############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ngsReports ### ############################################################################## ############################################################################## * checking for file ‘ngsReports/DESCRIPTION’ ... OK * preparing ‘ngsReports’: * 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. 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) No file Rd2.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)) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4] Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo d- Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m od- Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267 []\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le vels. [5] [6] [7] [8] [9] [10] [11] Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m /n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_tile_sequence_quality\T1/ptm/m/n/10 , Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/ ptm/m/n/10 , Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt m/m/n/10 , Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter _Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 . [12] [13] [14] [15] [16] [17] [18] [19] [20] Underfull \vbox (badness 10000) has occurred while \output is active [21] [22] [23] [24] [25] [26] Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560 []\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10 , this de-faults to a heatmap us-ing the mean Per_base_sequence_quality [27] [28] [29] [30] Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777 []\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas tQC mod-ule (eg. c("Per_base_sequence_quality", [31] [32] [33] [34] [35] Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076 []\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \ T1/zi4/m/n/10 grDevices::colorRampPalette() [36] [37] [38] Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tors of length 4. Passed to scale_*_continuous() [39] [40] [41] [42] Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538 \T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType [43] [44] Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630 []\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/ n/10 plotType = "heatmap" plotType = "line" Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] No file Rd2.ind. [56] (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.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){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts /enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola ta/i4-t1-0.enc} Output written on Rd2.pdf (56 pages, 175774 bytes). Transcript written on Rd2.log. 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. 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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.toc [3]) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5] Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo d- Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m od- Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267 []\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le vels. [6] [7] [8] [9] [10] [11] [12] Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m /n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_tile_sequence_quality\T1/ptm/m/n/10 , Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/ ptm/m/n/10 , Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt m/m/n/10 , Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter _Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 . [13] [14] [15] [16] [17] [18] [19] [20] [21] Underfull \vbox (badness 10000) has occurred while \output is active [22] [23] [24] [25] [26] [27] Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560 []\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10 , this de-faults to a heatmap us-ing the mean Per_base_sequence_quality [28] [29] [30] [31] Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777 []\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas tQC mod-ule (eg. c("Per_base_sequence_quality", [32] [33] [34] [35] [36] Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076 []\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \ T1/zi4/m/n/10 grDevices::colorRampPalette() [37] [38] [39] Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tors of length 4. Passed to scale_*_continuous() [40] [41] [42] [43] Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538 \T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType [44] [45] Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630 []\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/ n/10 plotType = "heatmap" plotType = "line" Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] No file Rd2.ind. [57] (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts /enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola ta/i4-t1-0.enc} Output written on Rd2.pdf (57 pages, 179824 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (145 entries accepted, 0 rejected). Sorting entries....done (1210 comparisons). Generating output file Rd2.ind....done (273 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. 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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.toc [3]) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5] Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo d- Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m od- Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267 []\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le vels. [6] [7] [8] [9] [10] [11] [12] Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m /n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_tile_sequence_quality\T1/ptm/m/n/10 , Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/ ptm/m/n/10 , Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt m/m/n/10 , Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter _Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 . [13] [14] [15] [16] [17] [18] [19] [20] [21] Underfull \vbox (badness 10000) has occurred while \output is active [22] [23] [24] [25] [26] [27] Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560 []\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10 , this de-faults to a heatmap us-ing the mean Per_base_sequence_quality [28] [29] [30] [31] Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777 []\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas tQC mod-ule (eg. c("Per_base_sequence_quality", [32] [33] [34] [35] [36] Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076 []\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \ T1/zi4/m/n/10 grDevices::colorRampPalette() [37] [38] [39] Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tors of length 4. Passed to scale_*_continuous() [40] [41] [42] [43] Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538 \T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType [44] [45] Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630 []\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/ n/10 plotType = "heatmap" plotType = "line" Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.ind [57] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 6. Overfull \hbox (55.01662pt too wide) in paragraph at lines 6--8 \T1/ptm/m/it/10 (\T1/zi4/m/n/10 [,FastqcDataList,numeric,missing-method\T1/ptm/ m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.8567pt too wide) in paragraph at lines 8--10 []\T1/zi4/m/it/10 [,FastqcDataList,character,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 8--10 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.8567pt too wide) in paragraph at lines 10--12 []\T1/zi4/m/it/10 [,FastqcDataList,logical,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 10--12 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (8.3567pt too wide) in paragraph at lines 12--14 []\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 77--79 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 80--82 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 82--84 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 84--86 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , [58] Overfull \hbox (10.8567pt too wide) in paragraph at lines 126--128 []\T1/zi4/m/it/10 plotAdapterContent,FastqcDataList-method [59] Overfull \hbox (10.8567pt too wide) in paragraph at lines 214--216 []\T1/zi4/m/it/10 plotSeqLengthDistn,FastqcDataList-method [60]) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts /enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola ta/i4-t1-0.enc} Output written on Rd2.pdf (60 pages, 197222 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (145 entries accepted, 0 rejected). Sorting entries....done (1210 comparisons). Generating output file Rd2.ind....done (273 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. 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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.toc [3]) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5] Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo d- Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m od- Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267 []\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le vels. [6] [7] [8] [9] [10] [11] [12] Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m /n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_tile_sequence_quality\T1/ptm/m/n/10 , Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/ ptm/m/n/10 , Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt m/m/n/10 , Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter _Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 . [13] [14] [15] [16] [17] [18] [19] [20] [21] Underfull \vbox (badness 10000) has occurred while \output is active [22] [23] [24] [25] [26] [27] Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560 []\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10 , this de-faults to a heatmap us-ing the mean Per_base_sequence_quality [28] [29] [30] [31] Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777 []\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas tQC mod-ule (eg. c("Per_base_sequence_quality", [32] [33] [34] [35] [36] Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076 []\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \ T1/zi4/m/n/10 grDevices::colorRampPalette() [37] [38] [39] Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tors of length 4. Passed to scale_*_continuous() [40] [41] [42] [43] Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538 \T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType [44] [45] Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630 []\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/ n/10 plotType = "heatmap" plotType = "line" Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.ind [57] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 6. Overfull \hbox (55.01662pt too wide) in paragraph at lines 6--8 \T1/ptm/m/it/10 (\T1/zi4/m/n/10 [,FastqcDataList,numeric,missing-method\T1/ptm/ m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.8567pt too wide) in paragraph at lines 8--10 []\T1/zi4/m/it/10 [,FastqcDataList,character,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 8--10 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.8567pt too wide) in paragraph at lines 10--12 []\T1/zi4/m/it/10 [,FastqcDataList,logical,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 10--12 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (8.3567pt too wide) in paragraph at lines 12--14 []\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 77--79 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 80--82 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 82--84 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 84--86 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , [58] Overfull \hbox (10.8567pt too wide) in paragraph at lines 126--128 []\T1/zi4/m/it/10 plotAdapterContent,FastqcDataList-method [59] Overfull \hbox (10.8567pt too wide) in paragraph at lines 214--216 []\T1/zi4/m/it/10 plotSeqLengthDistn,FastqcDataList-method [60]) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts /enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola ta/i4-t1-0.enc} Output written on Rd2.pdf (60 pages, 198086 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (145 entries accepted, 0 rejected). Sorting entries....done (1210 comparisons). Generating output file Rd2.ind....done (273 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. 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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.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/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.toc [3]) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [4] [5] Overfull \hbox (2.23863pt too wide) in paragraph at lines 240--242 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Per_sequence_quality_scores mo d- Overfull \hbox (6.28877pt too wide) in paragraph at lines 255--257 []\T1/ptm/m/n/10 The un-der-ly-ing data from the Se-quence_Duplication_Levels m od- Overfull \hbox (24.47815pt too wide) in paragraph at lines 265--267 []\T1/ptm/m/n/10 Estimate taken from the plot data for Se-quence_Duplication_Le vels. [6] [7] [8] [9] [10] [11] [12] Overfull \hbox (63.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Summary\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Basic_Statistics\T1/ptm/m /n/10 , \T1/zi4/m/n/10 Per_base_sequence_quality\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_tile_sequence_quality\T1/ptm/m/n/10 , Overfull \hbox (68.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_sequence_quality_scores\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_b ase_sequence_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Per_sequence_GC_content\T1/ ptm/m/n/10 , Overfull \hbox (58.59091pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Per_base_N_content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Lengt h_Distribution\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Sequence_Duplication_Levels\T1/pt m/m/n/10 , Overfull \hbox (103.11093pt too wide) in paragraph at lines 680--691 \T1/zi4/m/n/10 Overrepresented_sequences\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Adapter _Content\T1/ptm/m/n/10 , \T1/zi4/m/n/10 Kmer_Content\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 Total_Deduplicated_Percentage\T1/ptm/m/n/10 . [13] [14] [15] [16] [17] [18] [19] [20] [21] Underfull \vbox (badness 10000) has occurred while \output is active [22] [23] [24] [25] [26] [27] Overfull \hbox (23.0476pt too wide) in paragraph at lines 1555--1560 []\T1/ptm/m/n/10 When act-ing on a \T1/zi4/m/n/10 FastqcDataList\T1/ptm/m/n/10 , this de-faults to a heatmap us-ing the mean Per_base_sequence_quality [28] [29] [30] [31] Overfull \hbox (55.89735pt too wide) in paragraph at lines 1774--1777 []\T1/zi4/m/n/10 character \T1/ptm/m/n/10 vec-tor con-tain-ing the de-sired Fas tQC mod-ule (eg. c("Per_base_sequence_quality", [32] [33] [34] [35] [36] Overfull \hbox (43.32875pt too wide) in paragraph at lines 2074--2076 []\T1/ptm/m/n/10 The colour palette. If the vec-tor sup-plied is less than n, \ T1/zi4/m/n/10 grDevices::colorRampPalette() [37] [38] [39] Overfull \hbox (37.21838pt too wide) in paragraph at lines 2295--2297 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tors of length 4. Passed to scale_*_continuous() [40] [41] [42] [43] Overfull \hbox (0.38704pt too wide) in paragraph at lines 2534--2538 \T1/ptm/m/n/10 plot-ting from mul-ti-ple re-ports. The in-di-vid-ual line plots are able to be gen-er-ated by set-ting \T1/zi4/m/n/10 plotType [44] [45] Overfull \hbox (6.82005pt too wide) in paragraph at lines 2627--2630 []\T1/zi4/m/n/10 character\T1/ptm/m/n/10 . Can only take the val-ues \T1/zi4/m/ n/10 plotType = "heatmap" plotType = "line" Overfull \hbox (27.78935pt too wide) in paragraph at lines 2631--2633 []\T1/ptm/m/n/10 Output from \T1/zi4/m/n/10 expansion() \T1/ptm/m/n/10 or nu-me ric vec-tor of length 4. Passed to \T1/zi4/m/n/10 scale_x_discrete [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.ind [57] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 6. Overfull \hbox (55.01662pt too wide) in paragraph at lines 6--8 \T1/ptm/m/it/10 (\T1/zi4/m/n/10 [,FastqcDataList,numeric,missing-method\T1/ptm/ m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.8567pt too wide) in paragraph at lines 8--10 []\T1/zi4/m/it/10 [,FastqcDataList,character,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 8--10 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.8567pt too wide) in paragraph at lines 10--12 []\T1/zi4/m/it/10 [,FastqcDataList,logical,missing-method Overfull \hbox (55.01662pt too wide) in paragraph at lines 10--12 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm /m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (8.3567pt too wide) in paragraph at lines 12--14 []\T1/zi4/m/it/10 [,FastqcDataList,numeric,missing-method\T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 77--79 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 80--82 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 82--84 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , Overfull \hbox (5.01662pt too wide) in paragraph at lines 84--86 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 getSummary,.FastqcFile-method\T1/ptm/m/it/10 ) \T1/ptm/m/n/10 , [58] Overfull \hbox (10.8567pt too wide) in paragraph at lines 126--128 []\T1/zi4/m/it/10 plotAdapterContent,FastqcDataList-method [59] Overfull \hbox (10.8567pt too wide) in paragraph at lines 214--216 []\T1/zi4/m/it/10 plotSeqLengthDistn,FastqcDataList-method [60]) (/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/.Rd2pdf1546237/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts /enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola ta/i4-t1-0.enc} Output written on Rd2.pdf (60 pages, 198238 bytes). Transcript written on Rd2.log. Saving output to ‘/tmp/RtmpFrGBIm/Rbuild1797fdc38aad1/ngsReports/build/ngsReports.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 ‘ngsReports_1.10.0.tar.gz’