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@kasperdanielhansen
Created October 4, 2017 00:47
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Makefile for R packages
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
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