* checking for file 'MANOR/DESCRIPTION' ... OK
* preparing 'MANOR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/2.0d/tmpdir/Rinst516473559
---------- Making package MANOR ------------
adding build stamp to DESCRIPTION
making DLL ...
making Rnem_arg.d from Rnem_arg.c
making Rnem_exe.d from Rnem_exe.c
making exememo.d from exememo.c
making lib_io.d from lib_io.c
making nem_alg.d from nem_alg.c
making nem_hlp.d from nem_hlp.c
making nem_mod.d from nem_mod.c
making nem_nei.d from nem_nei.c
making nem_rnd.d from nem_rnd.c
making nem_ver.d from nem_ver.c
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c Rnem_arg.c -o Rnem_arg.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function `nem':
Rnem_exe.c:168: warning: 'tmpV' might be used uninitialized in this function
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c exememo.c -o exememo.o
exememo.c: In function `GenAlloc':
exememo.c:39: warning: long int format, size_t arg (arg 5)
exememo.c:39: warning: long int format, size_t arg (arg 6)
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c lib_io.c -o lib_io.o
lib_io.c: In function `CountLinesColumns':
lib_io.c:354: warning: 'mincols' might be used uninitialized in this function
lib_io.c:354: warning: 'maxcols' might be used uninitialized in this function
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_alg.c -o nem_alg.o
nem_alg.c: In function `ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' might be used uninitialized in this function
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_hlp.c -o nem_hlp.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_mod.c -o nem_mod.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_nei.c -o nem_nei.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_rnd.c -o nem_rnd.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c nem_ver.c -o nem_ver.o
windres --include-dir e:/biocbld/2.0d/R/include -i MANOR_res.rc -o MANOR_res.o
gcc -shared -s -o MANOR.dll MANOR.def Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o MANOR_res.o -Le:/biocbld/2.0d/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'MANOR'
Formats: text html latex example chm
MANOR-internal text html latex chm
arrayTrend text html latex example chm
detectSB text html latex example chm
flag text html latex example chm
flag.arrayCGH text html latex example chm
flag.summary text html latex example chm
flags text html latex example chm
genome.plot text html latex example chm
html.report text html latex example chm
import text html latex example chm
nem text html latex example chm
norm.arrayCGH text html latex example chm
qscore text html latex example chm
qscore.arrayCGH text html latex example chm
qscore.summary text html latex example chm
qscores text html latex example chm
report.plot text html latex example chm
sort.arrayCGH text html latex example chm
spatial text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\2.0d\Rpacks\MANOR\chm\MANOR.chm
Compile time: 0 minutes, 0 seconds
20 Topics
119 Local links
20 Internet links
1 Graphic
Created e:\biocbld\2.0d\Rpacks\MANOR\chm\MANOR.chm, 49,426 bytes
Compression decreased file by 59,497 bytes.
preparing package MANOR for lazy loading
Loading required package: GLAD
adding MD5 sums
* DONE (MANOR)
* creating vignettes ... ERROR
Loading required package: MANOR
Loading required package: GLAD
sed -e 's/\\newcommand{\\htmldoc}{}/\\newcommand{\\htmldoc}\[1\]{}/g' -e '/^\\begin{figure}/d' -e '/^\\end{figure}/d' -e '/^\\caption/d' < MANOR.tex > vignette.tex
latex vignette.tex
This is pdfeTeX, Version 3.141592-1.30.6-2.2 (MiKTeX 2.5)
entering extended mode
(vignette.tex
LaTeX2e <2005/12/01>
Babel and hyphenation patterns for english, dumylang, nohyphenation, ge
rman, ngerman, french, loaded.
("C:\Program Files\MiKTeX 2.5\tex\latex\base\article.cls"
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
("C:\Program Files\MiKTeX 2.5\tex\latex\base\size11.clo"))
("C:\Program Files\MiKTeX 2.5\tex\latex\amsmath\amsmath.sty"
For additional information on amsmath, use the `?' option.
("C:\Program Files\MiKTeX 2.5\tex\latex\amsmath\amstext.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\amsmath\amsgen.sty"))
("C:\Program Files\MiKTeX 2.5\tex\latex\amsmath\amsbsy.sty")
("C:\Program Files\MiKTeX 2.5\tex\latex\amsmath\amsopn.sty"))
("C:\Program Files\MiKTeX 2.5\tex\latex\natbib\natbib.sty") (html.sty)
("C:\Program Files\MiKTeX 2.5\tex\latex\float\float.sty")
("C:\Program Files\MiKTeX 2.5\tex\latex\base\fontenc.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\base\t1enc.def"))
("C:\Program Files\MiKTeX 2.5\tex\latex\graphics\graphicx.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\graphics\keyval.sty")
("C:\Program Files\MiKTeX 2.5\tex\latex\graphics\graphics.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\graphics\trig.sty")
("C:\Program Files\MiKTeX 2.5\tex\latex\00miktex\graphics.cfg")
("C:\Program Files\MiKTeX 2.5\tex\latex\graphics\dvips.def")))
("C:\Program Files\MiKTeX 2.5\tex\latex\ae\ae.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\base\fontenc.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\base\t1enc.def")
("C:\Program Files\MiKTeX 2.5\tex\latex\ae\t1aer.fd")))
("C:\Program Files\MiKTeX 2.5\tex\latex\fancyvrb\fancyvrb.sty"
Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
No file fancyvrb.cfg.
) ("C:\Program Files\MiKTeX 2.5\tex\latex\upquote\upquote.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\base\textcomp.sty"
("C:\Program Files\MiKTeX 2.5\tex\latex\base\ts1enc.def")))
======================================================================
starting package maintenance...
installation directory: "C:\Program Files\MiKTeX 2.5"
package repository: ftp://mirror.icis.pcz.pl/tex-archive/systems/win32/miktex/tm/packages/
DBlight digest: 91cf918982171a72864dc4b6c898f013
going to download 18540 bytes
going to install 5 file(s) (1 package(s))
downloading ftp://mirror.icis.pcz.pl/tex-archive/systems/win32/miktex/tm/packages/cite.cab...
18540 bytes, 1.54 KB/Sec
extracting files from cite.cab...
latex.exe: Windows API error 5: Access is denied.
make: *** [vignette.dvi] Error 1
Error in buildVignettes(dir = ".") : running make failed
Execution halted