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This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ldblock package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ldblock.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 978/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ldblock 1.22.1 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ldblock |
Version: 1.22.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ldblock |
StartedAt: 2021-10-14 07:35:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 07:36:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 90.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: ldblock_1.22.1.tar.gz |
PackageFileSize: 40.2 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/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/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-3.13-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 377. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 377. ) (/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) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) 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 [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] 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 1.22.1\cr Au- thor: \tab VJ Carey <stvjc@channing.harvard.edu>\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 2021-07-28\cr Date/Publication: \tab 2021-10-14\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 <stvjc@channing.harvard.edu> 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/share/texlive/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] (/tmp/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/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/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/ type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo nts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur w/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a. pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share /texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (10 pages, 102073 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-3.13-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 377. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 377. ) (/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/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/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/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/Rd2.out) (/tmp/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/Rd2.toc [1{/var/li b/texmf/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 1.22.1\cr Au- thor: \tab VJ Carey <stvjc@channing.harvard.edu>\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 2021-07-28\cr Date/Publication: \tab 2021-10-14\cr } c("\Sexpr[r esults=rd,stage=build]tools:::Rd_package_indices(\"#1\")", [2] 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 <stvjc@channing.harvard.edu> 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 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 [][]$\T1/zi4/m/n/ 10 hapmap . ncbi . nlm . nih . gov / downloads / [5] [6] Overfull \hbox (47.51794pt too wide) in paragraph at lines 345--346 []\T1/ptm/m/n/10 the API to-ken pro-vided by NCI, de-faults to value of en-vi-r on-ment vari-able LDLINK_TOKEN (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [7] [8] Overfull \hbox (4.78088pt too wide) in paragraph at lines 470--471 [][][]$\T1/zi4/m/n/10 ftp : / / ftp . 1000genomes . ebi . ac . uk / vol1 / ftp / technical / working / 20130606 _ sample _ info / [9] No file Rd2.ind. [10] (/tmp/RtmpeBAKIK/Rbuild2c9a55249d18f7/ldblock/.Rd2pdf2923093/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/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/ type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo nts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur w/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a. pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share /texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (10 pages, 103606 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 (148 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/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-3.13-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 377. 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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-3.13-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 377. 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