Last updated on 2015-01-27 12:47:39.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.4 | 25.80 | 17.14 | 42.94 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 3.4 | 37.28 | 16.36 | 53.63 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 3.4 | 98.65 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 3.4 | 94.58 | NOTE | |||
| r-devel-osx-x86_64-clang | 3.4 | 70.65 | OK | |||
| r-devel-windows-ix86+x86_64 | 3.4 | 5.00 | 1.00 | 6.00 | ERROR | |
| r-patched-linux-x86_64 | 3.4 | 37.30 | 18.24 | 55.53 | NOTE | |
| r-patched-solaris-sparc | 3.4 | 516.90 | OK | |||
| r-patched-solaris-x86 | 3.4 | 163.10 | OK | |||
| r-release-linux-ix86 | 3.4 | 49.27 | 18.96 | 68.23 | ERROR | |
| r-release-linux-x86_64 | 3.4 | 37.51 | 17.77 | 55.28 | NOTE | |
| r-release-osx-x86_64-mavericks | 3.4 | NOTE | ||||
| r-release-osx-x86_64-snowleopard | 3.4 | OK | ||||
| r-release-windows-ix86+x86_64 | 3.4 | 110.00 | 44.00 | 154.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 3.4 | 166.00 | 57.00 | 223.00 | OK |
Version: 3.4
Check: installed package size
Result: NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
libs 7.3Mb
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: 3.4
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-windows-ix86+x86_64
Version: 3.4
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