From a09ae123bb910d1a8e36a20ceddc4345c1f57b23 Mon Sep 17 00:00:00 2001
From: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
Date: Tue, 12 May 2020 14:43:59 +0200
Subject: [PATCH 1/2] use git clean for Makefile target clean, remove target
 superclean.  Fixes #104

---
 Makefile | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/Makefile b/Makefile
index d68a72b18..41279a47b 100644
--- a/Makefile
+++ b/Makefile
@@ -3,25 +3,11 @@ all: roxygenize pkg-data pkg-doc vignettes pkg-vignettes | fileio-tests
 DATE = $(shell date +%Y%m%d)
 
 clean:
-	@rm -f *~ .*~ \#*\#
-	@rm -f hyperSpec_*.tar.gz
-	@rm -rf hyperSpec.Rcheck
-	$(MAKE) -C Vignettes/baseline     clean
-	$(MAKE) -C Vignettes/chondro      clean
-	$(MAKE) -C Vignettes/fileio       clean
-	$(MAKE) -C Vignettes/flu          clean
-	$(MAKE) -C Vignettes/hyperspec clean
-	$(MAKE) -C Vignettes/laser        clean
-	$(MAKE) -C Vignettes/plotting     clean
-	$(MAKE) -C hyperSpec/inst/doc     clean
-	$(MAKE) -C hyperSpec/vignettes -f Makefile-local clean
-
-superclean:
-	@git clean -q -f -x -d
+	@git clean -q -f -x -d  --exclude .Rproj.user/ --exclude hyperSpec.Rproj
 
 # TODO: add dependency `clean`
 
-## bootstrap target does the required processing immediately after cloning, superclean, or
+## bootstrap target does the required processing immediately after cloning, clean, or
 ## if the installed version of hyperSpec is too old for building the vignettes
 
 bootstrap: installdeps bootstrapI chondro flu laser pkg-data | fileio-tests

From b0a78a3ab9d7527809d84b5192f7b42f8eb3267c Mon Sep 17 00:00:00 2001
From: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
Date: Tue, 12 May 2020 15:33:39 +0200
Subject: [PATCH 2/2] fix Makefiles for make bootstrap

---
 Makefile                           | 6 +++---
 hyperSpec/vignettes/Makefile-local | 3 +++
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 41279a47b..6d66ca16c 100644
--- a/Makefile
+++ b/Makefile
@@ -10,10 +10,10 @@ clean:
 ## bootstrap target does the required processing immediately after cloning, clean, or
 ## if the installed version of hyperSpec is too old for building the vignettes
 
-bootstrap: installdeps bootstrapI chondro flu laser pkg-data | fileio-tests
+bootstrap: installdeps pkg-data bootstrapI chondro flu laser  | fileio-tests
 	@R CMD build --no-build-vignettes hyperSpec/
 	@R CMD INSTALL hyperSpec_*-$(DATE).tar.gz
-	$(MAKE) -C hyperspec/vignettes -f Makefile-local
+	$(MAKE) -C hyperSpec/vignettes -f Makefile-local
 
 bootstrapI: roxygenize
 	@R CMD build --no-build-vignettes hyperSpec/
@@ -97,7 +97,7 @@ flu:
 
 hyperspec:
 	$(MAKE) -C Vignettes/hyperspec
-	$(MAKE) -C hyperSpec/vignettes -f Makefile-local hyperspec.Rnw
+	$(MAKE) -C hyperSpec/vignettes -f Makefile-local all
 
 # laser ............................................................................................
 
diff --git a/hyperSpec/vignettes/Makefile-local b/hyperSpec/vignettes/Makefile-local
index e5ef4fff0..9953efe03 100644
--- a/hyperSpec/vignettes/Makefile-local
+++ b/hyperSpec/vignettes/Makefile-local
@@ -50,6 +50,9 @@ rawdata:
 
 # hyperspec vignette (aka introduction)
 
+../../Vignettes/hyperspec/strukturhyperspec.pdf:
+	@$(MAKE) -C ../../Vignettes/hyperspec strukturhyperspec.pdf
+
 hyperspec.Rnw: ../../Vignettes/hyperspec/hyperspec.Rnw ../../Vignettes/hyperspec/strukturhyperspec.pdf \
                   ../../Vignettes/hyperspec/functions.RData ../../Vignettes/hyperspec/hyperspec.bib
 	cp -av $^ ./