HTSanalyzeR 2.21.0 Xin Wang
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSanalyzeR | Last Changed Rev: 102594 / Revision: 107602 | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | skipped | skipped | |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | ERROR | skipped | skipped | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### chmod a+r HTSanalyzeR -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HTSanalyzeR
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* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* preparing 'HTSanalyzeR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.2-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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:igraph':
normalize, union
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, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
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: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:igraph':
compare
Attaching package: 'IRanges'
The following object is masked from 'package:igraph':
simplify
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
The following objects are masked from 'package:igraph':
degree, edges, intersection
Loading required package: RColorBrewer
Loading required package: genefilter
Attaching package: 'genefilter'
The following object is masked from 'package:base':
anyNA
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
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. Users who want more
current data are encouraged to look at the KEGGREST or
reactome.db packages
Warning in FUN(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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(X[[i]], ...) :
--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 objects are masked from 'package:igraph':
bfs, dfs, transitivity
Warning in bumOptim(x = x, starts) :
One or both parameters are on the limit of the defined parameter space
Error: processing vignette 'HTSanalyzeR-Vignette.Rnw' failed with diagnostics:
chunk 36 (label = fitBUMplot)
Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
Execution halted