* 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 D:/biocbld/1.8d/tmpdir/Rinst794887973
---------- 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 -Id:/biocbld/1.8d/R/include -Wall -O2 -c Rnem_arg.c -o Rnem_arg.o
gcc -Id:/biocbld/1.8d/R/include -Wall -O2 -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 -Id:/biocbld/1.8d/R/include -Wall -O2 -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 -Id:/biocbld/1.8d/R/include -Wall -O2 -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 -Id:/biocbld/1.8d/R/include -Wall -O2 -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 -Id:/biocbld/1.8d/R/include -Wall -O2 -c nem_hlp.c -o nem_hlp.o
gcc -Id:/biocbld/1.8d/R/include -Wall -O2 -c nem_mod.c -o nem_mod.o
gcc -Id:/biocbld/1.8d/R/include -Wall -O2 -c nem_nei.c -o nem_nei.o
gcc -Id:/biocbld/1.8d/R/include -Wall -O2 -c nem_rnd.c -o nem_rnd.o
gcc -Id:/biocbld/1.8d/R/include -Wall -O2 -c nem_ver.c -o nem_ver.o
windres --include-dir d:/biocbld/1.8d/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 -Ld:/biocbld/1.8d/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 d:\biocbld\1.8d\Rpacks\MANOR\chm\MANOR.chm
Compile time: 0 minutes, 0 seconds
20 Topics
119 Local links
20 Internet links
1 Graphic
Created d:\biocbld\1.8d\Rpacks\MANOR\chm\MANOR.chm, 49,293 bytes
Compression decreased file by 59,402 bytes.
preparing package MANOR for lazy loading
adding MD5 sums
* DONE (MANOR)
* creating vignettes ... ERROR
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bibtex vignette
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Starting package installation...
Installation folder: "C:\MiKTex\texmf"
Package repository: "ftp://indian.cse.msu.edu/pub/mirrors/CTAN/systems/win32/miktex/tm/packages/"
DBlight signature: 85efbe718a92aaacce6c6b09bfbcb8a2
Estimating expenditure...
Error: The package
apalike
is unknown.
======================================================================
I couldn't open style file apalike.bst
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: \bibstyle{apalike
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I'm skipping whatever remains of this command
I found no style file---while reading file vignette.aux
(There were 2 error messages)
latex vignette.tex
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.4.2.3)...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (section.5) cvn /H /I...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsection.5.1) cvn ...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (section.6) cvn /H /I...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsection.6.1) cvn ...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsection.6.2) cvn ...
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][2
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.2) cvn H.B /D...
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Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (section.7) cvn /H /I...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsection.7.1) cvn ...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.1.1)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.1.2)...
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Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.1.3)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.1.4)...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsection.7.2) cvn ...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.2.1)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.2.2)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.2.3)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (subsubsection.7.2.4)...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.L end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /Subtype /Link /Dest (section.8) cvn /H /I...
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin 13.6 H.A end<--
Ignoring remaining special text following unknown PS operator: "SDict"
Remainder of line unparsed.
Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.1) cvn H.B...
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Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.R end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
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Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.S end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.R end<--
Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
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Ignoring remaining special text following unknown PS operator: "SDict"
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
<--
][3
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.3) cvn H.B /D...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.2) cvn H.B...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.3) cvn H.B...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.3.1) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.3.1....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section*.2) cvn H....
<--
][4
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.4) cvn H.B /D...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section*.3) cvn H....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.3.1....
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.3.2) cv...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.3.2....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
][5
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.5) cvn H.B /D...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.3.2....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.3.2....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.4) cvn H.B...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.4.1) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
][6
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.6) cvn H.B /D...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.4.2) cv...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.4.2....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /Color [1 0 0] /H /I /Border [0 0 12] /Sub...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.4.2....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.4.2....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.5) cvn H.B...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.5.1) cv...
<--
][7
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.7) cvn H.B /D...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.5.2) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.6) cvn H.B...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.6.1) cv...
<--
][8
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.8) cvn H.B /D...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.6.2) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.7) cvn H.B...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.7.1) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.1....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.1....
<--
][9
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.9) cvn H.B /D...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.1....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.1....
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsection.7.2) cv...
<--
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [
vignette.dvi -> vignette.pdf
/XYZ H.V] /Dest (subsubsection.7.2....
<--
][10
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.10) cvn H.B /...
<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.2....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.2....
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (subsubsection.7.2....
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][11
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Current input buffer is -->begin /product where{pop product(Distiller)search{...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (page.11) cvn H.B /...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin H.R end<--
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Current input buffer is -->begin [ /H /I /Border [0 0 12] /Color [0 1 1] /Act...
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Current input buffer is -->begin H.S end<--
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Current input buffer is -->begin 13.6 H.A end<--
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Current input buffer is -->begin [ /View [/XYZ H.V] /Dest (section.8) cvn H.B...
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]
156275 bytes written
cp vignette.pdf MANOR.pdf
rm -f vignette*
buildVignettes(dir = '.')