htSeqTools 1.31.1
Oscar Reina
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/htSeqTools |
| Branch: master |
| Last Commit: a8920e5 |
| Last Changed Date: 2019-01-04 09:43:17 -0400 (Fri, 04 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 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 | |
| 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 htSeqTools
###
##############################################################################
##############################################################################
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* preparing ‘htSeqTools’:
* checking DESCRIPTION meta-information ... OK
* 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: 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: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: MASS
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: rtracklayer
Warning: Package 'htSeqTools' is deprecated and will be removed from
Bioconductor version 3.10
Warning in showList(object, showFunction, print.classinfo = TRUE) :
Note that starting with BioC 3.7, the class attribute of all
GRangesList **instances** needs to be set to
"CompressedGRangesList". Please update this object with
'updateObject(object, verbose=TRUE)' and re-serialize it.
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Warning: RangedData objects are deprecated. Please migrate your code to
use GRanges or GRangesList objects instead. See IMPORTANT NOTE
in ?RangedData
Error: processing vignette 'htSeqTools.Rnw' failed with diagnostics:
chunk 6 (label = qcontrol1)
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