DASiR 1.12.0
Ricard Illa
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DASiR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -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 | |
| oaxaca | 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 DASiR -R && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data DASiR
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* checking for file 'DASiR/DESCRIPTION' ... OK
* preparing 'DASiR':
* 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: 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: GenomicRanges
Loading required package: GenomeInfoDb
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
version 3.3
DAS server for this session is: http://genome.ucsc.edu/cgi-bin/das
Querying url: http://genome.ucsc.edu/cgi-bin/das/dsn
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/entry_points
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/types
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/features
DAS server for this session is: http://vega.sanger.ac.uk/das
Quering url: http://vega.sanger.ac.uk/das/Homo_sapiens.VEGA51.reference/sequence
Error: could not find function "xmlStructuredStop"...
Quering url: http://vega.sanger.ac.uk/das/Homo_sapiens.VEGA51.reference/sequence
Error: could not find function "xmlStructuredStop"...
DAS server for this session is: http://das.cathdb.info/das
Quering url: http://das.cathdb.info/das/cath_pdb/structure?query=1hck
Warning in download.file(url, destfile = tf, quiet = TRUE) :
cannot open URL 'http://das.cathdb.info/das/cath_pdb/structure?query=1hck': HTTP status was '404 Not Found'
Error: processing vignette 'DASiR.Rnw' failed with diagnostics:
chunk 9 (label = getDasStructure)
Error in download.file(url, destfile = tf, quiet = TRUE) :
cannot open URL 'http://das.cathdb.info/das/cath_pdb/structure?query=1hck'
Execution halted