Last updated on 2018-12-29 10:50:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.3 | 16.13 | 93.96 | 110.09 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.7.3 | 10.87 | 72.28 | 83.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.7.3 | 126.74 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.7.3 | 123.40 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.7.3 | 26.00 | 207.00 | 233.00 | OK | |
| r-patched-linux-x86_64 | 1.7.3 | 16.52 | 88.54 | 105.06 | OK | |
| r-patched-solaris-x86 | 1.7.3 | 186.90 | OK | |||
| r-release-linux-x86_64 | 1.7.3 | 17.93 | 87.89 | 105.82 | OK | |
| r-release-windows-ix86+x86_64 | 1.7.3 | 32.00 | 144.00 | 176.00 | ERROR | |
| r-release-osx-x86_64 | 1.7.3 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.7.3 | 23.00 | 148.00 | 171.00 | OK | |
| r-oldrel-osx-x86_64 | 1.7.3 | OK |
Version: 1.7.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
duplicated vignette title:
‘Introduction’
--- re-building ‘readGTF.Rnw’ using Sweave
--- finished re-building ‘readGTF.Rnw’
--- re-building ‘refGenome.Rnw’ using Sweave
Loading required package: doBy
Loading required package: RSQLite
Missing matches for 1 gene_ID(s):
[getGenePositions.ucscGenome] Adding 'start_codon' and 'stop_codon' positions.
[overlapJuncs] Input preparation.
[overlapJuncs] Query size : 7 Ref size : 92
[overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[overlapJuncs] i: 1 seqid: 1 query set: 7 ref set: 82
[overlapJuncs] Result assemly.
[overlapJuncs] Finished.
--- finished re-building ‘refGenome.Rnw’
Error: Duplicate vignette titles
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.7.3
Check: running tests for arch ‘i386’
Result: ERROR
Running 'test-all.R' [3s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
>
>
> ##============================================================================##
> ## A Load prerequisites
> ##============================================================================##
>
> require(refGenome)
Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
>
>
> ##============================================================================##
> ## B Initialize example data
> ##============================================================================##
>
> ensfile <- system.file("extdata",
+ "hs.ensembl.62.small.RData",
+ package = "refGenome", mustWork=TRUE)
>
> ##----------------------------------------------------------------------------##
> ## B.1 Load Ensembl genome
> ##----------------------------------------------------------------------------##
> ens <- loadGenome(ensfile)
> enex<-refExons(ens)
[refExons.refGenome] Extracting tables.
[refExons.refGenome] Adding 'CDS'.
[refExons.refGenome] Adding 'start_codon'.
[refExons.refGenome] Adding 'stop_codon'.
[refExons.refGenome] Finished.
> gp <- getGenePositions(ens)
> junc<-getSpliceTable(ens)
>
>
>
> ##============================================================================##
> ## C Run tests
> ##============================================================================##
>
> ##----------------------------------------------------------------------------##
> ## C.1 Test overlap juncs
> ##----------------------------------------------------------------------------##
>
> ## ##
> ## Requires: Initialized objects (as done by test-all.R header)
> ## ##
>
> ## ##
> ## C.1.1 Overlap juncs
> ## ##
>
> ## 1 2 3 4 5 6 7 ##
> qry<-data.frame(id = 1:7, seqid = "1",
+ lstart = c(10100L, 11800L, 12220L, 12220L, 12220L, 32000L, 40000L),
+ lend = c(10100L, 12000L, 12225L, 12227L, 12227L, 32100L, 40100L),
+ rstart = c(10200L, 12200L, 12057L, 12613L, 12650L, 32200L, 40200L),
+ rend = c(10300L, 12250L, 12179L, 12620L, 12700L, 32300L, 40300L))
> ## 1 2 3 4 5 6 7 ##
>
> ## ##
> ## C.1.2
> ## ##
> res<-overlapJuncs(qry,junc)
[overlapJuncs] Input preparation.
[overlapJuncs] Query size : 7 Ref size : 92
[overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[overlapJuncs] i: 1 seqid: 1 query set: 7 ref set: 82
[overlapJuncs] Result assemly.
[overlapJuncs] Finished.
>
> if(! all(is.na(res$sod)==c(TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE)) )
+ stop("[test_overlap_juncs] Wrong res$sod NA's.")
Error: [test_overlap_juncs] Wrong res$sod NA's.
Execution halted
Flavor: r-release-windows-ix86+x86_64