Last updated on 2018-12-14 15:51:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 6.7 | 246.89 | 26.40 | 273.29 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 6.7 | 164.62 | 21.15 | 185.77 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 6.7 | 382.18 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 6.7 | 291.75 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 6.7 | 500.00 | 98.00 | 598.00 | NOTE | |
| r-patched-linux-x86_64 | 6.7 | 197.36 | 24.44 | 221.80 | NOTE | |
| r-patched-solaris-x86 | 6.7 | 265.30 | ERROR | |||
| r-release-linux-x86_64 | 6.7 | 186.45 | 25.01 | 211.46 | NOTE | |
| r-release-windows-ix86+x86_64 | 6.7 | 420.00 | 94.00 | 514.00 | NOTE | |
| r-release-osx-x86_64 | 6.7 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 6.7 | 300.00 | 74.00 | 374.00 | NOTE | |
| r-oldrel-osx-x86_64 | 6.7 | NOTE |
clang-ASAN clang-UBSAN gcc-ASAN gcc-UBSAN rchk valgrind
Version: 6.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64
Version: 6.7
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: 6.7
Check: installed package size
Result: NOTE
installed size is 25.5Mb
sub-directories of 1Mb or more:
libs 24.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+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: 6.7
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