triform 1.29.1
Thomas Carroll
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/triform |
| Branch: master |
| Last Commit: 127bc98 |
| Last Changed Date: 2019-11-18 09:05:04 -0500 (Mon, 18 Nov 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data triform
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* checking for file ‘triform/DESCRIPTION’ ... OK
* preparing ‘triform’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘triform.Rnw’ using Sweave
Loading required package: IRanges
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, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: yaml
Warning: Package 'triform' is deprecated and will be removed from Bioconductor
version 3.12
Using config file /private/tmp/RtmpuqqkYq/Rinst79e1784ea502/triform/extdata/config.yml
Converting BED to RangedData for file /private/tmp/RtmpuqqkYq/Rinst79e1784ea502/triform/extdata/backgr_huds_Gm12878_rep1.bed
Error: processing vignette 'triform.Rnw' failed with diagnostics:
chunk 2 (label = Preprocessing BED files using configuration file)
Error : RangedData objects are defunct. Please migrate your code to use GRanges
or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
--- failed re-building ‘triform.Rnw’
SUMMARY: processing the following file failed:
‘triform.Rnw’
Error: Vignette re-building failed.
Execution halted