Last updated on 2014-04-24 15:50:48.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0 | 27.34 | 21.60 | 48.95 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 3.0 | 41.74 | 21.51 | 63.24 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 3.0 | 91.83 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0 | 103.13 | NOTE | |||
| r-devel-osx-x86_64-clang | 3.0 | 35.65 | OK | |||
| r-devel-osx-x86_64-gcc | 2.7 | OK | ||||
| r-devel-windows-ix86+x86_64 | 3.0 | 114.00 | 44.00 | 158.00 | OK | |
| r-patched-linux-x86_64 | 3.0 | 41.94 | 21.60 | 63.54 | NOTE | |
| r-patched-solaris-sparc | 3.0 | 505.60 | OK | |||
| r-patched-solaris-x86 | 3.0 | 170.30 | OK | |||
| r-release-linux-ix86 | 3.0 | 68.00 | 31.00 | 99.00 | ERROR | |
| r-release-linux-x86_64 | 3.0 | 41.91 | 22.07 | 63.98 | NOTE | |
| r-release-osx-x86_64-mavericks | 3.0 | NOTE | ||||
| r-release-osx-x86_64-snowleopard | 3.0 | OK | ||||
| r-release-windows-ix86+x86_64 | 3.0 | 120.00 | 44.00 | 164.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 3.0 | 115.00 | 53.00 | 168.00 | OK |
Version: 3.0
Check: installed package size
Result: NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
libs 6.4Mb
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
Version: 3.0
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/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
> 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