rMAT 3.33.1
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rMAT |
| Branch: master |
| Last Commit: 5854505 |
| Last Changed Date: 2019-01-04 09:45:04 -0400 (Fri, 04 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT
###
##############################################################################
##############################################################################
* checking for file ‘rMAT/DESCRIPTION’ ... OK
* preparing ‘rMAT’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
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")'.
Loading required package: affxparser
Warning: Package 'rMAT' is deprecated and will be removed from Bioconductor
version 3.10
Reading Sequence Information from /private/tmp/Rtmp1WXe9Q/Rinst1d1b2c2abff/rMAT/extdata/Sc03b_MR_v04_10000.bpmap
Reading Sequence Information from /private/tmp/Rtmp1WXe9Q/Rinst1d1b2c2abff/rMAT/extdata/Sc03b_MR_v04_10000.bpmap
Warning: RangedData objects are deprecated. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
Error: processing vignette 'rMAT.Rnw' failed with diagnostics:
chunk 8 (label = COMPUTING rMAT SCORES)
Error : RangedData objects are deprecated and the "lapply" method for
RangedData objects is now defunct. Please migrate your code to use
GRanges or GRangesList objects instead. See IMPORTANT NOTE in
?RangedData
Execution halted