Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ppcseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ppcseq.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 1419/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ppcseq 1.0.0 (landing page) Stefano Mangiola
| 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: ppcseq |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ppcseq |
StartedAt: 2021-10-14 14:00:19 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 14:03:01 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 161.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: ppcseq_1.0.0.tar.gz |
PackageFileSize: 2.005 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ppcseq ### ############################################################################## ############################################################################## * checking for file ‘ppcseq/DESCRIPTION’ ... OK * preparing ‘ppcseq’: * checking DESCRIPTION meta-information ... OK * cleaning src * 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 377. 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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. ) [2] [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) Overfull \hbox (56.23795pt too wide) in paragraph at lines 223--223 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [5] Overfull \hbox (56.23795pt too wide) in paragraph at lines 272--272 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] No file Rd2.ind. [6] (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/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/inconsolata/i4-ts1.enc}{/usr/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}</usr/local/texlive/2019/texmf-dist/fonts/type1/p ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1 /urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times /utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pf b></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (6 pages, 85643 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 377. 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Found on input line 46. ) (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.toc) [2] [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd ) Overfull \hbox (56.23795pt too wide) in paragraph at lines 223--223 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [5] Overfull \hbox (56.23795pt too wide) in paragraph at lines 272--272 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [6] No file Rd2.ind. [7] (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.aux) ) (see the transcript file for additional information){/usr/local/texlive/2019/te xmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/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}</usr/local/texlive/2019/texmf-dist/fonts/type1/p ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1 /urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times /utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pf b></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (7 pages, 86563 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (6 entries accepted, 0 rejected). Sorting entries....done (17 comparisons). Generating output file Rd2.ind....done (21 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 377. 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This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (6 entries accepted, 0 rejected). Sorting entries....done (17 comparisons). Generating output file Rd2.ind....done (21 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 377. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 377. ) (/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/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/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/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.out) (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.out) [1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] (/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/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.toc) [2] [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd ) Overfull \hbox (56.23795pt too wide) in paragraph at lines 223--223 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [5] Overfull \hbox (56.23795pt too wide) in paragraph at lines 272--272 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [6] (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.ind [7] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 17. [8]) (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/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/inconsolata/i4-ts1.enc}{/usr/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}</usr/local/texlive/2019/texmf-dist/fonts/type1/p ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2019/texmf-dist/fonts /type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/ utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pfb ></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (8 pages, 95662 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (6 entries accepted, 0 rejected). Sorting entries....done (17 comparisons). Generating output file Rd2.ind....done (21 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 377. 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Found on input line 46. ) (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.toc) [2] [3] [4] (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/ts1zi4.fd ) Overfull \hbox (56.23795pt too wide) in paragraph at lines 223--223 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [5] Overfull \hbox (56.23795pt too wide) in paragraph at lines 272--272 [] \T1/zi4/m/n/9 dplyr::mutate( is_significant = ifelse(symbol %in% c("SLC16 A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%[] [6] (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/Rd2.ind [7] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 17. [8]) (/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/.Rd2pdf68248/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/inconsolata/i4-ts1.enc}{/usr/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}</usr/local/texlive/2019/texmf-dist/fonts/type1/p ublic/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2019/texmf-dist/font s/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2019/texmf-dist/fonts /type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/ utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmr8a.pfb ></usr/local/texlive/2019/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (8 pages, 95652 bytes). Transcript written on Rd2.log. Saving output to ‘/private/tmp/RtmpRAQ1mx/Rbuild10a982ce3c6a3/ppcseq/build/ppcseq.pdf’ ... Done * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘ppcseq_1.0.0.tar.gz’