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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data REMP
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* checking for file ‘REMP/DESCRIPTION’ ... OK
* preparing ‘REMP’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘REMP.Rnw’ using Sweave
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins,
    colOrderStats, colProds, colQuantiles, colRanges, colRanks,
    colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
    colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds, colWeightedVars,
    rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
    rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums,
    rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs,
    rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
    rowVars, rowWeightedMads, rowWeightedMeans,
    rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element,
    setdiff, setequal, union


Attaching package: ‘BiocGenerics’

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, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames,
    sapply, saveRDS, table, tapply, unique, unsplit, which.max,
    which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: minfi
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.10 	 2024-06-24
Warning: program compiled against libxml 212 using older 211
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

********************************************************************************
REMP version 1.31.0 (Devel)
To access full functionality of REMP, please make sure this version is current.

Citation:
  Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L.
  Prediction of genome-wide DNA methylation in repetitive elements.
  Nucleic Acids Research. 2017;45(15):8697-711.
  PubMed PMID: 28911103; PMCID: PMC5587781. http://dx.doi.org/10.1093/nar/gkx587
********************************************************************************
Start Alu annotation data initialization (hg19)...
Gene annotation database: AH
Illumina platform: 450k
Done.  (20 sec.)
REMParcel has been saved under the directory:
/home/biocbuild/tmp/Rtmp6sMcRW/REMP.data.450k
Using random seed = 777
Processing Alu with window +/- 1000 base pair ...
Done.  (2 sec.)
Start RE methylation prediction with 1 core(s) ...
Predicting sample GM12878 ...
    GM12878 completed! 0 sample(s) left ...  (4 sec.)
Done.
You have successfully set non-parallel mode (single worker).
58 Alu that have less than 2 CpGs predicted are not aggretated.
You have successfully set non-parallel mode (single worker).
Decoding Alu (aggregated by mean: min # of CpGs: 2) annotation to symbol ...
You have successfully set non-parallel mode (single worker).
414 Alu that have less than 2 CpGs predicted are not aggretated.
Error: processing vignette 'REMP.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'REMP.tex' failed.
Messages:
/usr/bin/texi2dvi: biber failed
--- failed re-building ‘REMP.Rnw’

SUMMARY: processing the following file failed:
  ‘REMP.Rnw’

Error: Vignette re-building failed.
Execution halted