[R] Error building package: LaTeX error when creating PDF version

Peter Dunn PDunn2 at usc.edu.au
Fri Apr 24 02:24:29 CEST 2009


Hi all
 
I am trying to build an R package, which I have successfully done many times before, but have an error I cannot trace.  I hope someone can help me.
 
Here's is some edited output (full output below if it is useful):
 
pdunn2 at PDunnUbuntu:~/DSdata$ R CMD build GLMsData
* checking for file 'GLMsData/DESCRIPTION' ... OK
* preparing 'GLMsData':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GLMsData_0.7.tar.gz'

pdunn2 at PDunnUbuntu:~/DSdata$ R CMD check GLMsData
* checking for working pdflatex ... OK
* using log directory '/home/pdunn2/DSdata/GLMsData.Rcheck'
* using R version 2.9.0 (2009-04-17)

<SNIP: No errors or warnings in sniped bit; everything is OK>
 
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
 
 
So there is an error making the PDf version of the package manual.  That's fine; I am happy to fix it.  But first I need to find it.
 
So I enter the directory GLMsData.Rcheck and find the corresponding tex file for the manual, and run  pdflatex  on this tex file:
 
pdunn2 at PDunnUbuntu:~/DSdata$ cd GLMsData.Rcheck/
pdunn2 at PDunnUbuntu:~/DSdata/GLMsData.Rcheck$ pdflatex GLMsData-manual.tex

<SNIP again; no errors>

Output written on GLMsData-manual.pdf (79 pages, 405091 bytes).
Transcript written on GLMsData-manual.log.
pdunn2 at PDunnUbuntu:~/DSdata/GLMsData.Rcheck$             
 
 
So from what I gather:
* R CMD check  finds an error when using  pdflatex  to make the PDF version of the manual
* But when I manually run  pdflatex  on the tex file, it works OK.
 
Obviously, I am missing something.  Can someone tell me what it is?  I can't find enlightenment on the archives or the manuals.

Thanks everyone.

P.



> sessionInfo()
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods    base





FULL OUTPUT:

pdunn2 at PDunnUbuntu:~/DSdata$ R CMD build GLMsData
* checking for file 'GLMsData/DESCRIPTION' ... OK
* preparing 'GLMsData':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GLMsData_0.7.tar.gz'

pdunn2 at PDunnUbuntu:~/DSdata$ R CMD check GLMsData
* checking for working pdflatex ... OK
* using log directory '/home/pdunn2/DSdata/GLMsData.Rcheck'
* using R version 2.9.0 (2009-04-17)
* using session charset: UTF-8
* checking for file 'GLMsData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GLMsData' version '0.7'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'GLMsData' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
pdunn2 at PDunnUbuntu:~/DSdata$ cd GLMsData.Rcheck/
pdunn2 at PDunnUbuntu:~/DSdata/GLMsData.Rcheck$ pdflatex GLMsData-manual.tex
This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
 %&-line parsing enabled.
entering extended mode
(./GLMsData-manual.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, ukenglish, loaded.

(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/usr/share/texmf/tex/latex/R/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf/tex/latex/R/upquote.sty
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) NOT loading ae
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) NOT loading lmodern
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/etc/texmf/tex/latex/config/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
)
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 315.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 315.

) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
Writing index file GLMsData-manual.idx
(./GLMsData-manual.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty))
(./GLMsData-manual.out) (./GLMsData-manual.out)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./GLMsData-manual.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2])
(/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd)
Underfull \vbox (badness 1014) has occurred while \output is active [3]
[4] [5] [6]
Overfull \hbox (51.62097pt too wide) in paragraph at lines 190--190
\T1/pcr/m/n/10 NorthWest\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Scotland\T1/ptm/m/n/10
, \T1/pcr/m/n/10 SouthEast\T1/ptm/m/n/10 , \T1/pcr/m/n/10 SouthWest\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 Wales\T1/ptm/m/n/10 , \T1/pcr/m/n/10 WestMidlands \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 YorksHumbers
[7] [8]
Overfull \hbox (34.07922pt too wide) in paragraph at lines 270--270
[]\T1/ptm/m/n/10 the cat-tle breed; a fac-tor with lev-els \T1/pcr/m/n/10 Ayrsh
ire\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Canadian\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Guer
nsey\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Holstein-Fresian
[9] [10] [11] [12] [13]
Overfull \hbox (10.57906pt too wide) in paragraph at lines 512--512
[]\T1/ptm/m/n/10 the lo-ca-tion of the plot; a fac-tor with lev-els \T1/pcr/m/n
/10 Bencubbin BindiBindi Gnowangerup
[14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27]
Overfull \vbox (38.56093pt too high) has occurred while \output is active
[28]
Overfull \hbox (0.30684pt too wide) in paragraph at lines 1201--1208
[]\T1/ptm/m/n/10 Brofeldt, Pekka: Bidrag till kaennedom on fiskbe-ston-det i va
ara sjoear. Laen-gel-maevesi. T.H.Jaervi:
[29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
Overfull \hbox (3.58647pt too wide) in paragraph at lines 1644--1644
[]\T1/ptm/m/n/10 the treat-ment method; a fac-tor with lev-els \T1/pcr/m/n/10 A
 \T1/ptm/m/n/10 (open surgery) or \T1/pcr/m/n/10 B \T1/ptm/m/n/10 (per-cu-ta-ne
ous nephrolitho-
[39] [40]
Overfull \hbox (2.34769pt too wide) in paragraph at lines 1725--1729
[]\T1/ptm/m/n/10 The av-er-age in-comes on Long Is-land com-mu-ni-ties in 1979
and 1989, in 1989 US dol-lars. Poospatuck
[41] [42] [43] [44] [45]
Overfull \hbox (10.14717pt too wide) in paragraph at lines 1927--1931
[]\T1/ptm/m/n/10 The orig-i-nal source is: \T1/ptm/m/it/10 Pro-ce-dures and Ana
l-y-ses for Staffing Stan-dards De-vel-op-ment: Data/Regression
[46] [47] [48]
Overfull \hbox (23.06664pt too wide) in paragraph at lines 2090--2093
[]\T1/ptm/m/n/10 Margolin, B. H., Ka-plan, N. and Zeiger, E. (1981). Sta-tis-ti
-cal anal-y-sis of the Ames Salmonella/microsome
[49] [50] [51] [52] [53] [54] [55] [56] [57] [58]
Overfull \hbox (46.54933pt too wide) in paragraph at lines 2514--2514
[]\T1/ptm/m/n/10 the type of ser-vice; al-ways \T1/pcr/m/n/10 Fixed \T1/ptm/m/n
/10 for \T1/pcr/m/n/10 ptransitfixed \T1/ptm/m/n/10 and al-ways \T1/pcr/m/n/10
Demand \T1/ptm/m/n/10 for \T1/pcr/m/n/10 ptransitdemand
[59] [60] [61] [62]
Underfull \vbox (badness 10000) has occurred while \output is active [63]
[64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74]
Overfull \hbox (14.48874pt too wide) in paragraph at lines 3230--3233
[]\T1/ptm/m/n/10 Cancer es-ti-mates from [][]$\T1/pcr/m/n/10 www . amazoncastle
 . com . feminism / action . htm$[][] \T1/ptm/m/n/10 (vis-ited 19 Septem-

Overfull \hbox (0.6288pt too wide) in paragraph at lines 3263--3267
\T1/ptm/m/n/10 mortality and sur-vival. Pub-lished on the in-ter-net [][]$\T1/p
cr/m/n/10 www . health . wa . gov . au / Publications /
[75]
Overfull \hbox (1.66795pt too wide) in paragraph at lines 3290--3290
[]\T1/ptm/m/n/10 the smok-ing sta-tus of the women in the \T1/ptm/m/it/10 orig-
i-nal \T1/ptm/m/n/10 sur-vey; a fac-tor with lev-els \T1/pcr/m/n/10 NonSmoker
[76] [77] [78]
No file GLMsData-manual.ind.
[79] (./GLMsData-manual.aux) )
(see the transcript file for additional information){/usr/share/texmf-texlive/f
onts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmm
i10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/
texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/t
ype1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cms
y7.pfb></usr/share/texmf-texlive/fonts/type1/urw/courier/ucrb8a.pfb></usr/share
/texmf-texlive/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texmf-texlive/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></usr/s
hare/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf-texlive/f
onts/type1/urw/times/utmri8a.pfb>
Output written on GLMsData-manual.pdf (79 pages, 405091 bytes).
Transcript written on GLMsData-manual.log.
pdunn2 at PDunnUbuntu:~/DSdata/GLMsData.Rcheck$             





-- 

Peter Dunn: Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education  ML-34
University of the Sunshine Coast, Locked Bag 4
Maroochydore DC Qld 4558
 
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdunn2 at usc.edu.au
www.usc.edu.au


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