############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data twilight ### ############################################################################## ############################################################################## * checking for file ‘twilight/DESCRIPTION’ ... OK * preparing ‘twilight’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘tr_2004_01.Rnw’ using Sweave Loading required package: Biobase 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, 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Error: processing vignette 'tr_2004_01.Rnw' failed with diagnostics: chunk 2 Error in library(vsn) : there is no package called ‘vsn’ --- failed re-building ‘tr_2004_01.Rnw’ pdflatex tr_2004_01 This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./tr_2004_01.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-02-24> (/usr/local/texlive/2022/texmf-dist/tex/latex/base/report.cls Document Class: report 2021/10/04 v1.4n Standard LaTeX document class (/usr/local/texlive/2022/texmf-dist/tex/latex/base/fleqn.clo) (/usr/local/texlive/2022/texmf-dist/tex/latex/base/size11.clo)) (./compdiag.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/ifpdf.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/graphics.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/trig.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/local/texlive/2022/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/local/texlive/2022/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/local/texlive/2022/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/local/texlive/2022/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2022/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/local/texlive/2022/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/local/texlive/2022/texmf-dist/tex/latex/url/url.sty) (/usr/local/texlive/2022/texmf-dist/tex/generic/bitset/bitset.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2022/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty ))) (/usr/local/texlive/2022/texmf-dist/tex/latex/ntgclass/a4.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/geometry/geometry.sty (/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/ifvtex.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/tools/theorem.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/tools/thp.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/tools/thb.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/caption/caption.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/caption/caption3.sty)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Sweave.sty (/usr/local/texlive/2022/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/base/textcomp.sty) (/usr/local/texlive/2022/texmf-dist/tex/latex/base/fontenc.sty)) (/usr/local/texlive/2022/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file tr_2004_01.aux. 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Transcript written on tr_2004_01.log. make: *** [vign] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted