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M. Jankowski

2007-Jun-20 02:23 UTC

[R] Help With Sweave:

Hi All,

I am running Ubuntu Feisty (7.04) on a Thinkpad T41. I've installed
the nowebm package for Ubuntu. Working from this HowTo:
http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw
I try to compile the example *.Snw as in the Sweave manual:

mdj at lapmdj:~/Desktop/Sweave/example1$ noweb example-1.Snw
Can't open output file

Despite the error, a *.tex file is produced. Now I am stuck because I
cannot seem to get the CTAN noweb package correctly installed  for my
Latex installation. I guess I am somewhat spoiled by the Synaptic
package manager. Here is the result of my best attempt to get the
noweb package installed:

Following the guidelines for installing packages found here:

http://www.ctan.org/tex-archive/info/beginlatex/html/chapter5.html#pk...

I try to install this package:

http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=noweb

But there are no *.ins or *.dtx files. There is a *.sty though...

I follow the instructions in the readme and this is the result (Here
are a few of the errors, the complete output is below):
make: [install-shell] Error 1 (ignored)
make: [install-tex] Error 1 (ignored)
make: [install-code] Error 1 (ignored)

A bunch of errors. What am I doing wrong? Any help is much
appreciated!

Of course, if there is a better place for me to ask this question
please let me know where! Thanks!

Matt

mdj at lapmdj:~/downloads/noweb-2.11b/src$ sudo make all install
cd c; make "CC=gcc -ansi -pedantic" "CFLAGS=" all
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/c'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/c'
for i in shell lib xdoc tex; do (cd $i; make all); done
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/
shell'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/shell'
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/lib'
chmod +x unmarkup emptydefn toascii nwmtime pipedocs h2a btdefn
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/lib'
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/xdoc'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/xdoc'
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/tex'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/tex'
cd awk; make "ICONT=icont" "ICONC=iconc" all
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/awk'
chmod +x noindex  totex noidx tohtml
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/awk'
mkdir /usr/local/noweb /usr/local/noweb/lib 2>/dev/null
make: [install-shell] Error 1 (ignored)
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/noweb >
/usr/local/noweb/
noweb
chmod +x /usr/local/noweb/noweb
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/notangle > /usr/local/
noweb/notangle
chmod +x /usr/local/noweb/notangle
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/noweave             >
/
usr/local/noweb/noweave
chmod +x /usr/local/noweb/noweave
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/nountangle >
/usr/local/
noweb/nountangle
chmod +x /usr/local/noweb/nountangle
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/nodefs >
/usr/local/noweb/
nodefs
chmod +x /usr/local/noweb/nodefs
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/noroots > /usr/local/
noweb/noroots
chmod +x /usr/local/noweb/noroots
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/nuweb2noweb >
/usr/local/
noweb/nuweb2noweb
chmod +x /usr/local/noweb/nuweb2noweb
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/cpif >
/usr/local/noweb/
cpif
chmod +x /usr/local/noweb/cpif
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/htmltoc > /usr/local/
noweb/htmltoc
chmod +x /usr/local/noweb/htmltoc
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/noroff >
/usr/local/noweb/
noroff
chmod +x /usr/local/noweb/noroff
sed "s@|LIBDIR|@/usr/local/noweb/lib@" shell/toroff >
/usr/local/noweb/
lib/toroff
chmod +x /usr/local/noweb/lib/toroff
cp shell/tmac.w /usr/local/noweb/lib
mkdir /usr/local/noweb /usr/local/noweb/lib 2>/dev/null
make: [install-code] Error 1 (ignored)
strip c/nt c/markup c/mnt c/finduses
cp c/nt c/markup c/mnt c/finduses /usr/local/noweb/lib
cd awk; make ICONT=icont ICONC=iconc LIB=/usr/local/noweb/lib BIN=/usr/
local/noweb install
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/awk'
chmod +x noindex  totex noidx tohtml
cp totex noidx tohtml /usr/local/noweb/lib
cp noindex  /usr/local/noweb
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/awk'
cd lib; make LIB=/usr/local/noweb/lib install
make[1]: Entering directory `/home/mdj/downloads/noweb-2.11b/src/lib'
chmod +x unmarkup emptydefn toascii nwmtime pipedocs h2a btdefn
cp unmarkup emptydefn toascii nwmtime h2a btdefn /usr/local/noweb/lib
sed 's@|LIBDIR|@/usr/local/noweb/lib at g' pipedocs >
/usr/local/noweb/
lib/pipedocs
chmod +x /usr/local/noweb/lib/pipedocs
make[1]: Leaving directory `/home/mdj/downloads/noweb-2.11b/src/lib'
mkdir /usr/local/noweb/man /usr/local/noweb/man/man1 /usr/local/noweb/
man/man7 2>/dev/null
make: [install-man] Error 1 (ignored)
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/cpif.1 > /usr/local/noweb/man/man1/cpif.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/nodefs.1 > /usr/local/noweb/man/man1/nodefs.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/noroots.1 > /usr/local/noweb/man/man1/noroots.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/noweb.1 > /usr/local/noweb/man/man1/noweb.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/noindex.1 > /usr/local/noweb/man/man1/noindex.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/nuweb2noweb.1 > /usr/local/noweb/man/man1/
nuweb2noweb.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/notangle.1 > /usr/local/noweb/man/man1/notangle.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/noroff.1 > /usr/local/noweb/man/man1/noroff.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/sl2h.1 > /usr/local/noweb/man/man1/sl2h.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/htmltoc.1 > /usr/local/noweb/man/man1/htmltoc.1
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/nowebstyle.7 > /usr/local/noweb/man/man7/nowebstyle.
7
sed -e "s@|LIBDIR|@/usr/local/noweb/lib@" -e
"s@|TEXINPUTS|@/usr/local/
tex/inputs@" xdoc/nowebfilters.7 > /usr/local/noweb/man/man7/
nowebfilters.7
rm -f /usr/local/noweb/man/man1/noweave.1
(cd /usr/local/noweb/man/man1; ln notangle.1 noweave.1)
rm -f /usr/local/noweb/man/man1/nountangle.1
(cd /usr/local/noweb/man/man1; ln notangle.1 nountangle.1)
mkdir /usr/local/tex/inputs 2>/dev/null
make: [install-tex] Error 1 (ignored)
cp tex/nwmac.tex tex/noweb.sty /usr/local/tex/inputs
texhash || echo "Program texhash not found or failed"
no
texhash: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
texhash: Updating /var/lib/texmf/ls-R-TEXMFDIST-TETEX...
texhash: Updating /var/lib/texmf/ls-R...
texhash: Done.
mkdir /dev/null 2>/dev/null
make: [install-elisp] Error 1 (ignored)
cp elisp/noweb-mode.el /dev/null
mdj at lapmdj:~/downloads/noweb-2.11b/src$ texhash
texhash: /var/lib/texmf/ls-R-TEXMFMAIN: no write permission.
Skipping...
texhash: /var/lib/texmf/ls-R-TEXMFDIST-TETEX: no write permission.
Skipping...
texhash: /var/lib/texmf/ls-R: no write permission. Skipping...
texhash: Done.
mdj at lapmdj:~/downloads/noweb-2.11b/src$ sudo texhash
no
texhash: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
texhash: Updating /var/lib/texmf/ls-R-TEXMFDIST-TETEX...
texhash: Updating /var/lib/texmf/ls-R...
texhash: Done.
mdj at lapmdj:~/downloads/noweb-2.11b/src$ cd /var/lib/texmf/
mdj at lapmdj:/var/lib/texmf$ ls
fonts  ls-R  ls-R-TEXMFDIST-TETEX  ls-R-TEXMFMAIN  tex  web2c
mdj at lapmdj:/var/lib/texmf$ texhash
texhash: /var/lib/texmf/ls-R-TEXMFMAIN: no write permission.
Skipping...
texhash: /var/lib/texmf/ls-R-TEXMFDIST-TETEX: no write permission.
Skipping...
texhash: /var/lib/texmf/ls-R: no write permission. Skipping...
texhash: Done.
mdj at lapmdj:/var/lib/texmf$ sudo texhash
no
texhash: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
texhash: Updating /var/lib/texmf/ls-R-TEXMFDIST-TETEX...
texhash: Updating /var/lib/texmf/ls-R...
texhash: Done.
mdj at lapmdj:/var/lib/texmf$

I thought that 'sudo texhash' would fix the installation error...but
apparently it did not because:

mdj at lapmdj:~/Desktop/Sweave/example1$ pdflatex example-1.tex
This is pdfeTeX, Version 3.141592-1.30.5-2.2 (Web2C 7.5.5)
entering extended mode
(./example-1.tex
LaTeX2e <2003/12/01>
Babel <v3.8g> and hyphenation patterns for english, usenglishmax,
dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (./
example-1.aux)
! Undefined control sequence.
l.13 \nwfilename
                {example-1.Snw}
\nwbegincode{1}\sublabel{NW3jPyRy-0-1}\nwmarg...

?
#Which apparently means that the noweb package has not yet been
installed correctly. What is going wrong?

Dirk Eddelbuettel

2007-Jun-20 02:44 UTC

head link

[R] Help With Sweave:

Matt,

On 19 June 2007 at 21:23, M. Jankowski wrote:
| Hi All,
| 
| I am running Ubuntu Feisty (7.04) on a Thinkpad T41. I've installed
| the nowebm package for Ubuntu. Working from this HowTo:
| http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw
| I try to compile the example *.Snw as in the Sweave manual:
| 
| mdj at lapmdj:~/Desktop/Sweave/example1$ noweb example-1.Snw
| Can't open output file
| 
| Despite the error, a *.tex file is produced. Now I am stuck because I
| cannot seem to get the CTAN noweb package correctly installed  for my
| Latex installation. I guess I am somewhat spoiled by the Synaptic
| package manager. Here is the result of my best attempt to get the
| noweb package installed:

i)   No external noweb package is needed
ii)  Synaptic is not used to install CRAN / CTAN packages
iii) Everything should be provided by r-base-core and tetex-extra.

Since relatively recently, a 'Sweave' command has been added.  So simply
do

	$ R CMD Sweave example-1.Snw 
	$ pdflatex example-1.tex
	$ kpdf example-1.pdf		# or xpdf, or gv, or ...

| A bunch of errors. What am I doing wrong? Any help is much
| appreciated!

You simply make your life too complicated when Debian and Ubuntu make it
easier for you :)

| Of course, if there is a better place for me to ask this question
| please let me know where! Thanks!

The r-sig-debian list is appropriate for problems with Debian / Ubuntu.

Dirk

PS  I usually use simple shell wrappers like this one. Others prefer
Makefile. 


edd at basebud:~> cat /home/edd/bin/sweave
#!/bin/bash -e

function errorexit () {
    echo "Error: $1"
    exit 1
}

function filetest () {
    if [ ! -f $1 ]; then
       errorexit "File $1 not found"
    fi
    return 0
}


if [ "$#" -lt 1 ]; then
    errorexit "Need to specify argument file"
fi


BASENAME=$(basename $1 .Rnw)

RNWFILE=$BASENAME.Rnw
filetest $RNWFILE
echo "library(tools); Sweave(\"$RNWFILE\")" \
      | R --no-save --no-restore --slave

LATEXFILE=$BASENAME.tex
filetest $LATEXFILE && pdflatex $LATEXFILE

PDFFILE=$BASENAME.pdf
#filetest $PDFFILE && acroread $PDFFILE &
#filetest $PDFFILE && xpdf $PDFFILE &
filetest $PDFFILE && kpdf $PDFFILE &


-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison

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