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BioC 3.2: BUILD report for triplex on perceval

This page was generated on 2015-11-10 14:48:07 -0800 (Tue, 10 Nov 2015).

Package 1068/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
triplex 1.10.0
Jiri Hon
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/triplex
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded [ ERROR ] skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: triplex
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data triplex
StartedAt: 2015-11-09 19:54:25 -0800 (Mon, 09 Nov 2015)
EndedAt: 2015-11-09 19:54:55 -0800 (Mon, 09 Nov 2015)
EllapsedTime: 30.4 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data triplex
###
##############################################################################
##############################################################################


* checking for file ‘triplex/DESCRIPTION’ ... OK
* preparing ‘triplex’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: S4Vectors
Loading required package: stats4
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’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

Loading required package: IRanges
Loading required package: XVector
Loading required package: Biostrings
NOTICE: There was no triplexes found with the given options.
TIP: Try to modify search options (p_value, min_score, etc.),
     for details see ?triplex.search.
Warning in triplex.search(seq, iso_pen = 2) :
  Default penalization options were changed. You should consider recalculation
			of P-value constants (mu, lambda, rn). For details see vignette.
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: biomaRt
Loading required package: grid

Error: processing vignette 'triplex.Rnw' failed with diagnostics:
 chunk 30 
Error : 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

Execution halted