htSeqTools 1.32.0
Oscar Reina
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/htSeqTools |
| Branch: RELEASE_3_9 |
| Last Commit: 8bb3e67 |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 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 | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data htSeqTools
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* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* preparing ‘htSeqTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘htSeqTools.Rnw’ using Sweave
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: 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
--- failed re-building ‘htSeqTools.Rnw’
SUMMARY: processing the following file failed:
‘htSeqTools.Rnw’
Error: Vignette re-building failed.
Execution halted