Last updated on 2017-08-19 05:48:40.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 6.0 | 40.49 | 20.95 | 61.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 6.0 | 43.63 | 21.13 | 64.76 | OK | |
| r-devel-linux-x86_64-fedora-clang | 6.0 | 104.68 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 6.0 | 103.26 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 6.0 | 180.00 | 48.00 | 228.00 | OK | |
| r-patched-linux-x86_64 | 6.0 | 43.48 | 21.14 | 64.61 | OK | |
| r-patched-solaris-x86 | 6.0 | 164.70 | ERROR | |||
| r-release-linux-x86_64 | 6.0 | 43.33 | 20.98 | 64.31 | OK | |
| r-release-windows-ix86+x86_64 | 6.0 | 177.00 | 78.00 | 255.00 | OK | |
| r-release-osx-x86_64 | 6.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 6.0 | 130.00 | 72.00 | 202.00 | OK | |
| r-oldrel-osx-x86_64 | 6.0 | NOTE |
Version: 6.0
Check: installed package size
Result: NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 8.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 6.0
Check: examples
Result: ERROR
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:
> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
>
> ### ** Examples
>
> param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+ geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
> param <- makeAnnotationParameter(param)
> print(param)
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"
$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"
$geneFileFormat
[1] "refFlat"
$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"
$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"
$upstreamRange
[1] 50
$downstreamRange
[1] 50
$spliceIntoExon
[1] 3
$spliceIntoIntron
[1] 8
$bed
NULL
$genomeScore
NULL
$tabix
NULL
$indexOutput
[1] FALSE
$inputFormat
[1] "vcf"
$checkReference
[1] TRUE
> annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.
*** caught segfault ***
address 0, cause 'memory not mapped'
Traceback:
1: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
2: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G", "C"))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86