_path <- system.file("extdata","maffile.txt",package = "ssMutPA")
> maf<-maftools::read.maf(mut_path ,isTCGA = FALSE)
-Reading
-Validating
--Removed 1121 duplicated variants
-Silent variants: 607
-Summarizing
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
--Missing clinical data
-Finished in 2.760s elapsed (2.011s cpu)
> pathway_path <- system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
> load(pathway_path)
> data(samp_class_onco,mut_onco,sur_onco)
> ##draw a waterfall plot
> #win.graph()
> Oncoplot(maf,samp_class_onco,sur_onco,mut_onco,kegg_323_gmt,"IL-17 signaling pathway")
--Possible FLAGS among top ten genes:
MUC16
TTN
-Processing clinical data
Error in FUN(X[[i]], ...) :
numeric annotation color for event must be a sequential color palette!
Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
Calls: Oncoplot -> oncoplot -> lapply -> FUN
Execution halted
Flavor: r-release-linux-x86_64