SCM

R Development Page

SciViews log file (build_src)

Thu Aug 18 13:25:52 2016: Building tarball for package SciViews (SVN revision 558)
using R version 3.3.1 Patched (2016-08-17 r71112) ...

* checking for file ‘SciViews/DESCRIPTION’ ... OK
* preparing ‘SciViews’:
* 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 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 79 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/srv/R/R-patched/build.16-08-18/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/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/inconsolata/zi4.sty
`inconsolata-zi4' v1.05, 2014/06/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.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/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/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}] [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4] [5] [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [8]
Overfull \hbox (26.54883pt too wide) in paragraph at lines 428--431
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 

Overfull \hbox (82.86093pt too wide) in paragraph at lines 445--449
\T1/zi4/m/n/10 "everything"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "all.obs"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "complete.obs"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "na.or.compl
ete"\T1/ptm/m/n/10 , or \T1/zi4/m/n/10 "pairwise.complete.obs"\T1/ptm/m/n/10 . 


Overfull \hbox (8.8376pt too wide) in paragraph at lines 460--462
[]\T1/ptm/m/n/10 color of the el-lipse. If \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 (
de-fault), the col-ors will be com-puted us-ing \T1/zi4/m/n/10 cutpoints
[9]
Overfull \hbox (17.14748pt too wide) in paragraph at lines 489--491
[]\T1/ptm/m/n/10 Philippe Gros-jean , wrap-ping code
 in pack-age el-lipse, func-tion \T1/zi4/m/n/10 plotcorr()
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10] [11] [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []\T1/zi4/m/n/10 panel.cor(x, y, use = "everything", method = c("pearson", "ke
ndall", "spearman"),[] 
[15] [16] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17]
Overfull \hbox (18.71768pt too wide) in paragraph at lines 938--940
[]\T1/ptm/m/n/10 further ar-gu-ments to plot func-tions, or func-tions that con
-struct items, like \T1/zi4/m/n/10 density()\T1/ptm/m/n/10 ,

Overfull \hbox (3.72015pt too wide) in paragraph at lines 944--947
[]\T1/ptm/m/n/10 Panel func-tions \T1/zi4/m/n/10 panel.boxplot()\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 panel.density()\T1/ptm/m/n/10 , \T1/zi4/m/n/10 panel.hist() \T
1/ptm/m/n/10 and \T1/zi4/m/n/10 panel.qqnorm() \T1/ptm/m/n/10 should
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18] [19]
Overfull \hbox (26.54883pt too wide) in paragraph at lines 1065--1068
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 

Overfull \hbox (8.02902pt too wide) in paragraph at lines 1074--1076
[]\T1/ptm/m/n/10 either \T1/zi4/m/n/10 "svd" \T1/ptm/m/n/10 (the func-tion uses
 [][]\T1/zi4/m/n/10 prcomp[][][]\T1/ptm/m/n/10 ), or \T1/zi4/m/n/10 "eigen" \T1
/ptm/m/n/10 (the func-tion uses \T1/zi4/m/n/10 princomp\T1/ptm/m/n/10 ),
[20] [21] [22] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
No file Rd2.ind.
[25] (./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.loadings} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.princomp} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.biplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.prcomp} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.qqnorm} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hist} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.density} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.smooth} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.test} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.lm} has been referenced but does not exist, rep
laced by a fixed one

pdfTeX warning (dest): name{Rfn.pairs} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.log} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.plotcorr} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.wt} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov2cor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.symnum} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.omit} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.fail} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.options} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.frame} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.colorRampPalette} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cm.colors} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.palette} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hsv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.character} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cat} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.strtoi} has been referenced but does not exist,
 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}
Output written on Rd2.pdf (25 pages, 123626 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015/dev] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (209 entries accepted, 0 rejected).
Sorting entries.....done (1741 comparisons).
Generating output file Rd2.ind....done (363 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 79 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/srv/R/R-patched/build.16-08-18/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/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/inconsolata/zi4.sty
`inconsolata-zi4' v1.05, 2014/06/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.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/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/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/li
b/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Underfull \vbox (badness 10000) has occurred while \output is active [4]
[5] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (26.54883pt too wide) in paragraph at lines 428--431
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 
[8]
Overfull \hbox (82.86093pt too wide) in paragraph at lines 445--449
\T1/zi4/m/n/10 "everything"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "all.obs"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "complete.obs"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "na.or.compl
ete"\T1/ptm/m/n/10 , or \T1/zi4/m/n/10 "pairwise.complete.obs"\T1/ptm/m/n/10 . 


Overfull \hbox (8.8376pt too wide) in paragraph at lines 460--462
[]\T1/ptm/m/n/10 color of the el-lipse. If \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 (
de-fault), the col-ors will be com-puted us-ing \T1/zi4/m/n/10 cutpoints

Overfull \hbox (17.14748pt too wide) in paragraph at lines 489--491
[]\T1/ptm/m/n/10 Philippe Gros-jean , wrap-ping code
 in pack-age el-lipse, func-tion \T1/zi4/m/n/10 plotcorr()
[9] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
Underfull \vbox (badness 10000) has occurred while \output is active [11]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []\T1/zi4/m/n/10 panel.cor(x, y, use = "everything", method = c("pearson", "ke
ndall", "spearman"),[] 
[14] [15] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
Overfull \hbox (18.71768pt too wide) in paragraph at lines 938--940
[]\T1/ptm/m/n/10 further ar-gu-ments to plot func-tions, or func-tions that con
-struct items, like \T1/zi4/m/n/10 density()\T1/ptm/m/n/10 ,

Overfull \hbox (3.72015pt too wide) in paragraph at lines 944--947
[]\T1/ptm/m/n/10 Panel func-tions \T1/zi4/m/n/10 panel.boxplot()\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 panel.density()\T1/ptm/m/n/10 , \T1/zi4/m/n/10 panel.hist() \T
1/ptm/m/n/10 and \T1/zi4/m/n/10 panel.qqnorm() \T1/ptm/m/n/10 should
[17] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (26.54883pt too wide) in paragraph at lines 1065--1068
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 

Overfull \hbox (8.02902pt too wide) in paragraph at lines 1074--1076
[]\T1/ptm/m/n/10 either \T1/zi4/m/n/10 "svd" \T1/ptm/m/n/10 (the func-tion uses
 [][]\T1/zi4/m/n/10 prcomp[][][]\T1/ptm/m/n/10 ), or \T1/zi4/m/n/10 "eigen" \T1
/ptm/m/n/10 (the func-tion uses \T1/zi4/m/n/10 princomp\T1/ptm/m/n/10 ),
[19] [20] [21] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24] (./Rd2.ind
[25]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 26.

[26] [27] [28]) (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.loadings} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.princomp} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.biplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.prcomp} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.qqnorm} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hist} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.density} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.smooth} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.test} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.lm} has been referenced but does not exist, rep
laced by a fixed one

pdfTeX warning (dest): name{Rfn.pairs} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.log} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.plotcorr} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.wt} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov2cor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.symnum} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.omit} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.fail} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.options} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.frame} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.colorRampPalette} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cm.colors} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.palette} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hsv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.character} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cat} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.strtoi} has been referenced but does not exist,
 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}
Output written on Rd2.pdf (28 pages, 144028 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2015/dev] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (209 entries accepted, 0 rejected).
Sorting entries.....done (1738 comparisons).
Generating output file Rd2.ind....done (365 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 79 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/srv/R/R-patched/build.16-08-18/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/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/inconsolata/zi4.sty
`inconsolata-zi4' v1.05, 2014/06/22 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.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/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/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/li
b/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Underfull \vbox (badness 10000) has occurred while \output is active [4]
[5] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (26.54883pt too wide) in paragraph at lines 428--431
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 
[8]
Overfull \hbox (82.86093pt too wide) in paragraph at lines 445--449
\T1/zi4/m/n/10 "everything"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "all.obs"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "complete.obs"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "na.or.compl
ete"\T1/ptm/m/n/10 , or \T1/zi4/m/n/10 "pairwise.complete.obs"\T1/ptm/m/n/10 . 


Overfull \hbox (8.8376pt too wide) in paragraph at lines 460--462
[]\T1/ptm/m/n/10 color of the el-lipse. If \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 (
de-fault), the col-ors will be com-puted us-ing \T1/zi4/m/n/10 cutpoints

Overfull \hbox (17.14748pt too wide) in paragraph at lines 489--491
[]\T1/ptm/m/n/10 Philippe Gros-jean , wrap-ping code
 in pack-age el-lipse, func-tion \T1/zi4/m/n/10 plotcorr()
[9] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
Underfull \vbox (badness 10000) has occurred while \output is active [11]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786
 []\T1/zi4/m/n/10 panel.cor(x, y, use = "everything", method = c("pearson", "ke
ndall", "spearman"),[] 
[14] [15] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
Overfull \hbox (18.71768pt too wide) in paragraph at lines 938--940
[]\T1/ptm/m/n/10 further ar-gu-ments to plot func-tions, or func-tions that con
-struct items, like \T1/zi4/m/n/10 density()\T1/ptm/m/n/10 ,

Overfull \hbox (3.72015pt too wide) in paragraph at lines 944--947
[]\T1/ptm/m/n/10 Panel func-tions \T1/zi4/m/n/10 panel.boxplot()\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 panel.density()\T1/ptm/m/n/10 , \T1/zi4/m/n/10 panel.hist() \T
1/ptm/m/n/10 and \T1/zi4/m/n/10 panel.qqnorm() \T1/ptm/m/n/10 should
[17] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (26.54883pt too wide) in paragraph at lines 1065--1068
\T1/ptm/m/n/10 the for-mula \T1/zi4/m/n/10 formula\T1/ptm/m/n/10 . By de-fault 
the vari-ables are taken from \T1/zi4/m/n/10 environment(formula)\T1/ptm/m/n/10
 . 

Overfull \hbox (8.02902pt too wide) in paragraph at lines 1074--1076
[]\T1/ptm/m/n/10 either \T1/zi4/m/n/10 "svd" \T1/ptm/m/n/10 (the func-tion uses
 [][]\T1/zi4/m/n/10 prcomp[][][]\T1/ptm/m/n/10 ), or \T1/zi4/m/n/10 "eigen" \T1
/ptm/m/n/10 (the func-tion uses \T1/zi4/m/n/10 princomp\T1/ptm/m/n/10 ),
[19] [20] [21] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24] (./Rd2.ind
[25]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 26.

[26] [27] [28]) (./Rd2.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.loadings} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.princomp} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.biplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.prcomp} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.qqnorm} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hist} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.density} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.smooth} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.test} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.lm} has been referenced but does not exist, rep
laced by a fixed one

pdfTeX warning (dest): name{Rfn.pairs} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coplot} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.log} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.plotcorr} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.wt} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov2cor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.symnum} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.omit} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.na.fail} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.options} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.frame} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.colorRampPalette} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cm.colors} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.par} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.palette} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.hsv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.character} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cat} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.strtoi} has been referenced but does not exist,
 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}
Output written on Rd2.pdf (28 pages, 144424 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpaRAsTE/Rbuild322a7e88b164/SciViews/build/SciViews.pdf’ ...
Done
* creating vignettes ... OK
* compacting vignettes and other PDF files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘SciViews_0.9-12.tar.gz’

Run time: 9.77 seconds.
Thanks to:
Vienna University of Economics and Business Powered By FusionForge