############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidySummarizedExperiment ### ############################################################################## ############################################################################## * checking for file ‘tidySummarizedExperiment/DESCRIPTION’ ... OK * preparing ‘tidySummarizedExperiment’: * checking DESCRIPTION meta-information ... OK * installing the package to process help pages * building the PDF package manual Hmm ... looks like a package Converting Rd files to LaTeX . Creating pdf output from LaTeX ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) [2] Overfull \hbox (36.74829pt too wide) in paragraph at lines 102--105 []\T1/ptm/m/n/10 This is an ef-fi-cient im-ple-men-ta-tion of the com-mon pat-t ern of \T1/zi4/m/n/10 do.call(rbind,dfs) \T1/ptm/m/n/10 or \T1/zi4/m/n/10 do.ca ll(cbind,dfs) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [3] [4] Overfull \hbox (93.17853pt too wide) in paragraph at lines 262--267 []\T1/ptm/m/n/10 Width of text out-put to gen-er-ate. This de-faults to \T1/zi4 /m/n/10 NULL\T1/ptm/m/n/10 , which means use \T1/zi4/m/n/10 getOption("tibble.w idth") [5] [6] Overfull \hbox (23.15576pt too wide) in paragraph at lines 399--400 []\T1/ptm/m/n/10 A Sum-ma-rized-Ex-per-i-ment dataset con-tain-ing the tran-scr ip-tome in-for-ma-tion for Drosophila Melanogaster. [7] Overfull \hbox (49.34036pt too wide) in paragraph at lines 461--466 \T1/ptm/m/n/10 ments (e.g. \T1/zi4/m/n/10 plot_ly(x=1:10,y=1:10,color=I("red"), marker=list(color="blue"))\T1/ptm/m/n/10 ). [8] Overfull \hbox (25.8094pt too wide) in paragraph at lines 475--483 \T1/ptm/m/n/10 trolled us-ing \T1/zi4/m/n/10 colors \T1/ptm/m/n/10 and \T1/zi4/ m/n/10 alpha\T1/ptm/m/n/10 , or avoided al-to-gether via [][]\T1/zi4/m/n/10 I() [][][] \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 color=I("red")\T1/ptm/m/n/10 ). Overfull \hbox (5.47838pt too wide) in paragraph at lines 492--496 \T1/ptm/m/n/10 (e.g., [][]marker.line.color[][] and [][]line.color[][] for fill ed poly-gons). 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[11] [12] Overfull \hbox (23.13869pt too wide) in paragraph at lines 750--753 []\T1/ptm/m/n/10 Can be a char-ac-ter vec-tor, cre-at-ing mul-ti-ple columns, i f \T1/zi4/m/n/10 names_sep \T1/ptm/m/n/10 or \T1/zi4/m/n/10 names_pattern [13] Overfull \hbox (18.55855pt too wide) in paragraph at lines 776--781 []\T1/ptm/m/n/10 What hap-pens if the out-put has in-valid col-umn names? The d e-fault, \T1/zi4/m/n/10 "check_unique" Overfull \hbox (36.14949pt too wide) in paragraph at lines 793--797 \T1/ptm/m/n/10 the type of spe-cific columns. For ex-am-ple, \T1/zi4/m/n/10 nam es_transform=list(week=as.integer) [14] [15] [16] No file Rd2.ind. [17] (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.pivot.Rul.wider.Rul.spec} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spread} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gather} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rlang::ensym\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.quasiquotation} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.vctrs::vec.Rul.as.Rul.names\(\)} has been refer enced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.tidyr.Rul.tidy.Rul.select} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.type.convert} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plotly.Rul.json} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::bscols\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.subplot} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.highlight} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.style} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.layout} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplotly} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.mapbox} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.geo} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formula} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.add.Rul.trace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.event.Rul.data} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.pch} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.grDevices::col2rgb\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.I} has been referenced but does not exist, repl aced by a fixed one pdfTeX warning (dest): name{Rfn.schema} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::SharedData} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplot2::qplot\(\)} has been referenced but doe s not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.animation} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.fortify} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dplyr.Rul.data.Rul.masking} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mutate.Rdash.joins} has been referenced but doe s not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc} {/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (17 pages, 114117 bytes). Transcript written on Rd2.log. 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Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 378. ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) Writing index file Rd2.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.out) (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/ texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.toc) [2] Overfull \hbox (36.74829pt too wide) in paragraph at lines 102--105 []\T1/ptm/m/n/10 This is an ef-fi-cient im-ple-men-ta-tion of the com-mon pat-t ern of \T1/zi4/m/n/10 do.call(rbind,dfs) \T1/ptm/m/n/10 or \T1/zi4/m/n/10 do.ca ll(cbind,dfs) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [3] [4] Overfull \hbox (93.17853pt too wide) in paragraph at lines 262--267 []\T1/ptm/m/n/10 Width of text out-put to gen-er-ate. This de-faults to \T1/zi4 /m/n/10 NULL\T1/ptm/m/n/10 , which means use \T1/zi4/m/n/10 getOption("tibble.w idth") [5] [6] Overfull \hbox (23.15576pt too wide) in paragraph at lines 399--400 []\T1/ptm/m/n/10 A Sum-ma-rized-Ex-per-i-ment dataset con-tain-ing the tran-scr ip-tome in-for-ma-tion for Drosophila Melanogaster. [7] Overfull \hbox (49.34036pt too wide) in paragraph at lines 461--466 \T1/ptm/m/n/10 ments (e.g. \T1/zi4/m/n/10 plot_ly(x=1:10,y=1:10,color=I("red"), marker=list(color="blue"))\T1/ptm/m/n/10 ). [8] Overfull \hbox (25.8094pt too wide) in paragraph at lines 475--483 \T1/ptm/m/n/10 trolled us-ing \T1/zi4/m/n/10 colors \T1/ptm/m/n/10 and \T1/zi4/ m/n/10 alpha\T1/ptm/m/n/10 , or avoided al-to-gether via [][]\T1/zi4/m/n/10 I() [][][] \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 color=I("red")\T1/ptm/m/n/10 ). Overfull \hbox (5.47838pt too wide) in paragraph at lines 492--496 \T1/ptm/m/n/10 (e.g., [][]marker.line.color[][] and [][]line.color[][] for fill ed poly-gons). 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[11] [12] Overfull \hbox (23.13869pt too wide) in paragraph at lines 750--753 []\T1/ptm/m/n/10 Can be a char-ac-ter vec-tor, cre-at-ing mul-ti-ple columns, i f \T1/zi4/m/n/10 names_sep \T1/ptm/m/n/10 or \T1/zi4/m/n/10 names_pattern [13] Overfull \hbox (18.55855pt too wide) in paragraph at lines 776--781 []\T1/ptm/m/n/10 What hap-pens if the out-put has in-valid col-umn names? The d e-fault, \T1/zi4/m/n/10 "check_unique" Overfull \hbox (36.14949pt too wide) in paragraph at lines 793--797 \T1/ptm/m/n/10 the type of spe-cific columns. For ex-am-ple, \T1/zi4/m/n/10 nam es_transform=list(week=as.integer) [14] [15] [16] No file Rd2.ind. 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Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (62 entries accepted, 6 rejected). Sorting entries....done (440 comparisons). Generating output file Rd2.ind....done (118 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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This de-faults to \T1/zi4 /m/n/10 NULL\T1/ptm/m/n/10 , which means use \T1/zi4/m/n/10 getOption("tibble.w idth") [5] [6] Overfull \hbox (23.15576pt too wide) in paragraph at lines 399--400 []\T1/ptm/m/n/10 A Sum-ma-rized-Ex-per-i-ment dataset con-tain-ing the tran-scr ip-tome in-for-ma-tion for Drosophila Melanogaster. [7] Overfull \hbox (49.34036pt too wide) in paragraph at lines 461--466 \T1/ptm/m/n/10 ments (e.g. \T1/zi4/m/n/10 plot_ly(x=1:10,y=1:10,color=I("red"), marker=list(color="blue"))\T1/ptm/m/n/10 ). [8] Overfull \hbox (25.8094pt too wide) in paragraph at lines 475--483 \T1/ptm/m/n/10 trolled us-ing \T1/zi4/m/n/10 colors \T1/ptm/m/n/10 and \T1/zi4/ m/n/10 alpha\T1/ptm/m/n/10 , or avoided al-to-gether via [][]\T1/zi4/m/n/10 I() [][][] \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 color=I("red")\T1/ptm/m/n/10 ). Overfull \hbox (5.47838pt too wide) in paragraph at lines 492--496 \T1/ptm/m/n/10 (e.g., [][]marker.line.color[][] and [][]line.color[][] for fill ed poly-gons). 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.pivot.Rul.wider.Rul.spec} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spread} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gather} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rlang::ensym\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.quasiquotation} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.vctrs::vec.Rul.as.Rul.names\(\)} has been refer enced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.tidyr.Rul.tidy.Rul.select} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.type.convert} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plotly.Rul.json} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::bscols\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.subplot} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.highlight} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.style} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.layout} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplotly} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.mapbox} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.geo} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formula} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.add.Rul.trace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.event.Rul.data} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.pch} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.grDevices::col2rgb\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.I} has been referenced but does not exist, repl aced by a fixed one pdfTeX warning (dest): name{Rfn.schema} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::SharedData} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplot2::qplot\(\)} has been referenced but doe s not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.animation} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.fortify} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dplyr.Rul.data.Rul.masking} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mutate.Rdash.joins} has been referenced but doe s not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc} {/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (18 pages, 127259 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (62 entries accepted, 6 rejected). Sorting entries....done (440 comparisons). Generating output file Rd2.ind....done (118 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. 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This de-faults to \T1/zi4 /m/n/10 NULL\T1/ptm/m/n/10 , which means use \T1/zi4/m/n/10 getOption("tibble.w idth") [5] [6] Overfull \hbox (23.15576pt too wide) in paragraph at lines 399--400 []\T1/ptm/m/n/10 A Sum-ma-rized-Ex-per-i-ment dataset con-tain-ing the tran-scr ip-tome in-for-ma-tion for Drosophila Melanogaster. [7] [8] Overfull \hbox (49.34036pt too wide) in paragraph at lines 461--466 \T1/ptm/m/n/10 ments (e.g. \T1/zi4/m/n/10 plot_ly(x=1:10,y=1:10,color=I("red"), marker=list(color="blue"))\T1/ptm/m/n/10 ). Overfull \hbox (25.8094pt too wide) in paragraph at lines 475--483 \T1/ptm/m/n/10 trolled us-ing \T1/zi4/m/n/10 colors \T1/ptm/m/n/10 and \T1/zi4/ m/n/10 alpha\T1/ptm/m/n/10 , or avoided al-to-gether via [][]\T1/zi4/m/n/10 I() [][][] \T1/ptm/m/n/10 (e.g., \T1/zi4/m/n/10 color=I("red")\T1/ptm/m/n/10 ). Overfull \hbox (5.47838pt too wide) in paragraph at lines 492--496 \T1/ptm/m/n/10 (e.g., [][]marker.line.color[][] and [][]line.color[][] for fill ed poly-gons). 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[18]) (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.pivot.Rul.wider.Rul.spec} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spread} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gather} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rlang::ensym\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.quasiquotation} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.vctrs::vec.Rul.as.Rul.names\(\)} has been refer enced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.tidyr.Rul.tidy.Rul.select} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.type.convert} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plotly.Rul.json} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::bscols\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.subplot} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.highlight} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.style} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.layout} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplotly} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.mapbox} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot.Rul.geo} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formula} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.add.Rul.trace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.event.Rul.data} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.pch} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.grDevices::col2rgb\(\)} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.I} has been referenced but does not exist, repl aced by a fixed one pdfTeX warning (dest): name{Rfn.schema} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.crosstalk::SharedData} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ggplot2::qplot\(\)} has been referenced but doe s not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.animation} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.fortify} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dplyr.Rul.data.Rul.masking} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mutate.Rdash.joins} has been referenced but doe s not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc} {/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (18 pages, 128034 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (62 entries accepted, 6 rejected). Sorting entries....done (439 comparisons). Generating output file Rd2.ind....done (119 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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[11] [12] Overfull \hbox (23.13869pt too wide) in paragraph at lines 750--753 []\T1/ptm/m/n/10 Can be a char-ac-ter vec-tor, cre-at-ing mul-ti-ple columns, i f \T1/zi4/m/n/10 names_sep \T1/ptm/m/n/10 or \T1/zi4/m/n/10 names_pattern [13] Overfull \hbox (18.55855pt too wide) in paragraph at lines 776--781 []\T1/ptm/m/n/10 What hap-pens if the out-put has in-valid col-umn names? The d e-fault, \T1/zi4/m/n/10 "check_unique" Overfull \hbox (36.14949pt too wide) in paragraph at lines 793--797 \T1/ptm/m/n/10 the type of spe-cific columns. For ex-am-ple, \T1/zi4/m/n/10 nam es_transform=list(week=as.integer) [14] [15] [16] (/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/.Rd2pdf1900721/R d2.ind [17] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 26. 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Transcript written on Rd2.log. Saving output to ‘/tmp/RtmpBIa33M/Rbuild1d00b1630b4b0b/tidySummarizedExperiment/build/tidySummarizedExperiment.pdf’ ... Done * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘tidySummarizedExperiment_1.4.1.tar.gz’