spliceR 1.14.0
Johannes Waage , Kristoffer Vitting-Seerup
| 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/spliceR | | 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 | NotNeeded | [ ERROR ] | skipped | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spliceR
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* checking for file ‘spliceR/DESCRIPTION’ ... OK
* preparing ‘spliceR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: cummeRbund
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: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
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: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: RColorBrewer
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:cummeRbund':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Attaching package: 'spliceR'
The following object is masked from 'package:cummeRbund':
conditions
The following object is masked from 'package:BiocGenerics':
conditions
Creating database /tmp/Rtmp6m38Rh/cuffData.db
Reading Run Info File /tmp/Rtmp6m38Rh/run.info
Writing runInfo Table
Reading Read Group Info /tmp/Rtmp6m38Rh/read_groups.info
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/Rtmp6m38Rh/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing geneData table
Reading /tmp/Rtmp6m38Rh/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/Rtmp6m38Rh/promoters.diff
Writing promoterDiffData table
Reading /tmp/Rtmp6m38Rh/genes.count_tracking
Reshaping geneCount table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing geneCount table
Reading read group info in /tmp/Rtmp6m38Rh/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/Rtmp6m38Rh/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing isoformData table
Reading /tmp/Rtmp6m38Rh/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/Rtmp6m38Rh/isoforms.count_tracking
Reshaping isoformCount table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing isoformCount table
Reading read group info in /tmp/Rtmp6m38Rh/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/Rtmp6m38Rh/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing TSSData table
Reading /tmp/Rtmp6m38Rh/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/Rtmp6m38Rh/splicing.diff
Writing splicingDiffData table
Reading /tmp/Rtmp6m38Rh/tss_groups.count_tracking
Reshaping TSSCount table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing TSSCount table
Reading read group info in /tmp/Rtmp6m38Rh/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/Rtmp6m38Rh/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing CDSData table
Reading /tmp/Rtmp6m38Rh/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/Rtmp6m38Rh/cds.diff
Writing CDSDiffData table
Reading /tmp/Rtmp6m38Rh/cds.count_tracking
Reshaping CDSCount table
Warning: attributes are not identical across measure variables; they will be dropped
Recasting
Writing CDSCount table
Reading read group info in /tmp/Rtmp6m38Rh/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
Fixing cufflinks annotation problem...
Cufflinks annotation problem was fixed for 65 Cuff_genes
Creating spliceRList...
Error: processing vignette 'spliceR.Rnw' failed with diagnostics:
chunk 3 (label = GRanges_1)
Error in `genome<-`(`*tmp*`, value = "hg19") :
Failed to set session genome to 'hg19'
Execution halted