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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data ITALICS
###
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* checking for file ‘ITALICS/DESCRIPTION’ ... OK
* preparing ‘ITALICS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ITALICS.Rnw’ using Sweave
Loading required package: ITALICS
Loading required package: GLAD

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Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

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New options are available in daglad: see help for details.

Loading required package: ITALICSData
Loading required package: oligo
Loading required package: BiocGenerics

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, 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.max, which.min

Loading required package: oligoClasses
Welcome to oligoClasses version 1.63.0
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    strsplit

================================================================================
Welcome to oligo version 1.65.0
================================================================================
Loading required package: affxparser
Loading required package: pd.mapping50k.xba240
Loading required package: RSQLite
Loading required package: DBI
Welcome to ITALICS 
#################################################################################################
# This implementation of the ITALICS algorithm was developped for bioconductor 
# This implementation is sligthly different 
 than the original one which is available at : 
# http://xfer.curie.fr/get/Zsx2xwOnH2l/ITALICSData_0.0.2.tar.gz 
 and# http://xfer.curie.fr/get/diXljlXCEev/ITALICS_0.1.0.tar.gz 
#################################################################################################
# The two main functions of the package are ITALICS and trainITALICS
 # ITALICS : See the help of the ITALICS function (?ITALICS) or read the vignette vignette to see how to normalize 
# using ITALICS.
# 
# trainITALICS : See the help of the trainITALICS function (?trainITALICS)
#################################################################################################

In function OutliersGNL: Inconsistency for smoothing values vs. GNL status has been corrected)
Error: processing vignette 'ITALICS.Rnw' failed with diagnostics:
unable to run pdflatex on 'ITALICS.tex'
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ITALICS.Rnw’

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

Error: Vignette re-building failed.
Execution halted