HTSanalyzeR 2.9.2
Xin Wang
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSanalyzeR | | Last Changed Rev: 66700 / Revision: 66885 | | Last Changed Date: 2012-06-13 09:23:29 -0700 (Wed, 13 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | ERROR | skipped | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | skipped | skipped |
| pitt | Mac OS X Leopard (10.5.8) / i386 | [ ERROR ] | skipped | skipped |
| perceval | Mac OS X Leopard (10.5.8) / i386 | ERROR | skipped | skipped |
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* preparing 'HTSanalyzeR':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: igraph
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
/////////////////////////////////////////////////////////////////////////////
//------------------Thanks for using HTSanalyzeR v 2.9.2-------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to xin.wang@cancer.org.uk--------------//
/////////////////////////////////////////////////////////////////////////////
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object(s) are masked from 'package:stats':
xtabs
The following object(s) are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply,
mapply, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, rownames, sapply, setdiff,
table, tapply, union, unique
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")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: graph
Attaching package: 'graph'
The following object(s) are masked from 'package:igraph':
degree, edges
Loading required package: RColorBrewer
Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-8 2012-04-25
Loading required package: grid
Loading required package: DBI
KEGG.db contains mappings based on older data because the
original resource was removed from the the public domain
before the most recent update was produced. This package
should now be considered deprecated and future versions of
Bioconductor may not have it available. One possible
alternative to consider is to look at the reactome.db
package
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[1L]], ...) :
--Gene Set terms already exsit in gene set collection GO_MF of HyperGeo.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[2L]], ...) :
--Gene Set terms already exsit in gene set collection GO_BP of HyperGeo.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[3L]], ...) :
--Gene Set terms already exsit in gene set collection GO_CC of HyperGeo.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[4L]], ...) :
--Gene Set terms already exsit in gene set collection PW_KEGG of HyperGeo.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[1L]], ...) :
--Gene Set terms already exsit in gene set collection GO_MF of GSEA.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[2L]], ...) :
--Gene Set terms already exsit in gene set collection GO_BP of GSEA.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[3L]], ...) :
--Gene Set terms already exsit in gene set collection GO_CC of GSEA.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[4L]], ...) :
--Gene Set terms already exsit in gene set collection PW_KEGG of GSEA.results, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[1L]], ...) :
--Gene Set terms already exsit in gene set collection GO_MF of Sig.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[2L]], ...) :
--Gene Set terms already exsit in gene set collection GO_BP of Sig.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[3L]], ...) :
--Gene Set terms already exsit in gene set collection GO_CC of Sig.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[4L]], ...) :
--Gene Set terms already exsit in gene set collection PW_KEGG of Sig.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[1L]], ...) :
--Gene Set terms already exsit in gene set collection GO_MF of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[2L]], ...) :
--Gene Set terms already exsit in gene set collection GO_BP of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[3L]], ...) :
--Gene Set terms already exsit in gene set collection GO_CC of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!
Warning in FUN(c("GO_MF", "GO_BP", "GO_CC", "PW_KEGG")[[4L]], ...) :
--Gene Set terms already exsit in gene set collection PW_KEGG of Sig.adj.pvals.in.both, and will be overwritten by new gene set terms!
Loading required package: RBGL
Attaching package: 'RBGL'
The following object(s) are masked from 'package:igraph':
transitivity
Warning in bumOptim(x = x, starts) :
One or both parameters are on the limit of the defined parameter space
Warning in subgraph(network, v = nodeList) :
At structural_properties.c:1809 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Error: processing vignette 'HTSanalyzeR-Vignette.Rnw' failed with diagnostics:
chunk 36 (label = fitBUMplot)
Error in get.all.shortest.paths(mst, from = mst.cluster.id[j], to = mst.cluster.id[(j + :
At structural_properties.c:5484 : Weight vector must be non-negative, Invalid value
Execution halted