############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ldblock ### ############################################################################## ############################################################################## * checking for file ‘ldblock/DESCRIPTION’ ... OK * preparing ‘ldblock’: * 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) (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) 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. ) Underfull \hbox (badness 10000) in paragraph at lines 45--45 []\T1/ptm/m/it/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"# 1\")", Underfull \hbox (badness 1342) in paragraph at lines 45--45 \T1/ptm/m/it/10 "ld-block")data struc-tures for link-age dis-e-qui-lib-rium mea -sures in Overfull \hbox (15.39606pt too wide) in paragraph at lines 50--52 []\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_descriptio n(\"#1\")", "ld-block")Define data struc- [1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (25.26584pt too wide) in paragraph at lines 55--66 []\T1/ptm/m/n/10 The DE-SCRIP-TION file: c("\Sexpr[results=rd,stage=build]tools :::Rd_package_DESCRIPTION(\"#1\")", Overfull \hbox (49.72574pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 rium mea-sures in pop-u-la-tions\cr Ver-sion: \tab 1.24.0\cr Au- thor: \tab VJ Carey \cr Overfull \hbox (140.18497pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 Builder: \tab knitr\cr Rox-y-gen-Note: \tab 7.1.1\cr En-cod-ing: \tab UTF-8\cr git_url: \tab https://git.bioconductor.org/packages/ldblock\cr Overfull \hbox (100.5054pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 2021-10-26\cr Date/Publication: \tab 2022-04-12\cr } c("\Sexpr[r esults=rd,stage=build]tools:::Rd_package_indices(\"#1\")", Overfull \hbox (91.02522pt too wide) in paragraph at lines 69--71 []\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"# 1\")", "ld-block")VJ Carey Overfull \hbox (4.40584pt too wide) in paragraph at lines 72--75 []\T1/ptm/m/n/10 Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_packag e_maintainer(\"#1\")", "ld-block")VJ [2] Overfull \hbox (179.76044pt too wide) in paragraph at lines 98--98 [] \T1/zi4/m/n/10 urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/l d_data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",[] [3] Overfull \hbox (4.78088pt too wide) in paragraph at lines 153--154 [][][]$\T1/zi4/m/n/10 ftp : / / ftp . 1000genomes . ebi . ac . uk / vol1 / ftp / technical / working / 20130606 _ sample _ info / [4] Overfull \hbox (14.65924pt too wide) in paragraph at lines 237--240 []\T1/ptm/m/n/10 name of gzipped text file as dis-tributed at [][]$\T1/zi4/m/n/ 10 hapmap . ncbi . nlm . nih . gov / downloads / [5] [6] Overfull \hbox (47.51794pt too wide) in paragraph at lines 345--346 []\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r on-ment vari-able LDLINK_TOKEN (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [7] [8] Overfull \hbox (4.78088pt too wide) in paragraph at lines 470--471 [][][]$\T1/zi4/m/n/10 ftp : / / ftp . 1000genomes . ebi . ac . uk / vol1 / ftp / technical / working / 20130606 _ sample _ info / [9] No file Rd2.ind. [10] (/private/tmp/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/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)pdfTeX warning (dest): name {Rfn.TabixFile} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep laced by a fixed one pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex ist, replaced by a fixed one {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/local/texlive/2019/texmf-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 (10 pages, 101934 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) Writing index file Rd2.idx (/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def) (/private/tmp/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/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/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/Rd2.out) (/private/tmp/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/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/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/Rd2.toc [1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]) Underfull \hbox (badness 10000) in paragraph at lines 45--45 []\T1/ptm/m/it/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"# 1\")", Underfull \hbox (badness 1342) in paragraph at lines 45--45 \T1/ptm/m/it/10 "ld-block")data struc-tures for link-age dis-e-qui-lib-rium mea -sures in Overfull \hbox (15.39606pt too wide) in paragraph at lines 50--52 []\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_descriptio n(\"#1\")", "ld-block")Define data struc- Overfull \hbox (25.26584pt too wide) in paragraph at lines 55--66 []\T1/ptm/m/n/10 The DE-SCRIP-TION file: c("\Sexpr[results=rd,stage=build]tools :::Rd_package_DESCRIPTION(\"#1\")", Overfull \hbox (49.72574pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 rium mea-sures in pop-u-la-tions\cr Ver-sion: \tab 1.24.0\cr Au- thor: \tab VJ Carey \cr Overfull \hbox (140.18497pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 Builder: \tab knitr\cr Rox-y-gen-Note: \tab 7.1.1\cr En-cod-ing: \tab UTF-8\cr git_url: \tab https://git.bioconductor.org/packages/ldblock\cr Overfull \hbox (100.5054pt too wide) in paragraph at lines 55--66 \T1/ptm/m/n/10 2021-10-26\cr Date/Publication: \tab 2022-04-12\cr } c("\Sexpr[r esults=rd,stage=build]tools:::Rd_package_indices(\"#1\")", Overfull \hbox (91.02522pt too wide) in paragraph at lines 69--71 []\T1/ptm/m/n/10 c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"# 1\")", "ld-block")VJ Carey Overfull \hbox (4.40584pt too wide) in paragraph at lines 72--75 []\T1/ptm/m/n/10 Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_packag e_maintainer(\"#1\")", "ld-block")VJ [2] Overfull \hbox (179.76044pt too wide) in paragraph at lines 98--98 [] \T1/zi4/m/n/10 urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/l d_data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",[] [3] Overfull \hbox (4.78088pt too wide) in paragraph at lines 153--154 [][][]$\T1/zi4/m/n/10 ftp : / / ftp . 1000genomes . ebi . ac . uk / vol1 / ftp / technical / working / 20130606 _ sample _ info / [4] Overfull \hbox (14.65924pt too wide) in paragraph at lines 237--240 []\T1/ptm/m/n/10 name of gzipped text file as dis-tributed at [][]$\T1/zi4/m/n/ 10 hapmap . ncbi . nlm . nih . gov / downloads / [5] [6] Overfull \hbox (47.51794pt too wide) in paragraph at lines 345--346 []\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r on-ment vari-able LDLINK_TOKEN (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [7] [8] Overfull \hbox (4.78088pt too wide) in paragraph at lines 470--471 [][][]$\T1/zi4/m/n/10 ftp : / / ftp . 1000genomes . ebi . ac . uk / vol1 / ftp / technical / working / 20130606 _ sample _ info / [9] No file Rd2.ind. [10] (/private/tmp/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.TabixFile} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep laced by a fixed one pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex ist, replaced by a fixed one {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/local/texlive/2019/texmf-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 (10 pages, 103372 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (29 entries accepted, 1 rejected). Sorting entries....done (147 comparisons). Generating output file Rd2.ind....done (60 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. 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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.TabixFile} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep laced by a fixed one pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex ist, replaced by a fixed one {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/local/texlive/2019/texmf-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 (11 pages, 112770 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (29 entries accepted, 1 rejected). Sorting entries....done (147 comparisons). Generating output file Rd2.ind....done (60 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. 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[11]) (/private/tmp/RtmpcZf9cQ/Rbuildeb879d6e989/ldblock/.Rd2pdf60295/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.TabixFile} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ld} has been referenced but does not exist, rep laced by a fixed one pdfTeX warning (dest): name{Rfn.readVcf} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.genemodel} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.delim} has been referenced but does not ex ist, replaced by a fixed one {/usr/local/texlive/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/local/texlive/2019/texmf-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 (11 pages, 113003 bytes). 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