cummeRbund 2.14.0
Loyal A. Goff
| 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/cummeRbund | | 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 | [ ERROR ] | skipped | | |
| 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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cummeRbund
###
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* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* preparing ‘cummeRbund’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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
Creating database /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cuffData.db
Reading Run Info File /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/read_groups.info
Writing replicates Table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Getting gene information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Getting splicing information:
distData
Getting relCDS information:
distData
Creating database /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cuffData.db
Reading Run Info File /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/read_groups.info
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Reading /tmp/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/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/RtmpBD5unL/Rinst2fdfc888be5/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Scale for 'x' is already present. Adding another scale for
'x', which will replace the existing scale.
Scale for 'x' is already present. Adding another scale for
'x', which will replace the existing scale.
Warning: Removed 204 rows containing non-finite values (stat_density).
Warning: Removed 492 rows containing non-finite values (stat_density).
Warning: Removed 204 rows containing non-finite values (stat_density).
Warning: Removed 492 rows containing non-finite values (stat_density).
Warning: Removed 204 rows containing non-finite values (stat_density).
Warning: Removed 492 rows containing non-finite values (stat_density).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).
Warning: Removed 40 rows containing missing values (geom_point).
Warning: Removed 40 rows containing missing values (geom_point).
Warning: Removed 40 rows containing missing values (geom_point).
Getting gene information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Getting splicing information:
distData
Getting relCDS information:
distData
Getting gene information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Getting splicing information:
distData
Getting relCDS information:
distData
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Scale for 'colour' is already present. Adding another scale
for 'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale
for 'colour', which will replace the existing scale.
Using tracking_id, sample_name as id variables
Warning: Removed 4 rows containing non-finite values (stat_smooth).
Using tracking_id, sample_name as id variables
Warning: Removed 4 rows containing non-finite values (stat_smooth).
Warning: Removed 4 rows containing non-finite values (stat_smooth).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
Using tracking_id, sample_name as id variables
Error: processing vignette 'cummeRbund-manual.Rnw' failed with diagnostics:
chunk 68 (label = features_3)
Error in `genome<-`(`*tmp*`, value = "hg19") :
Failed to set session genome to 'hg19'
Execution halted