Dirk Eddelbuettel
2018-May-29 20:53 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
On 29 May 2018 at 16:37, R P Herrold wrote:
| On Tue, 29 May 2018, Dirk Eddelbuettel wrote:
|
| > On a CentOS 7 machine, I am at a loss with respect to an inability to run
a
| > full R CMD check as anything involving tex files ends in tears.
|
| Hi, Dirk
|
| Have fun at the upcoming conference at UIC
|
| I seem to have 56 font packages installed under CentOS 7
| locally, but then I work pretty carefully to cull them down
|
| What is the specific 'leaf node' package you are trying to
I noticed it with a local, not-public package -- but it appears to apply with
any source package. I replicated with pkgKitten straight off CRAN and after
checking that it has a six page manual there. Here, I get an aborted (!!)
source file, same happens with the local, non-public package:
-----------------------------------------------------------------------------
\documentclass[a4paper]{book}
\usepackage[times,hyper]{Rd}
\usepackage{makeidx}
\usepackage[latin1]{inputenc} % @SET ENCODING@
% \usepackage{graphicx} % @USE GRAPHICX@
\makeindex{}
\begin{document}
\chapter*{}
\begin{center}
{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of
\file{pkgKitten\_0.1.4.tar.gz}}}
\par\bigskip{\large \today}
\end{center}
-----------------------------------------------------------------------------
Note that it ends on \end{center}, not \end{document}.
Dirk
| attain. Long ago and far away, I packaged several hundred,
| inspired by your Debian effort, and I may have a working .spec
| file about
|
| with my regards,
|
| -- Russ herrold
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Tom Callaway
2018-May-30 15:34 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
On 05/29/2018 04:53 PM, Dirk Eddelbuettel wrote:> I noticed it with a local, not-public package -- but it appears to apply with > any source package. I replicated with pkgKitten straight off CRAN and after > checking that it has a six page manual there.I'm having trouble reproducing this one. In my fresh CentOS 7 VM, I can pull the pkgKitten source down, and run R CMD Rd2pdf pkgKitten without issue: [spot at localhost ~]$ tar xf pkgKitten_0.1.4.tar.gz [spot at localhost ~]$ R CMD Rd2pdf pkgKitten Hmm ... looks like a package Converting Rd files to LaTeX Creating pdf output from LaTeX ... This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode LaTeX2e <2011/06/27> Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/R/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/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx No file Rd2.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/usr/share/texlive/t exmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65 []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".", author, maintainer, e mail,[] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] No file Rd2.ind. [3] (./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.email.Rul.address} has been referenced but does not exist, replaced by a f ixed one pdfTeX warning (dest): name{Rfn.fullname} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.package.skeleton} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/ texmf-dist/fonts/type1/urw/courier/ucrr8a.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 (3 pages, 69080 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support). Scanning input file Rd2.idx....done (9 entries accepted, 0 rejected). Sorting entries....done (36 comparisons). Generating output file Rd2.ind....done (26 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode LaTeX2e <2011/06/27> Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/R/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/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty)) (./Rd2.out) (./Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/usr/share/texlive/t exmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65 []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".", author, maintainer, e mail,[] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] (./Rd2.ind [3] [4]) (./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.email.Rul.address} has been referenced but does not exist, replaced by a f ixed one pdfTeX warning (dest): name{Rfn.fullname} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.package.skeleton} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/ texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf- dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/ty pe1/urw/courier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helv etic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/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-dis t/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (4 pages, 85455 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support). Scanning input file Rd2.idx....done (9 entries accepted, 0 rejected). Sorting entries....done (36 comparisons). Generating output file Rd2.ind....done (26 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode LaTeX2e <2011/06/27> Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/R/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/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty)) (./Rd2.out) (./Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/usr/share/texlive/t exmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65 []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".", author, maintainer, e mail,[] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] (./Rd2.ind [3] [4]) (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.email.Rul.address} has been referenced but does not exist, replaced by a f ixed one pdfTeX warning (dest): name{Rfn.fullname} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.package.skeleton} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/ texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf- dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/ty pe1/urw/courier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helv etic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/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-dis t/fonts/type1/urw/times/utmri8a.pfb> Output written on Rd2.pdf (4 pages, 85995 bytes). Transcript written on Rd2.log. Saving output to ?pkgKitten.pdf? ... Done ***** Do you have a ~/.texlive2013 ? If so, try deleting it and retrying. Here's the list of texlive components I have on my CentOS 7 system: texlive-ae-svn15878.1.4-38.el7.noarch texlive-algorithms-svn15878.0.1-38.el7.noarch texlive-amscls-svn29207.0-38.el7.noarch texlive-amsfonts-svn29208.3.04-38.el7.noarch texlive-amsmath-svn29327.2.14-38.el7.noarch texlive-anysize-svn15878.0-38.el7.noarch texlive-attachfile-svn21866.v1.5b-38.el7.noarch texlive-avantgar-svn28614.0-38.el7.noarch texlive-babelbib-svn25245.1.31-38.el7.noarch texlive-babel-svn24756.3.8m-38.el7.noarch texlive-base-2012-38.20130427_r30134.el7.noarch texlive-beamer-svn29349.3.26-38.el7.noarch texlive-bera-svn20031.0-38.el7.noarch texlive-beton-svn15878.0-38.el7.noarch texlive-bibtex-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-bibtex-svn26689.0.99d-38.el7.noarch texlive-bookman-svn28614.0-38.el7.noarch texlive-booktabs-svn15878.1.61803-38.el7.noarch texlive-breakurl-svn15878.1.30-38.el7.noarch texlive-caption-svn29026.3.3__2013_02_03_-38.el7.noarch texlive-carlisle-svn18258.0-38.el7.noarch texlive-charter-svn15878.0-38.el7.noarch texlive-chngcntr-svn17157.1.0a-38.el7.noarch texlive-cite-svn19955.5.3-38.el7.noarch texlive-cmap-svn26568.0-38.el7.noarch texlive-cmextra-svn14075.0-38.el7.noarch texlive-cm-super-svn15878.0-38.el7.noarch texlive-cm-svn29581.0-38.el7.noarch texlive-collection-basic-svn26314.0-38.20130427_r30134.el7.noarch texlive-collection-documentation-base-svn17091.0-38.20130427_r30134.el7.noarch texlive-collection-fontsrecommended-svn28082.0-38.20130427_r30134.el7.noarch texlive-collection-latexrecommended-svn25795.0-38.20130427_r30134.el7.noarch texlive-collection-latex-svn25030.0-38.20130427_r30134.el7.noarch texlive-colortbl-svn25394.v1.0a-38.el7.noarch texlive-courier-svn28614.0-38.el7.noarch texlive-crop-svn15878.1.5-38.el7.noarch texlive-csquotes-svn24393.5.1d-38.el7.noarch texlive-ctable-svn26694.1.23-38.el7.noarch texlive-currfile-svn29012.0.7b-38.el7.noarch texlive-dvipdfm-bin-svn13663.0-38.20130427_r30134.el7.noarch texlive-dvipdfm-svn26689.0.13.2d-38.el7.noarch texlive-dvipdfmx-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-dvipdfmx-def-svn15878.0-38.el7.noarch texlive-dvipdfmx-svn26765.0-38.el7.noarch texlive-dvips-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-dvips-svn29585.0-38.el7.noarch texlive-ec-svn25033.1.0-38.el7.noarch texlive-enctex-svn28602.0-38.el7.noarch texlive-enumitem-svn24146.3.5.2-38.el7.noarch texlive-epsf-svn21461.2.7.4-38.el7.noarch texlive-eso-pic-svn21515.2.0c-38.el7.noarch texlive-etex-pkg-svn15878.2.0-38.el7.noarch texlive-etex-svn22198.2.1-38.el7.noarch texlive-etoolbox-svn20922.2.1-38.el7.noarch texlive-euler-svn17261.2.5-38.el7.noarch texlive-euro-svn22191.1.1-38.el7.noarch texlive-eurosym-svn17265.1.4_subrfix-38.el7.noarch texlive-extsizes-svn17263.1.4a-38.el7.noarch texlive-fancybox-svn18304.1.4-38.el7.noarch texlive-fancyhdr-svn15878.3.1-38.el7.noarch texlive-fancyref-svn15878.0.9c-38.el7.noarch texlive-fancyvrb-svn18492.2.8-38.el7.noarch texlive-filecontents-svn24250.1.3-38.el7.noarch texlive-filehook-svn24280.0.5d-38.el7.noarch texlive-fix2col-svn17133.0-38.el7.noarch texlive-float-svn15878.1.3d-38.el7.noarch texlive-fontspec-svn29412.v2.3a-38.el7.noarch texlive-footmisc-svn23330.5.5b-38.el7.noarch texlive-fpl-svn15878.1.002-38.el7.noarch texlive-fp-svn15878.0-38.el7.noarch texlive-geometry-svn19716.5.6-38.el7.noarch texlive-glyphlist-svn28576.0-38.el7.noarch texlive-graphics-svn25405.1.0o-38.el7.noarch texlive-gsftopk-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-gsftopk-svn26689.1.19.2-38.el7.noarch texlive-helvetic-svn28614.0-38.el7.noarch texlive-hyperref-svn28213.6.83m-38.el7.noarch texlive-hyphen-base-svn29197.0-38.el7.noarch texlive-hyph-utf8-svn29641.0-38.el7.noarch texlive-ifetex-svn24853.1.2-38.el7.noarch texlive-ifluatex-svn26725.1.3-38.el7.noarch texlive-ifxetex-svn19685.0.5-38.el7.noarch texlive-index-svn24099.4.1beta-38.el7.noarch texlive-jknapltx-svn19440.0-38.el7.noarch texlive-kastrup-svn15878.0-38.el7.noarch texlive-koma-script-svn27255.3.11b-38.el7.noarch texlive-kpathsea-bin-svn27347.0-38.20130427_r30134.el7.x86_64 texlive-kpathsea-lib-2012-38.20130427_r30134.el7.x86_64 texlive-kpathsea-svn28792.0-38.el7.noarch texlive-l3experimental-svn29361.SVN_4467-38.el7.noarch texlive-l3kernel-svn29409.SVN_4469-38.el7.noarch texlive-l3packages-svn29361.SVN_4467-38.el7.noarch texlive-latex-bin-bin-svn14050.0-38.20130427_r30134.el7.noarch texlive-latex-bin-svn26689.0-38.el7.noarch texlive-latexconfig-svn28991.0-38.el7.noarch texlive-latex-fonts-svn28888.0-38.el7.noarch texlive-latex-svn27907.0-38.el7.noarch texlive-listings-svn15878.1.4-38.el7.noarch texlive-lm-math-svn29044.1.958-38.el7.noarch texlive-lm-svn28119.2.004-38.el7.noarch texlive-ltxmisc-svn21927.0-38.el7.noarch texlive-lua-alt-getopt-svn29349.0.7.0-38.el7.noarch texlive-lualatex-math-svn29346.1.2-38.el7.noarch texlive-luaotfload-bin-svn18579.0-38.20130427_r30134.el7.noarch texlive-luaotfload-svn26718.1.26-38.el7.noarch texlive-luatexbase-svn22560.0.31-38.el7.noarch texlive-luatex-bin-svn26912.0-38.20130427_r30134.el7.x86_64 texlive-luatex-svn26689.0.70.1-38.el7.noarch texlive-makeindex-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-makeindex-svn26689.2.12-38.el7.noarch texlive-marginnote-svn25880.v1.1i-38.el7.noarch texlive-marvosym-svn29349.2.2a-38.el7.noarch texlive-mathpazo-svn15878.1.003-38.el7.noarch texlive-mdwtools-svn15878.1.05.4-38.el7.noarch texlive-memoir-svn21638.3.6j_patch_6.0g-38.el7.noarch texlive-metafont-bin-svn26912.0-38.20130427_r30134.el7.x86_64 texlive-metafont-svn26689.2.718281-38.el7.noarch texlive-metalogo-svn18611.0.12-38.el7.noarch texlive-mflogo-svn17487.0-38.el7.noarch texlive-mfnfss-svn19410.0-38.el7.noarch texlive-mfware-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-mfware-svn26689.0-38.el7.noarch texlive-mh-svn29420.0-38.el7.noarch texlive-microtype-svn29392.2.5-38.el7.noarch texlive-misc-svn24955.0-38.el7.noarch texlive-mparhack-svn15878.1.4-38.el7.noarch texlive-mptopdf-bin-svn18674.0-38.20130427_r30134.el7.noarch texlive-mptopdf-svn26689.0-38.el7.noarch texlive-ms-svn24467.0-38.el7.noarch texlive-multido-svn18302.1.42-38.el7.noarch texlive-natbib-svn20668.8.31b-38.el7.noarch texlive-ncntrsbk-svn28614.0-38.el7.noarch texlive-ntgclass-svn15878.0-38.el7.noarch texlive-oberdiek-svn26725.0-38.el7.noarch texlive-palatino-svn28614.0-38.el7.noarch texlive-paralist-svn15878.2.3b-38.el7.noarch texlive-parallel-svn15878.0-38.el7.noarch texlive-parskip-svn19963.2.0-38.el7.noarch texlive-pdfpages-svn27574.0.4t-38.el7.noarch texlive-pdftex-bin-svn27321.0-38.20130427_r30134.el7.x86_64 texlive-pdftex-def-svn22653.0.06d-38.el7.noarch texlive-pdftex-svn29585.1.40.11-38.el7.noarch texlive-pgf-svn22614.2.10-38.el7.noarch texlive-plain-svn26647.0-38.el7.noarch texlive-powerdot-svn25656.1.4i-38.el7.noarch texlive-psfrag-svn15878.3.04-38.el7.noarch texlive-pslatex-svn16416.0-38.el7.noarch texlive-psnfss-svn23394.9.2a-38.el7.noarch texlive-pspicture-svn15878.0-38.el7.noarch texlive-pst-3d-svn17257.1.10-38.el7.noarch texlive-pst-blur-svn15878.2.0-38.el7.noarch texlive-pst-coil-svn24020.1.06-38.el7.noarch texlive-pst-eps-svn15878.1.0-38.el7.noarch texlive-pst-fill-svn15878.1.01-38.el7.noarch texlive-pst-grad-svn15878.1.06-38.el7.noarch texlive-pst-math-svn20176.0.61-38.el7.noarch texlive-pst-node-svn27799.1.25-38.el7.noarch texlive-pst-plot-svn28729.1.44-38.el7.noarch texlive-pstricks-add-svn28750.3.59-38.el7.noarch texlive-pstricks-svn29678.2.39-38.el7.noarch texlive-pst-slpe-svn24391.1.31-38.el7.noarch texlive-pst-text-svn15878.1.00-38.el7.noarch texlive-pst-tree-svn24142.1.12-38.el7.noarch texlive-pxfonts-svn15878.0-38.el7.noarch texlive-qstest-svn15878.0-38.el7.noarch texlive-rcs-svn15878.0-38.el7.noarch texlive-rotating-svn16832.2.16b-38.el7.noarch texlive-rsfs-svn15878.0-38.el7.noarch texlive-sansmath-svn17997.1.1-38.el7.noarch texlive-sauerj-svn15878.0-38.el7.noarch texlive-section-svn20180.0-38.el7.noarch texlive-seminar-svn18322.1.5-38.el7.noarch texlive-sepnum-svn20186.2.0-38.el7.noarch texlive-setspace-svn24881.6.7a-38.el7.noarch texlive-showexpl-svn27790.v0.3j-38.el7.noarch texlive-soul-svn15878.2.4-38.el7.noarch texlive-subfig-svn15878.1.3-38.el7.noarch texlive-symbol-svn28614.0-38.el7.noarch texlive-tetex-bin-svn27344.0-38.20130427_r30134.el7.noarch texlive-tetex-svn29585.3.0-38.el7.noarch texlive-tex-bin-svn26912.0-38.20130427_r30134.el7.x86_64 texlive-texconfig-bin-svn27344.0-38.20130427_r30134.el7.noarch texlive-texconfig-svn29349.0-38.el7.noarch texlive-tex-gyre-math-svn29045.0-38.el7.noarch texlive-tex-gyre-svn18651.2.004-38.el7.noarch texlive-texlive.infra-bin-svn22566.0-38.20130427_r30134.el7.x86_64 texlive-texlive.infra-svn28217.0-38.el7.noarch texlive-tex-svn26689.3.1415926-38.el7.noarch texlive-textcase-svn15878.0-38.el7.noarch texlive-thumbpdf-bin-svn6898.0-38.20130427_r30134.el7.noarch texlive-thumbpdf-svn26689.3.15-38.el7.noarch texlive-times-svn28614.0-38.el7.noarch texlive-tipa-svn29349.1.3-38.el7.noarch texlive-tools-svn26263.0-38.el7.noarch texlive-txfonts-svn15878.0-38.el7.noarch texlive-type1cm-svn21820.0-38.el7.noarch texlive-typehtml-svn17134.0-38.el7.noarch texlive-ucs-svn27549.2.1-38.el7.noarch texlive-underscore-svn18261.0-38.el7.noarch texlive-unicode-math-svn29413.0.7d-38.el7.noarch texlive-url-svn16864.3.2-38.el7.noarch texlive-utopia-svn15878.0-38.el7.noarch texlive-varwidth-svn24104.0.92-38.el7.noarch texlive-wasy-svn15878.0-38.el7.noarch texlive-wasysym-svn15878.2.0-38.el7.noarch texlive-xcolor-svn15878.2.11-38.el7.noarch texlive-xdvi-bin-svn26509.0-38.20130427_r30134.el7.x86_64 texlive-xdvi-svn26689.22.85-38.el7.noarch texlive-xkeyval-svn27995.2.6a-38.el7.noarch texlive-xunicode-svn23897.0.981-38.el7.noarch texlive-zapfchan-svn28614.0-38.el7.noarch texlive-zapfding-svn28614.0-38.el7.noarch
Dirk Eddelbuettel
2018-May-30 16:10 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
Tom,
On 30 May 2018 at 11:34, Tom Callaway wrote:
| On 05/29/2018 04:53 PM, Dirk Eddelbuettel wrote:
| > I noticed it with a local, not-public package -- but it appears to apply
with
| > any source package. I replicated with pkgKitten straight off CRAN and
after
| > checking that it has a six page manual there.
|
| I'm having trouble reproducing this one. In my fresh CentOS 7 VM, I can
| pull the pkgKitten source down, and run R CMD Rd2pdf pkgKitten without
| issue:
Thank you. That is the expected behaviour and also what I see on Ubuntu /
Debian. We may be missing a font metrics or font package. Will check
locally.
Dirk
|
| [spot at localhost ~]$ tar xf pkgKitten_0.1.4.tar.gz
| [spot at localhost ~]$ R CMD Rd2pdf pkgKitten
| Hmm ... looks like a package
| Converting Rd files to LaTeX
| Creating pdf output from LaTeX ...
|
| This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
| restricted \write18 enabled.
| entering extended mode
| LaTeX2e <2011/06/27>
| Babel <v3.8m> and hyphenation patterns for english, dumylang,
| nohyphenation, lo
| aded.
| (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
| Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
| (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
| (/usr/share/R/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/ts1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
| (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
|
| Package hyperref Message: Driver (autodetected): hpdftex.
|
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
|
| Package hyperref Warning: Option `hyperindex' has already been used,
| (hyperref) setting the option has no effect on input line
| 366.
|
|
| Package hyperref Warning: Option `pagebackref' has already been used,
| (hyperref) setting the option has no effect on input line
| 366.
|
| ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
| (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
| Writing index file Rd2.idx
| No file Rd2.aux.
| (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
| (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
| [1{/usr/share/texlive/t
| exmf/fonts/map/pdftex/updmap/pdftex.map}]
| Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65
| []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".",
author,
| maintainer, e
| mail,[]
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
| No file Rd2.ind.
| [3] (./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.email.Rul.address} has been referenced but does not exist, replaced
| by a f
| ixed one
|
| pdfTeX warning (dest): name{Rfn.fullname} has been referenced but does
| not exis
| t, replaced by a fixed one
|
| pdfTeX warning (dest): name{Rfn.package.skeleton} has been referenced
| but does
| not exist, replaced by a fixed one
|
|
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
|
texmf-dist/fonts/type1/urw/courier/ucrr8a.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 (3 pages, 69080 bytes).
| Transcript written on Rd2.log.
| This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
| Scanning input file Rd2.idx....done (9 entries accepted, 0 rejected).
| Sorting entries....done (36 comparisons).
| Generating output file Rd2.ind....done (26 lines written, 0 warnings).
| Output written in Rd2.ind.
| Transcript written in Rd2.ilg.
| This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
| restricted \write18 enabled.
| entering extended mode
| LaTeX2e <2011/06/27>
| Babel <v3.8m> and hyphenation patterns for english, dumylang,
| nohyphenation, lo
| aded.
| (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
| Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
| (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
| (/usr/share/R/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/ts1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
| (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
|
| Package hyperref Message: Driver (autodetected): hpdftex.
|
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
|
| Package hyperref Warning: Option `hyperindex' has already been used,
| (hyperref) setting the option has no effect on input line
| 366.
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| Package hyperref Warning: Option `pagebackref' has already been used,
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| 366.
|
| ) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
| (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
| Writing index file Rd2.idx
| (./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
| (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty))
| (./Rd2.out) (./Rd2.out)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
| [1{/usr/share/texlive/t
| exmf/fonts/map/pdftex/updmap/pdftex.map}]
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| Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65
| []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".",
author,
| maintainer, e
| mail,[]
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] (./Rd2.ind [3]
| [4]) (./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.email.Rul.address} has been referenced but does not exist, replaced
| by a f
| ixed one
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| not exis
| t, replaced by a fixed one
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{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
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texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-
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dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/ty
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pe1/urw/courier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helv
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etic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb
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></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/te
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| t/fonts/type1/urw/times/utmri8a.pfb>
| Output written on Rd2.pdf (4 pages, 85455 bytes).
| Transcript written on Rd2.log.
| This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
| Scanning input file Rd2.idx....done (9 entries accepted, 0 rejected).
| Sorting entries....done (36 comparisons).
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| Output written in Rd2.ind.
| Transcript written in Rd2.ilg.
| This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
| restricted \write18 enabled.
| entering extended mode
| LaTeX2e <2011/06/27>
| Babel <v3.8m> and hyphenation patterns for english, dumylang,
| nohyphenation, lo
| aded.
| (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
| Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
| (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
| (/usr/share/R/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/ts1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
| (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
| (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
| (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
| (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
| (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
|
| Package hyperref Message: Driver (autodetected): hpdftex.
|
| (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
| (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
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| (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
| (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
| (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
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| Writing index file Rd2.idx
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| (/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty))
| (./Rd2.out) (./Rd2.out)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
| (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
| [1{/usr/share/texlive/t
| exmf/fonts/map/pdftex/updmap/pdftex.map}]
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
| Overfull \hbox (0.78088pt too wide) in paragraph at lines 65--65
| []\T1/pcr/m/n/10 kitten(name = "anRpackage", path = ".",
author,
| maintainer, e
| mail,[]
| (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] (./Rd2.ind [3]
| [4]) (./Rd2.aux) )
| (see the transcript file for additional information)pdfTeX warning
| (dest): name
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| by a f
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{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/
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dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/ty
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pe1/urw/courier/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helv
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etic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb
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></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/te
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| Output written on Rd2.pdf (4 pages, 85995 bytes).
| Transcript written on Rd2.log.
| Saving output to ?pkgKitten.pdf? ...
| Done
|
| *****
|
| Do you have a ~/.texlive2013 ? If so, try deleting it and retrying.
|
| Here's the list of texlive components I have on my CentOS 7 system:
|
| texlive-ae-svn15878.1.4-38.el7.noarch
| texlive-algorithms-svn15878.0.1-38.el7.noarch
| texlive-amscls-svn29207.0-38.el7.noarch
| texlive-amsfonts-svn29208.3.04-38.el7.noarch
| texlive-amsmath-svn29327.2.14-38.el7.noarch
| texlive-anysize-svn15878.0-38.el7.noarch
| texlive-attachfile-svn21866.v1.5b-38.el7.noarch
| texlive-avantgar-svn28614.0-38.el7.noarch
| texlive-babelbib-svn25245.1.31-38.el7.noarch
| texlive-babel-svn24756.3.8m-38.el7.noarch
| texlive-base-2012-38.20130427_r30134.el7.noarch
| texlive-beamer-svn29349.3.26-38.el7.noarch
| texlive-bera-svn20031.0-38.el7.noarch
| texlive-beton-svn15878.0-38.el7.noarch
| texlive-bibtex-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-bibtex-svn26689.0.99d-38.el7.noarch
| texlive-bookman-svn28614.0-38.el7.noarch
| texlive-booktabs-svn15878.1.61803-38.el7.noarch
| texlive-breakurl-svn15878.1.30-38.el7.noarch
| texlive-caption-svn29026.3.3__2013_02_03_-38.el7.noarch
| texlive-carlisle-svn18258.0-38.el7.noarch
| texlive-charter-svn15878.0-38.el7.noarch
| texlive-chngcntr-svn17157.1.0a-38.el7.noarch
| texlive-cite-svn19955.5.3-38.el7.noarch
| texlive-cmap-svn26568.0-38.el7.noarch
| texlive-cmextra-svn14075.0-38.el7.noarch
| texlive-cm-super-svn15878.0-38.el7.noarch
| texlive-cm-svn29581.0-38.el7.noarch
| texlive-collection-basic-svn26314.0-38.20130427_r30134.el7.noarch
| texlive-collection-documentation-base-svn17091.0-38.20130427_r30134.el7.noarch
| texlive-collection-fontsrecommended-svn28082.0-38.20130427_r30134.el7.noarch
| texlive-collection-latexrecommended-svn25795.0-38.20130427_r30134.el7.noarch
| texlive-collection-latex-svn25030.0-38.20130427_r30134.el7.noarch
| texlive-colortbl-svn25394.v1.0a-38.el7.noarch
| texlive-courier-svn28614.0-38.el7.noarch
| texlive-crop-svn15878.1.5-38.el7.noarch
| texlive-csquotes-svn24393.5.1d-38.el7.noarch
| texlive-ctable-svn26694.1.23-38.el7.noarch
| texlive-currfile-svn29012.0.7b-38.el7.noarch
| texlive-dvipdfm-bin-svn13663.0-38.20130427_r30134.el7.noarch
| texlive-dvipdfm-svn26689.0.13.2d-38.el7.noarch
| texlive-dvipdfmx-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-dvipdfmx-def-svn15878.0-38.el7.noarch
| texlive-dvipdfmx-svn26765.0-38.el7.noarch
| texlive-dvips-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-dvips-svn29585.0-38.el7.noarch
| texlive-ec-svn25033.1.0-38.el7.noarch
| texlive-enctex-svn28602.0-38.el7.noarch
| texlive-enumitem-svn24146.3.5.2-38.el7.noarch
| texlive-epsf-svn21461.2.7.4-38.el7.noarch
| texlive-eso-pic-svn21515.2.0c-38.el7.noarch
| texlive-etex-pkg-svn15878.2.0-38.el7.noarch
| texlive-etex-svn22198.2.1-38.el7.noarch
| texlive-etoolbox-svn20922.2.1-38.el7.noarch
| texlive-euler-svn17261.2.5-38.el7.noarch
| texlive-euro-svn22191.1.1-38.el7.noarch
| texlive-eurosym-svn17265.1.4_subrfix-38.el7.noarch
| texlive-extsizes-svn17263.1.4a-38.el7.noarch
| texlive-fancybox-svn18304.1.4-38.el7.noarch
| texlive-fancyhdr-svn15878.3.1-38.el7.noarch
| texlive-fancyref-svn15878.0.9c-38.el7.noarch
| texlive-fancyvrb-svn18492.2.8-38.el7.noarch
| texlive-filecontents-svn24250.1.3-38.el7.noarch
| texlive-filehook-svn24280.0.5d-38.el7.noarch
| texlive-fix2col-svn17133.0-38.el7.noarch
| texlive-float-svn15878.1.3d-38.el7.noarch
| texlive-fontspec-svn29412.v2.3a-38.el7.noarch
| texlive-footmisc-svn23330.5.5b-38.el7.noarch
| texlive-fpl-svn15878.1.002-38.el7.noarch
| texlive-fp-svn15878.0-38.el7.noarch
| texlive-geometry-svn19716.5.6-38.el7.noarch
| texlive-glyphlist-svn28576.0-38.el7.noarch
| texlive-graphics-svn25405.1.0o-38.el7.noarch
| texlive-gsftopk-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-gsftopk-svn26689.1.19.2-38.el7.noarch
| texlive-helvetic-svn28614.0-38.el7.noarch
| texlive-hyperref-svn28213.6.83m-38.el7.noarch
| texlive-hyphen-base-svn29197.0-38.el7.noarch
| texlive-hyph-utf8-svn29641.0-38.el7.noarch
| texlive-ifetex-svn24853.1.2-38.el7.noarch
| texlive-ifluatex-svn26725.1.3-38.el7.noarch
| texlive-ifxetex-svn19685.0.5-38.el7.noarch
| texlive-index-svn24099.4.1beta-38.el7.noarch
| texlive-jknapltx-svn19440.0-38.el7.noarch
| texlive-kastrup-svn15878.0-38.el7.noarch
| texlive-koma-script-svn27255.3.11b-38.el7.noarch
| texlive-kpathsea-bin-svn27347.0-38.20130427_r30134.el7.x86_64
| texlive-kpathsea-lib-2012-38.20130427_r30134.el7.x86_64
| texlive-kpathsea-svn28792.0-38.el7.noarch
| texlive-l3experimental-svn29361.SVN_4467-38.el7.noarch
| texlive-l3kernel-svn29409.SVN_4469-38.el7.noarch
| texlive-l3packages-svn29361.SVN_4467-38.el7.noarch
| texlive-latex-bin-bin-svn14050.0-38.20130427_r30134.el7.noarch
| texlive-latex-bin-svn26689.0-38.el7.noarch
| texlive-latexconfig-svn28991.0-38.el7.noarch
| texlive-latex-fonts-svn28888.0-38.el7.noarch
| texlive-latex-svn27907.0-38.el7.noarch
| texlive-listings-svn15878.1.4-38.el7.noarch
| texlive-lm-math-svn29044.1.958-38.el7.noarch
| texlive-lm-svn28119.2.004-38.el7.noarch
| texlive-ltxmisc-svn21927.0-38.el7.noarch
| texlive-lua-alt-getopt-svn29349.0.7.0-38.el7.noarch
| texlive-lualatex-math-svn29346.1.2-38.el7.noarch
| texlive-luaotfload-bin-svn18579.0-38.20130427_r30134.el7.noarch
| texlive-luaotfload-svn26718.1.26-38.el7.noarch
| texlive-luatexbase-svn22560.0.31-38.el7.noarch
| texlive-luatex-bin-svn26912.0-38.20130427_r30134.el7.x86_64
| texlive-luatex-svn26689.0.70.1-38.el7.noarch
| texlive-makeindex-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-makeindex-svn26689.2.12-38.el7.noarch
| texlive-marginnote-svn25880.v1.1i-38.el7.noarch
| texlive-marvosym-svn29349.2.2a-38.el7.noarch
| texlive-mathpazo-svn15878.1.003-38.el7.noarch
| texlive-mdwtools-svn15878.1.05.4-38.el7.noarch
| texlive-memoir-svn21638.3.6j_patch_6.0g-38.el7.noarch
| texlive-metafont-bin-svn26912.0-38.20130427_r30134.el7.x86_64
| texlive-metafont-svn26689.2.718281-38.el7.noarch
| texlive-metalogo-svn18611.0.12-38.el7.noarch
| texlive-mflogo-svn17487.0-38.el7.noarch
| texlive-mfnfss-svn19410.0-38.el7.noarch
| texlive-mfware-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-mfware-svn26689.0-38.el7.noarch
| texlive-mh-svn29420.0-38.el7.noarch
| texlive-microtype-svn29392.2.5-38.el7.noarch
| texlive-misc-svn24955.0-38.el7.noarch
| texlive-mparhack-svn15878.1.4-38.el7.noarch
| texlive-mptopdf-bin-svn18674.0-38.20130427_r30134.el7.noarch
| texlive-mptopdf-svn26689.0-38.el7.noarch
| texlive-ms-svn24467.0-38.el7.noarch
| texlive-multido-svn18302.1.42-38.el7.noarch
| texlive-natbib-svn20668.8.31b-38.el7.noarch
| texlive-ncntrsbk-svn28614.0-38.el7.noarch
| texlive-ntgclass-svn15878.0-38.el7.noarch
| texlive-oberdiek-svn26725.0-38.el7.noarch
| texlive-palatino-svn28614.0-38.el7.noarch
| texlive-paralist-svn15878.2.3b-38.el7.noarch
| texlive-parallel-svn15878.0-38.el7.noarch
| texlive-parskip-svn19963.2.0-38.el7.noarch
| texlive-pdfpages-svn27574.0.4t-38.el7.noarch
| texlive-pdftex-bin-svn27321.0-38.20130427_r30134.el7.x86_64
| texlive-pdftex-def-svn22653.0.06d-38.el7.noarch
| texlive-pdftex-svn29585.1.40.11-38.el7.noarch
| texlive-pgf-svn22614.2.10-38.el7.noarch
| texlive-plain-svn26647.0-38.el7.noarch
| texlive-powerdot-svn25656.1.4i-38.el7.noarch
| texlive-psfrag-svn15878.3.04-38.el7.noarch
| texlive-pslatex-svn16416.0-38.el7.noarch
| texlive-psnfss-svn23394.9.2a-38.el7.noarch
| texlive-pspicture-svn15878.0-38.el7.noarch
| texlive-pst-3d-svn17257.1.10-38.el7.noarch
| texlive-pst-blur-svn15878.2.0-38.el7.noarch
| texlive-pst-coil-svn24020.1.06-38.el7.noarch
| texlive-pst-eps-svn15878.1.0-38.el7.noarch
| texlive-pst-fill-svn15878.1.01-38.el7.noarch
| texlive-pst-grad-svn15878.1.06-38.el7.noarch
| texlive-pst-math-svn20176.0.61-38.el7.noarch
| texlive-pst-node-svn27799.1.25-38.el7.noarch
| texlive-pst-plot-svn28729.1.44-38.el7.noarch
| texlive-pstricks-add-svn28750.3.59-38.el7.noarch
| texlive-pstricks-svn29678.2.39-38.el7.noarch
| texlive-pst-slpe-svn24391.1.31-38.el7.noarch
| texlive-pst-text-svn15878.1.00-38.el7.noarch
| texlive-pst-tree-svn24142.1.12-38.el7.noarch
| texlive-pxfonts-svn15878.0-38.el7.noarch
| texlive-qstest-svn15878.0-38.el7.noarch
| texlive-rcs-svn15878.0-38.el7.noarch
| texlive-rotating-svn16832.2.16b-38.el7.noarch
| texlive-rsfs-svn15878.0-38.el7.noarch
| texlive-sansmath-svn17997.1.1-38.el7.noarch
| texlive-sauerj-svn15878.0-38.el7.noarch
| texlive-section-svn20180.0-38.el7.noarch
| texlive-seminar-svn18322.1.5-38.el7.noarch
| texlive-sepnum-svn20186.2.0-38.el7.noarch
| texlive-setspace-svn24881.6.7a-38.el7.noarch
| texlive-showexpl-svn27790.v0.3j-38.el7.noarch
| texlive-soul-svn15878.2.4-38.el7.noarch
| texlive-subfig-svn15878.1.3-38.el7.noarch
| texlive-symbol-svn28614.0-38.el7.noarch
| texlive-tetex-bin-svn27344.0-38.20130427_r30134.el7.noarch
| texlive-tetex-svn29585.3.0-38.el7.noarch
| texlive-tex-bin-svn26912.0-38.20130427_r30134.el7.x86_64
| texlive-texconfig-bin-svn27344.0-38.20130427_r30134.el7.noarch
| texlive-texconfig-svn29349.0-38.el7.noarch
| texlive-tex-gyre-math-svn29045.0-38.el7.noarch
| texlive-tex-gyre-svn18651.2.004-38.el7.noarch
| texlive-texlive.infra-bin-svn22566.0-38.20130427_r30134.el7.x86_64
| texlive-texlive.infra-svn28217.0-38.el7.noarch
| texlive-tex-svn26689.3.1415926-38.el7.noarch
| texlive-textcase-svn15878.0-38.el7.noarch
| texlive-thumbpdf-bin-svn6898.0-38.20130427_r30134.el7.noarch
| texlive-thumbpdf-svn26689.3.15-38.el7.noarch
| texlive-times-svn28614.0-38.el7.noarch
| texlive-tipa-svn29349.1.3-38.el7.noarch
| texlive-tools-svn26263.0-38.el7.noarch
| texlive-txfonts-svn15878.0-38.el7.noarch
| texlive-type1cm-svn21820.0-38.el7.noarch
| texlive-typehtml-svn17134.0-38.el7.noarch
| texlive-ucs-svn27549.2.1-38.el7.noarch
| texlive-underscore-svn18261.0-38.el7.noarch
| texlive-unicode-math-svn29413.0.7d-38.el7.noarch
| texlive-url-svn16864.3.2-38.el7.noarch
| texlive-utopia-svn15878.0-38.el7.noarch
| texlive-varwidth-svn24104.0.92-38.el7.noarch
| texlive-wasy-svn15878.0-38.el7.noarch
| texlive-wasysym-svn15878.2.0-38.el7.noarch
| texlive-xcolor-svn15878.2.11-38.el7.noarch
| texlive-xdvi-bin-svn26509.0-38.20130427_r30134.el7.x86_64
| texlive-xdvi-svn26689.22.85-38.el7.noarch
| texlive-xkeyval-svn27995.2.6a-38.el7.noarch
| texlive-xunicode-svn23897.0.981-38.el7.noarch
| texlive-zapfchan-svn28614.0-38.el7.noarch
| texlive-zapfding-svn28614.0-38.el7.noarch
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org