ggtut 0.9.0
VJ Carey
| Snapshot Date: 2015-10-24 10:15:05 -0400 (Sat, 24 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ggtut | | Last Changed Rev: 3462 / Revision: 3473 | | Last Changed Date: 2015-10-13 16:20:35 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### chmod a+r ggtut -R && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ggtut
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* checking for file 'ggtut/DESCRIPTION' ... OK
* preparing 'ggtut':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"c:/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: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
No methods found in "IRanges" for requests: aggregate
Attaching package: 'GGtools'
The following object is masked from 'package:stats':
getCall
Loading required package: Biobase
Loading required package: BiocGenerics
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:Matrix':
as.vector
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,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: illuminaHumanv1.db
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:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:Matrix':
expand
Loading required package: org.Hs.eg.db
Loading required package: DBI
To get a tailored smlSet, use getSS("GGdata", [chrvec])
available chromosomes are named 1, 10, ..., X, Y
Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object is masked from 'package:data.table':
setattr
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="c:/biocbld/bbs-3.3-data-experiment/tmpdir/RtmpKGQTno"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==322112061.44 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==16105603072 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:bit':
clone, clone.default, clone.list
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following objects are masked from 'package:ff':
mismatch, pattern
Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: Rsamtools
Loading required package: cheung2010
Loading required package: hgfocus.db
To get a tailored smlSet, use getSS("cheung2010", [chrvec])
available chromosomes are named chr1chr10...chr8chr9
Loading required package: SNPlocs.Hsapiens.dbSNP.20120608
Loading required package: BSgenome
Loading required package: rtracklayer
Please note that the SNPlocs.Hsapiens.dbSNP.20120608 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: hmyriB36
To get a tailored smlSet, use getSS("hmyriB36", [chrvec])
available chromosomes are named 1, 10, ..., X, Y
NOTE: expanding gene ranges by radius 50000 leads to negative start positions that are reset to 1.
opening ff c:/biocbld/bbs-3.3-data-experiment/tmpdir/Rtmp69ZotS/Rinst244cc4e2018/ggtut/ffarchives/twfilt_perm17/17_tssco1_1.ff
opening ff c:/biocbld/bbs-3.3-data-experiment/tmpdir/Rtmp69ZotS/Rinst244cc4e2018/ggtut/ffarchives/twfilt17/17_tssco1_1.ff
opening ff c:/biocbld/bbs-3.3-data-experiment/tmpdir/Rtmp69ZotS/Rinst244cc4e2018/ggtut/ffarchives/twfilt17/17_tsinds1_1.ff
Error: processing vignette 'tut15.Rnw' failed with diagnostics:
chunk 58 (label = lkm)
Error in lapply(killchr(select(Homo.sapiens, keys = m, keytype = "ENTREZID", :
error in evaluating the argument 'X' in selecting a method for function 'lapply': Error in gsub("chr", "", x) :
error in evaluating the argument 'x' in selecting a method for function 'gsub': Error in select(Homo.sapiens, keys = m, keytype = "ENTREZID", columns = "TXCHROM") :
error in evaluating the argument 'x' in selecting a method for function 'select': Error: object 'Homo.sapiens' not found
Calls: killchr -> gsub
Execution halted