Last updated on 2016-09-29 14:47:43.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 5.3 | 38.88 | 17.11 | 55.99 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 5.3 | 42.72 | 16.85 | 59.57 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 5.3 | 92.55 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 5.3 | 97.96 | NOTE | |||
| r-devel-macos-x86_64-clang | 5.3 | 65.72 | OK | |||
| r-devel-windows-ix86+x86_64 | 5.3 | 112.00 | 54.00 | 166.00 | OK | |
| r-patched-linux-x86_64 | 5.3 | 38.07 | 16.47 | 54.53 | NOTE | |
| r-patched-solaris-sparc | 5.3 | 510.80 | ERROR | |||
| r-patched-solaris-x86 | 5.3 | 141.30 | ERROR | |||
| r-release-linux-x86_64 | 5.3 | 39.12 | 16.70 | 55.82 | NOTE | |
| r-release-osx-x86_64-mavericks | 5.3 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 5.3 | 159.00 | 41.00 | 200.00 | OK | |
| r-oldrel-windows-ix86+x86_64 | 5.3 | 175.00 | 55.00 | 230.00 | OK |
Memtest notes: valgrind
Version: 5.3
Check: installed package size
Result: NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
libs 7.8Mb
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-x86_64, r-release-osx-x86_64-mavericks
Version: 5.3
Check: examples
Result: ERROR
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:
> ### Name: tabix.read.table
> ### Title: Read tabix file, similar to running tabix in command line.
> ### Aliases: tabix.read.table
>
> ### ** Examples
>
> fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
> snp <- tabix.read.table(fileName, "1:196623337-196632470")
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
Error in strsplit(body, "\t") : non-character argument
Calls: tabix.read.table -> do.call -> strsplit
Execution halted
Flavor: r-patched-solaris-sparc
Version: 5.3
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