ind1KG 0.10.0
VJ Carey
| Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/ind1KG | | Last Changed Rev: 3760 / Revision: 3935 | | Last Changed Date: 2016-05-03 14:35:06 -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 | [ ERROR ] | skipped | skipped | |
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### Running command:
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### chmod a+r ind1KG -R && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ind1KG
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* checking for file 'ind1KG/DESCRIPTION' ... OK
* preparing 'ind1KG':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"E:/biocbld/bbs-3.3-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: chopsticks
Loading required package: survival
Warning: Package 'ind1KG' is deprecated and will be removed from Bioconductor
version 3.3
Loading required package: Biostrings
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: 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: XVector
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.
Warning: The 'vals' argument has been renamed 'filter'. Please use the 'filter'
argument instead.
Warning in read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
Loading required package: BSgenome
Loading required package: rtracklayer
Please note that the SNPlocs.Hsapiens.dbSNP.20090506 package contains
outdated dbSNP data and will be deprecated in the near future. We
highly recommend that you use a SNPlocs package based on a more recent
dbSNP build for your analyses instead. See available.SNPs() for the
list of SNPlocs packages currently available and make sure to pick up
the most recent one.
Loading required package: lumi
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'nov09rv.Rnw' failed with diagnostics:
chunk 8 (label = lklu)
Error in eval(expr, envir, enclos) :
could not find function "dbListTables"
Execution halted