MethylSeekR 1.12.0
Lukas Burger
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MethylSeekR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MethylSeekR
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* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* preparing ‘MethylSeekR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: mhsmm
Loading required package: mvtnorm
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
reading methylome data
Read 200000 records
reading SNP table
Read 11750 records
removing SNPs
11604 (6.2%) CpGs removed
determining alpha distribution for chromosome: chr22
training PMD-HMM on chromosome chr22
performing viterbi segmentation
creating GRanges object
determining alpha distribution for chromosome: chr22
Error: processing vignette 'MethylSeekR.Rnw' failed with diagnostics:
chunk 18
Error in normArgTable(value, x) : unknown table name 'chromInfo'
Execution halted