Browse code

replace reference to texi2dvi with pdflatex as the former has been removed from MikTex

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112478 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 12/01/2016 20:52:19
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@@ -7,8 +7,8 @@ vignettes: AffyGW.tex
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 	cp ../inst/scripts/Infrastructure.pdf .
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 	cp ../inst/scripts/gtypeDownstream.pdf .
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 	cp ../inst/scripts/crlmmIllumina.pdf .
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-	"$(R_HOME)/bin/R" CMD texi2dvi --pdf genotyping.tex
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-	"$(R_HOME)/bin/R" CMD texi2dvi --pdf CopyNumberOverview.tex
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+	"$(R_HOME)/bin/R" CMD pdflatex genotyping.tex
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+	"$(R_HOME)/bin/R" CMD pdflatex CopyNumberOverview.tex
12 12
 
13 13
 clean:
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 	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
Browse code

run texi2dvi with R CMD to avoid windows build error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72377 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 08/01/2013 20:00:26
Showing1 changed files
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@@ -7,8 +7,8 @@ vignettes: AffyGW.tex
7 7
 	cp ../inst/scripts/Infrastructure.pdf .
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 	cp ../inst/scripts/gtypeDownstream.pdf .
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 	cp ../inst/scripts/crlmmIllumina.pdf .
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-	texi2dvi --pdf genotyping.tex
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-	texi2dvi --pdf CopyNumberOverview.tex
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+	"$(R_HOME)/bin/R" CMD texi2dvi --pdf genotyping.tex
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+	"$(R_HOME)/bin/R" CMD texi2dvi --pdf CopyNumberOverview.tex
12 12
 
13 13
 clean:
14 14
 	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
Browse code

merge collab branch

* collab:
update vignettes/Makefile
update .gitignore
update table in CopyNumberViewiew
bump dependency on oligoClasses version
Update alias for "[" method for PredictionRegion objects
Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch. The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:49:34
Showing1 changed files
... ...
@@ -7,6 +7,8 @@ vignettes: AffyGW.tex
7 7
 	cp ../inst/scripts/Infrastructure.pdf .
8 8
 	cp ../inst/scripts/gtypeDownstream.pdf .
9 9
 	cp ../inst/scripts/crlmmIllumina.pdf .
10
+	texi2dvi --pdf genotyping.tex
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+	texi2dvi --pdf CopyNumberOverview.tex
10 12
 
11 13
 clean:
12 14
 	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
Browse code

don't need to call texi2dvi explicitly in Makefile, plus it doesn't work in Windows

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@70209 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 04/10/2012 22:30:56
Showing1 changed files
... ...
@@ -7,8 +7,6 @@ vignettes: AffyGW.tex
7 7
 	cp ../inst/scripts/Infrastructure.pdf .
8 8
 	cp ../inst/scripts/gtypeDownstream.pdf .
9 9
 	cp ../inst/scripts/crlmmIllumina.pdf .
10
-	texi2dvi --pdf genotyping.tex
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-	texi2dvi --pdf CopyNumberOverview.tex
12 10
 
13 11
 clean:
14 12
 	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
Browse code

Merge branch 'collab'

* collab:
Update AffyGW.pdf and IlluminaPreprocessCN.pdf
crlmmIlluminaV2 calls crlmmGT. comment call to crlmmGT2
Update AffyGW vignette to step through construction of CNSet, normalization, and genotyping
v 1.15.27: Fix bug in crlmmGT2. clean up comments in crlmmIllumina.
update getFeatureData

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69561 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/09/2012 12:31:51
Showing1 changed files
... ...
@@ -6,6 +6,7 @@ vignettes: AffyGW.tex
6 6
 	cp ../inst/scripts/IlluminaPreprocessCN.pdf .
7 7
 	cp ../inst/scripts/Infrastructure.pdf .
8 8
 	cp ../inst/scripts/gtypeDownstream.pdf .
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+	cp ../inst/scripts/crlmmIllumina.pdf .
9 10
 	texi2dvi --pdf genotyping.tex
10 11
 	texi2dvi --pdf CopyNumberOverview.tex
11 12
 
Browse code

Merge branch 'collab'

* collab:
fixing vignettes dir
fixing vignettes dir
removing old vignettes
removing old vignettes
Adding GGdata to suggests
Fixed vignette for genotyping + association; Moved oligoClasses back to Depends b/c final users do need access to calls()/confs() when using crlmm()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64350 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 17:35:35
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new file mode 100644
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@@ -0,0 +1,13 @@
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+All: vignettes clean
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+
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+## all pdfs must be generated from the first target of the Makefile
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+vignettes: AffyGW.tex
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+	cp ../inst/scripts/AffyGW.pdf .
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+	cp ../inst/scripts/IlluminaPreprocessCN.pdf .
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+	cp ../inst/scripts/Infrastructure.pdf .
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+	cp ../inst/scripts/gtypeDownstream.pdf .
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+	texi2dvi --pdf genotyping.tex
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+	texi2dvi --pdf CopyNumberOverview.tex
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+
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+clean:
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+	-$(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex