############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM ### ############################################################################## ############################################################################## * checking for file ‘rTRM/DESCRIPTION’ ... OK * preparing ‘rTRM’: * 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 Loading required package: igraph Attaching package: ‘igraph’ The following objects are masked from ‘package:stats’: decompose, spectrum The following object is masked from ‘package:base’: union ... Creating pdf output from LaTeX ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-02-25> (./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/local/texlive/2019/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/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) No file Rd2.aux. (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s ty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 20. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 23. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 26. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 46. ) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/te xlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] Overfull \hbox (116.38962pt too wide) in paragraph at lines 217--217 []\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext ended = FALSE, strict = FALSE, type = "igraph") [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Overfull \hbox (944.66843pt too wide) in paragraph at lines 871--871 []\T1/zi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge. lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE) [15] Overfull \hbox (801.34872pt too wide) in paragraph at lines 915--915 []\T1/zi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F ALSE, normalize.layout = TRUE) [16] [17] Overfull \hbox (44.73999pt too wide) in paragraph at lines 979--979 []\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) [18] No file Rd2.ind. [19] (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/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/local/texlive/2019/te xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/ enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (19 pages, 106801 bytes). Transcript written on Rd2.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-02-25> (./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/local/texlive/2019/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/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.aux) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s ty)) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 20. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 23. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 26. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 46. ) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.toc [1{/usr/ local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/utf8.def) [2] [3] [4] Overfull \hbox (116.38962pt too wide) in paragraph at lines 217--217 []\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext ended = FALSE, strict = FALSE, type = "igraph") [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (944.66843pt too wide) in paragraph at lines 871--871 []\T1/zi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge. lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE) [16] Overfull \hbox (801.34872pt too wide) in paragraph at lines 915--915 []\T1/zi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F ALSE, normalize.layout = TRUE) [17] Overfull \hbox (44.73999pt too wide) in paragraph at lines 979--979 []\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) [18] No file Rd2.ind. [19] [20] (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.aux) ) (see the transcript file for additional information){/usr/local/texlive/2019/te xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/ enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (20 pages, 110629 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (37 entries accepted, 0 rejected). Sorting entries....done (228 comparisons). Generating output file Rd2.ind....done (71 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) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-02-25> (./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/local/texlive/2019/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/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.aux) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s ty)) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 20. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 23. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 26. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 46. ) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.toc [1{/usr/ local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/utf8.def) [2] [3] [4] Overfull \hbox (116.38962pt too wide) in paragraph at lines 217--217 []\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext ended = FALSE, strict = FALSE, type = "igraph") [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (944.66843pt too wide) in paragraph at lines 871--871 []\T1/zi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge. lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE) [16] Overfull \hbox (801.34872pt too wide) in paragraph at lines 915--915 []\T1/zi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F ALSE, normalize.layout = TRUE) [17] Overfull \hbox (44.73999pt too wide) in paragraph at lines 979--979 []\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) [18] (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.ind [19] [20] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 63. [21]) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/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/local/texlive/2019/te xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/ enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (21 pages, 120346 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (37 entries accepted, 0 rejected). Sorting entries....done (228 comparisons). Generating output file Rd2.ind....done (71 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) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 5 L3 programming layer <2020-02-25> (./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty (/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/local/texlive/2019/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/local/texlive/2019/texmf-dist/tex/latex/base/makeidx.sty) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.aux) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s ty)) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.out) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 20. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 23. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 26. LaTeX Warning: Font shape declaration has incorrect series value `mc'. It should not contain an `m'! Please correct it. Found on input line 46. ) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.toc [1{/usr/ local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/utf8.def) Underfull \vbox (badness 7116) has occurred while \output is active [2] [3] [4] Overfull \hbox (116.38962pt too wide) in paragraph at lines 217--217 []\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext ended = FALSE, strict = FALSE, type = "igraph") [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (944.66843pt too wide) in paragraph at lines 871--871 []\T1/zi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge. lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE) [16] Overfull \hbox (801.34872pt too wide) in paragraph at lines 915--915 []\T1/zi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F ALSE, normalize.layout = TRUE) [17] Overfull \hbox (44.73999pt too wide) in paragraph at lines 979--979 []\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE) [18] (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.ind [19] [20] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 63. [21]) (/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/.Rd2pdf57671/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information){/usr/local/texlive/2019/te xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2019/texmf-dist/fonts/ enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (21 pages, 120641 bytes). Transcript written on Rd2.log. Saving output to ‘/private/tmp/RtmpQr7Ilv/Rbuilde147c38f41f/rTRM/build/rTRM.pdf’ ... Done * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘rTRM_1.32.0.tar.gz’