Last updated on 2019-02-22 05:50:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 7.1 | 233.13 | 27.06 | 260.19 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 7.1 | 158.65 | 21.52 | 180.17 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 7.1 | 405.19 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 7.1 | 292.17 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 7.1 | 487.00 | 96.00 | 583.00 | NOTE | |
| r-patched-linux-x86_64 | 7.1 | 180.90 | 24.99 | 205.89 | NOTE | |
| r-patched-solaris-x86 | 7.1 | 366.60 | ERROR | |||
| r-release-linux-x86_64 | 7.1 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 7.1 | 388.00 | 104.00 | 492.00 | NOTE | |
| r-release-osx-x86_64 | 7.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 7.1 | 403.00 | 165.00 | 568.00 | NOTE | |
| r-oldrel-osx-x86_64 | 7.1 | NOTE |
Version: 7.1
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 7.1
Check: installed package size
Result: NOTE
installed size is 24.4Mb
sub-directories of 1Mb or more:
libs 23.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 7.1
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
>
> if (.Platform$endian == "little") {
+ param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+ geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
+ param <- makeAnnotationParameter(param)
+ print(param)
+ annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
+ } else {
+ message("Tabix does not work well for big endian for now")
+ }
$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
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: 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