Last updated on 2014-07-31 11:51:17.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1 | 27.62 | 20.88 | 48.50 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 3.1 | 43.80 | 19.71 | 63.51 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 3.1 | 92.07 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 3.1 | 101.44 | NOTE | |||
| r-devel-osx-x86_64-clang | 3.1 | 82.12 | OK | |||
| r-devel-windows-ix86+x86_64 | 3.1 | 148.00 | 47.00 | 195.00 | OK | |
| r-patched-linux-x86_64 | 3.1 | 43.77 | 20.02 | 63.78 | NOTE | |
| r-patched-solaris-sparc | 3.1 | 568.00 | OK | |||
| r-patched-solaris-x86 | 3.1 | 172.00 | OK | |||
| r-release-linux-ix86 | 3.1 | 60.30 | 22.05 | 82.35 | ERROR | |
| r-release-linux-x86_64 | 3.1 | 46.47 | 20.06 | 66.54 | NOTE | |
| r-release-osx-x86_64-mavericks | 3.1 | NOTE | ||||
| r-release-osx-x86_64-snowleopard | 3.1 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 3.1 | 189.00 | 59.00 | 248.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 3.1 | 124.00 | 52.00 | 176.00 | OK |
Version: 3.1
Check: installed package size
Result: NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
libs 6.6Mb
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard
Version: 3.1
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/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.fa"
$geneFile
[1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt"
$geneFileFormat
[1] "refFlat"
$codonFile
[1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/codon.txt"
$priorityFile
[1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/tabanno/test.gene.txt.
*** caught segfault ***
address (nil), 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"))
aborting ...
Flavor: r-release-linux-ix86