tRanslatome 1.11.0
Toma Tebaldi , Erik Dassi
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tRanslatome | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | ERROR | ERROR | |
| morelia | 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-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tRanslatome
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* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* preparing ‘tRanslatome’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from ‘package:limma’:
plotMA
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, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: Rmpfr
Loading required package: gmp
Attaching package: ‘gmp’
The following objects are masked from ‘package:base’:
%*%, apply, crossprod, matrix, tcrossprod
C code of R package 'Rmpfr': GMP using 64 bits per limb
Attaching package: ‘Rmpfr’
The following objects are masked from ‘package:BiocGenerics’:
cbind, pmax, pmin, rbind
The following objects are masked from ‘package:stats’:
dbinom, dnorm, dpois, pnorm
The following objects are masked from ‘package:base’:
cbind, pmax, pmin, rbind
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:Rmpfr’:
colMeans, colSums, rowMeans, rowSums
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: ‘SparseM’
The following object is masked from ‘package:base’:
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: ‘topGO’
The following object is masked from ‘package:IRanges’:
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:IRanges’:
space
The following object is masked from ‘package:S4Vectors’:
space
The following object is masked from ‘package:stats’:
lowess
Loading required package: plotrix
Attaching package: ‘plotrix’
The following object is masked from ‘package:gplots’:
plotCI
Building most specific GOs .....
( 1480 GO terms found. )
Build GO DAG topology ..........
( 1747 GO terms and 3424 relations. )
Annotating nodes ...............
( 17839 genes annotated to the GO terms. )
-- Elim Algorithm --
the algorithm is scoring 186 nontrivial nodes
parameters:
test statistic: fisher
cutOff: 0.01
Level 13: 2 nodes to be scored (0 eliminated genes)
Level 12: 6 nodes to be scored (0 eliminated genes)
Level 11: 15 nodes to be scored (64 eliminated genes)
Level 10: 19 nodes to be scored (79 eliminated genes)
Level 9: 26 nodes to be scored (668 eliminated genes)
Level 8: 20 nodes to be scored (668 eliminated genes)
Level 7: 13 nodes to be scored (877 eliminated genes)
Level 6: 14 nodes to be scored (927 eliminated genes)
Level 5: 19 nodes to be scored (3431 eliminated genes)
Level 4: 29 nodes to be scored (3460 eliminated genes)
Level 3: 13 nodes to be scored (14477 eliminated genes)
Level 2: 9 nodes to be scored (14477 eliminated genes)
Level 1: 1 nodes to be scored (14597 eliminated genes)
Building most specific GOs .....
( 1480 GO terms found. )
Build GO DAG topology ..........
( 1747 GO terms and 3424 relations. )
Annotating nodes ...............
( 17839 genes annotated to the GO terms. )
-- Elim Algorithm --
the algorithm is scoring 163 nontrivial nodes
parameters:
test statistic: fisher
cutOff: 0.01
Level 12: 6 nodes to be scored (0 eliminated genes)
Level 11: 16 nodes to be scored (0 eliminated genes)
Level 10: 18 nodes to be scored (39 eliminated genes)
Level 9: 26 nodes to be scored (440 eliminated genes)
Level 8: 17 nodes to be scored (440 eliminated genes)
Level 7: 11 nodes to be scored (3644 eliminated genes)
Level 6: 11 nodes to be scored (3662 eliminated genes)
Level 5: 13 nodes to be scored (5508 eliminated genes)
Level 4: 20 nodes to be scored (5533 eliminated genes)
Level 3: 14 nodes to be scored (5533 eliminated genes)
Level 2: 10 nodes to be scored (5533 eliminated genes)
Level 1: 1 nodes to be scored (5533 eliminated genes)
Error: processing vignette 'tRanslatome_package.Rnw' failed with diagnostics:
chunk 1
Error in goSim(go1[i, 1], go2[j, 1], organism = "human", measure = "Wang", :
unused arguments (organism = "human", ont = ontology)
Execution halted