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

Fri Apr 24 02:40:25 CEST 2009

On 23/04/2009 8:24 PM, Peter Dunn wrote:
> 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.

You should also have a .log file in the same directory as the .tex file. 
  You probably have a new one now that pdflatex works; please move that 
one aside and run R CMD check again.  If you get a .log file, it should 
list whatever the error was; you could compare it to the .log that 
worked if you can't spot it.  If you don't get a new log, that means R 
CMD check couldn't run pdflatex.

Duncan Murdoch

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