Makefile for R packages

Makefile

R_TIMING=_R_CHECK_TIMINGS_=0 /usr/bin/time
R_VER=3.4.x
R_CHECK_ARGS=--timings
## --no-codoc --no-examples --no-vignettes
## --codoc
R_BUILD_ARGS=--no-build-vignettes

R_INSTALL_ARGS=

###
bioc:
	rm -Rf tutorial.450k/inst
	R-3.2.x CMD build tutorial.450k
	tar xvzf tutorial.450k_0.1.tar.gz tutorial.450k/inst/doc/methylation450k.html

##############
base_minfi: minfi
ifneq (,$(wildcard minfi/DESCRIPTION))
minfi_VERSION:=$(shell grep ^Version minfi/DESCRIPTION | sed 's_Version: __')
endif

build_minfi: base_minfi
	rm -Rf minfi/inst/doc
	R-$(R_VER) CMD build $(R_BUILD_ARGS) minfi

check_minfi: build_minfi
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) minfi_$(minfi_VERSION).tar.gz

bioccheck_minfi: build_minfi
	$(R_TIMING) R-$(R_VER) CMD BiocCheck minfi_$(minfi_VERSION).tar.gz

install_minfi: build_minfi
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) minfi_$(minfi_VERSION).tar.gz

system_install_minfi: build_minfi
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"minfi_$(minfi_VERSION).tar.gz\") }"

vignette_minfi: base_minfi
	rm -Rf minfi/inst/doc
	R-$(R_VER) CMD build minfi
	tar xvzf minfi_$(minfi_VERSION).tar.gz minfi/inst/doc/minfi.pdf
	open minfi/inst/doc/minfi.pdf

open_vignette_minfi:
	tar xvzf minfi_$(minfi_VERSION).tar.gz minfi/inst/doc/minfi.pdf
	open minfi/inst/doc/minfi.pdf


##############
base_gsvdData: gsvdData
ifneq (,$(wildcard gsvdData/DESCRIPTION))
gsvdData_VERSION:=$(shell grep ^Version gsvdData/DESCRIPTION | sed 's_Version: __')
endif

build_gsvdData: base_gsvdData
	R-$(R_VER) CMD build $(R_BUILD_ARGS) gsvdData

check_gsvdData: build_gsvdData
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) gsvdData_$(gsvdData_VERSION).tar.gz

install_gsvdData: build_gsvdData
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) gsvdData_$(gsvdData_VERSION).tar.gz

system_install_gsvdData: build_gsvdData
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"gsvdData_$(gsvdData_VERSION).tar.gz\") }"

##############

base_biocMultiAssay: biocMultiAssay
ifneq (,$(wildcard biocMultiAssay/DESCRIPTION))
biocMultiAssay_VERSION:=$(shell grep ^Version biocMultiAssay/DESCRIPTION | sed 's_Version: __')
endif

build_biocMultiAssay: base_biocMultiAssay
	R-$(R_VER) CMD build $(R_BUILD_ARGS) biocMultiAssay

check_biocMultiAssay: build_biocMultiAssay
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) biocMultiAssay_$(biocMultiAssay_VERSION).tar.gz

install_biocMultiAssay: build_biocMultiAssay
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) biocMultiAssay_$(biocMultiAssay_VERSION).tar.gz

system_install_biocMultiAssay: build_biocMultiAssay
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"biocMultiAssay_$(biocMultiAssay_VERSION).tar.gz\") }"

##############

base_massay: massay
ifneq (,$(wildcard massay/DESCRIPTION))
massay_VERSION:=$(shell grep ^Version massay/DESCRIPTION | sed 's_Version: __')
endif

build_massay: base_massay
	R-$(R_VER) CMD build $(R_BUILD_ARGS) massay

check_massay: build_massay
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) massay_$(massay_VERSION).tar.gz

install_massay: build_massay
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) massay_$(massay_VERSION).tar.gz

system_install_massay: build_massay
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"massay_$(massay_VERSION).tar.gz\") }"

###################


base_minfiData: minfiData
ifneq (,$(wildcard minfiData/DESCRIPTION))
minfiData_VERSION:=$(shell grep ^Version minfiData/DESCRIPTION | sed 's_Version: __')
endif

build_minfiData: base_minfiData
	R-$(R_VER) CMD build $(R_BUILD_ARGS) minfiData

check_minfiData: build_minfiData
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) minfiData_$(minfiData_VERSION).tar.gz

install_minfiData: build_minfiData
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) minfiData_$(minfiData_VERSION).tar.gz

##############
base_bumphunter: bumphunter
ifneq (,$(wildcard bumphunter/DESCRIPTION))
bumphunter_VERSION:=$(shell grep ^Version bumphunter/DESCRIPTION | sed 's_Version: __')
endif

build_bumphunter: base_bumphunter
	R-$(R_VER) CMD build $(R_BUILD_ARGS) bumphunter

check_bumphunter: build_bumphunter
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) bumphunter_$(bumphunter_VERSION).tar.gz

install_bumphunter: build_bumphunter
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) bumphunter_$(bumphunter_VERSION).tar.gz

system_install_bumphunter: build_bumphunter
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"bumphunter_$(bumphunter_VERSION).tar.gz\") }"

##############
base_cqn:
ifneq (,$(wildcard cqn/DESCRIPTION))
cqn_VERSION:=$(shell grep ^Version cqn/DESCRIPTION | sed 's_Version: __')
endif

build_cqn: base_cqn
	R-$(R_VER) CMD build $(R_BUILD_ARGS) cqn

check_cqn: build_cqn
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) cqn_$(cqn_VERSION).tar.gz

install_cqn: build_cqn
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) cqn_$(cqn_VERSION).tar.gz

##############
base_Rgraphviz: Rgraphviz
ifneq (,$(wildcard Rgraphviz/DESCRIPTION))
Rgraphviz_VERSION:=$(shell grep ^Version Rgraphviz/DESCRIPTION | sed 's_Version: __')
endif

build_Rgraphviz: base_Rgraphviz
	R-$(R_VER) CMD build $(R_BUILD_ARGS) Rgraphviz

check_Rgraphviz: build_Rgraphviz
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) Rgraphviz_$(Rgraphviz_VERSION).tar.gz

install_Rgraphviz: build_Rgraphviz
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) Rgraphviz_$(Rgraphviz_VERSION).tar.gz

##############
base_bsseq: bsseq
ifneq (,$(wildcard bsseq/DESCRIPTION))
bsseq_VERSION:=$(shell grep ^Version bsseq/DESCRIPTION | sed 's_Version: __')
endif

build_bsseq: base_bsseq
	rm -Rf bsseq/inst/doc
	R-$(R_VER) CMD build $(R_BUILD_ARGS) bsseq

check_bsseq: build_bsseq
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) bsseq_$(bsseq_VERSION).tar.gz

vignettes_bsseq: base_bsseq
	rm -Rf bsseq/inst/doc
	R-$(R_VER) CMD build bsseq
	tar xvzf bsseq_$(bsseq_VERSION).tar.gz bsseq/inst/doc

install_bsseq: build_bsseq
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) bsseq_$(bsseq_VERSION).tar.gz

system_install_bsseq: build_bsseq
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"bsseq_$(bsseq_VERSION).tar.gz\") }"

##############
base_bsseqData: bsseqData
ifneq (,$(wildcard bsseqData/DESCRIPTION))
base_bsseqData: bsseqData_VERSION:=$(shell grep ^Version bsseqData/DESCRIPTION | sed 's_Version: __')
endif

build_bsseqData: base_bsseqData
	R-$(R_VER) CMD build $(R_BUILD_ARGS) bsseqData

check_bsseqData: build_bsseqData
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) bsseqData_$(bsseqData_VERSION).tar.gz

install_bsseqData: build_bsseqData
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) bsseqData_$(bsseqData_VERSION).tar.gz

##############
base_illuminaio: illuminaio
ifneq (,$(wildcard illuminaio/DESCRIPTION))
illuminaio_VERSION:=$(shell grep ^Version illuminaio/DESCRIPTION | sed 's_Version: __')
endif

build_illuminaio: base_illuminaio
	R-$(R_VER) CMD build $(R_BUILD_ARGS) illuminaio

check_illuminaio: build_illuminaio
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) illuminaio_$(illuminaio_VERSION).tar.gz

install_illuminaio: build_illuminaio
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) illuminaio_$(illuminaio_VERSION).tar.gz


###############
base_affxparser: affxparser
ifneq (,$(wildcard affxparser/DESCRIPTION))
affxparser_VERSION:=$(shell grep ^Version affxparser/DESCRIPTION | sed 's_Version: __')
endif

build_affxparser: base_affxparser
	R-$(R_VER) CMD build $(R_BUILD_ARGS) affxparser

check_affxparser: build_affxparser
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) affxparser_$(affxparser_VERSION).tar.gz

install_affxparser: build_affxparser
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) affxparser_$(affxparser_VERSION).tar.gz

system_install_affxparser: build_affxparser
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"affxparser_$(affxparser_VERSION).tar.gz\") }"

###

base_mpra: mpra
ifneq (,$(wildcard mpra/DESCRIPTION))
mpra_VERSION:=$(shell grep ^Version mpra/DESCRIPTION | sed 's_Version: __')
endif

build_mpra: base_mpra
	rm -Rf mpra/inst/doc
	R-$(R_VER) CMD build $(R_BUILD_ARGS) mpra

check_mpra: build_mpra
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) mpra_$(mpra_VERSION).tar.gz

bioccheck_mpra: build_mpra
	$(R_TIMING) R-$(R_VER) CMD BiocCheck mpra_$(mpra_VERSION).tar.gz

install_mpra: build_mpra
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) mpra_$(mpra_VERSION).tar.gz

system_install_mpra: build_mpra
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"mpra_$(mpra_VERSION).tar.gz\") }"

vignette_mpra: base_mpra
	rm -Rf mpra/inst/doc
	R-$(R_VER) CMD build mpra
	tar xvzf mpra_$(mpra_VERSION).tar.gz mpra/inst/doc/mpra.html
	open mpra/inst/doc/mpra.html

open_vignette_mpra:
	tar xvzf mpra_$(mpra_VERSION).tar.gz mpra/inst/doc/mpra.html
	open mpra/inst/doc/mpra.html



###

base_bnbc: bnbc
ifneq (,$(wildcard bnbc/DESCRIPTION))
bnbc_VERSION:=$(shell grep ^Version bnbc/DESCRIPTION | sed 's_Version: __')
endif

build_bnbc: base_bnbc
	rm -Rf bnbc/inst/doc
	R-$(R_VER) CMD build $(R_BUILD_ARGS) bnbc

check_bnbc: build_bnbc
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) bnbc_$(bnbc_VERSION).tar.gz

bioccheck_bnbc: build_bnbc
	$(R_TIMING) R-$(R_VER) CMD BiocCheck bnbc_$(bnbc_VERSION).tar.gz

install_bnbc: build_bnbc
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) bnbc_$(bnbc_VERSION).tar.gz

system_install_bnbc: build_bnbc
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"bnbc_$(bnbc_VERSION).tar.gz\") }"

vignette_bnbc: base_bnbc
	rm -Rf bnbc/inst/doc
	R-$(R_VER) CMD build bnbc
	tar xvzf bnbc_$(bnbc_VERSION).tar.gz bnbc/inst/doc/bnbc.html
	open bnbc/inst/doc/bnbc.html

open_vignette_bnbc:
	tar xvzf bnbc_$(bnbc_VERSION).tar.gz bnbc/inst/doc/bnbc.html
	open bnbc/inst/doc/bnbc.html


###

base_yamss: yamss
ifneq (,$(wildcard yamss/DESCRIPTION))
yamss_VERSION:=$(shell grep ^Version yamss/DESCRIPTION | sed 's_Version: __')
endif

build_yamss: base_yamss
	rm -Rf yamss/inst/doc
	R-$(R_VER) CMD build $(R_BUILD_ARGS) yamss

check_yamss: build_yamss
	$(R_TIMING) R-$(R_VER) CMD check $(R_CHECK_ARGS) yamss_$(yamss_VERSION).tar.gz

bioccheck_yamss: build_yamss
	$(R_TIMING) R-$(R_VER) CMD BiocCheck yamss_$(yamss_VERSION).tar.gz

install_yamss: build_yamss
	R-$(R_VER) CMD INSTALL $(R_INSTALL_ARGS) yamss_$(yamss_VERSION).tar.gz

system_install_yamss: build_yamss
	Rscript-$(R_VER) -e "{ base::hopkins\$$local.install(\"yamss_$(yamss_VERSION).tar.gz\") }"

vignette_yamss: base_yamss
	rm -Rf yamss/inst/doc
	R-$(R_VER) CMD build yamss
	tar xvzf yamss_$(yamss_VERSION).tar.gz yamss/inst/doc/yamss.pdf
	open yamss/inst/doc/yamss.pdf

open_vignette_yamss:
	tar xvzf yamss_$(yamss_VERSION).tar.gz yamss/inst/doc/yamss.pdf
	open yamss/inst/doc/yamss.pdf