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[pkgsrc/trunk]: pkgsrc/pkgtools/R2pkg pkgtools/R2pkg: separate R code from sh...
details: https://anonhg.NetBSD.org/pkgsrc/rev/dc2e22b9a29e
branches: trunk
changeset: 415763:dc2e22b9a29e
user: rillig <rillig%pkgsrc.org@localhost>
date: Sun Oct 13 13:26:22 2019 +0000
description:
pkgtools/R2pkg: separate R code from shell code
Before, it was difficult to edit the R code since all dollars,
backslashes and backticks had to be escaped. Separating the code also
makes the R part testable on its own.
diffstat:
pkgtools/R2pkg/Makefile | 36 +-
pkgtools/R2pkg/PLIST | 3 +-
pkgtools/R2pkg/files/R2pkg.R | 1265 +++++++++++++++++++++++++++++++++++++++++
pkgtools/R2pkg/files/R2pkg.sh | 1249 +---------------------------------------
pkgtools/R2pkg/files/RELEASE | 4 +-
5 files changed, 1303 insertions(+), 1254 deletions(-)
diffs (truncated from 2661 to 300 lines):
diff -r 787688ca1074 -r dc2e22b9a29e pkgtools/R2pkg/Makefile
--- a/pkgtools/R2pkg/Makefile Sun Oct 13 12:22:27 2019 +0000
+++ b/pkgtools/R2pkg/Makefile Sun Oct 13 13:26:22 2019 +0000
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2019/10/13 09:43:26 rillig Exp $
+# $NetBSD: Makefile,v 1.7 2019/10/13 13:26:22 rillig Exp $
#
-VERS= 0.6.1
+VERS= 0.6.2
PKGNAME= R2pkg-${VERS}
CATEGORIES= pkgtools
@@ -10,33 +10,25 @@
COMMENT= Tool to automate initial steps in building an R package
LICENSE= modified-bsd
-WRKSRC= ${WRKDIR}
-NO_BUILD= yes
-USE_LANGUAGES= # none
-AUTO_MKDIRS= yes
-
-DEPENDS+= curl>=7.52.1:../../www/curl
+WRKSRC= ${WRKDIR}
+NO_BUILD= yes
+USE_LANGUAGES= # none
+AUTO_MKDIRS= yes
-SUBST_CLASSES+= version
-SUBST_STAGE.version= pre-configure
-SUBST_MESSAGE.version= Substituting version in R2pkg.sh.
-SUBST_FILES.version= R2pkg.sh
-SUBST_VARS.version= VERS
+DEPENDS+= curl>=7.52.1:../../www/curl
-SUBST_CLASSES+= tools
-SUBST_STAGE.tools= pre-configure
-SUBST_MESSAGE.tools= Substituting tool locations.
-SUBST_FILES.tools= R2pkg.sh
-SUBST_VARS.tools= MAKE
-
-INSTALLATION_DIRS+= sbin ${PKGMANDIR}/man8
+SUBST_CLASSES+= R
+SUBST_STAGE.R= pre-configure
+SUBST_FILES.R= R2pkg.sh
+SUBST_VARS.R= VERS MAKE LIBDIR
+LIBDIR= ${PREFIX}/lib/R2pkg
do-extract:
- ${CP} ${FILESDIR}/R2pkg.sh ${WRKSRC}
- ${CP} ${FILESDIR}/R2pkg.8 ${WRKSRC}
+ cd ${FILESDIR} && ${CP} R2pkg.* ${WRKSRC}
do-install:
${INSTALL_SCRIPT} ${WRKSRC}/R2pkg.sh ${DESTDIR}${PREFIX}/sbin/R2pkg
+ ${INSTALL_DATA} ${WRKSRC}/R2pkg.R ${DESTDIR}${LIBDIR}/R2pkg.R
${INSTALL_MAN} ${WRKSRC}/R2pkg.8 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man8/R2pkg.8
.include "../../math/R/buildlink3.mk"
diff -r 787688ca1074 -r dc2e22b9a29e pkgtools/R2pkg/PLIST
--- a/pkgtools/R2pkg/PLIST Sun Oct 13 12:22:27 2019 +0000
+++ b/pkgtools/R2pkg/PLIST Sun Oct 13 13:26:22 2019 +0000
@@ -1,3 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2015/04/25 22:06:34 brook Exp $
+@comment $NetBSD: PLIST,v 1.2 2019/10/13 13:26:22 rillig Exp $
+lib/R2pkg/R2pkg.R
man/man8/R2pkg.8
sbin/R2pkg
diff -r 787688ca1074 -r dc2e22b9a29e pkgtools/R2pkg/files/R2pkg.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pkgtools/R2pkg/files/R2pkg.R Sun Oct 13 13:26:22 2019 +0000
@@ -0,0 +1,1265 @@
+# $NetBSD: R2pkg.R,v 1.1 2019/10/13 13:26:22 rillig Exp $
+#
+# Copyright (c) 2014,2015,2016,2017,2018,2019
+# Brook Milligan. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# 3. Neither the name of the author nor the names of any contributors
+# may be used to endorse or promote products derived from this software
+# without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+# OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+# SUCH DAMAGE.
+#
+#
+# Create an R package in the current directory
+#
+
+arg.level <- Sys.getenv('LEVEL')
+arg.rpkg <- Sys.getenv('RPKG')
+arg.packages_list <- Sys.getenv('PACKAGES_LIST')
+arg.r2pkg <- Sys.getenv('R2PKG')
+arg.args <- Sys.getenv('ARGS')
+arg.recursive <- as.logical(Sys.getenv('RECURSIVE'))
+arg.update <- as.logical(Sys.getenv('UPDATE'))
+arg.dependency_list <- Sys.getenv('DEPENDENCY_LIST')
+arg.maintainer_email <- Sys.getenv('MAINTAINER_EMAIL')
+arg.rpkg_description_url <- Sys.getenv('RPKG_DESCRIPTION_URL')
+arg.quiet_curl <- as.logical(Sys.getenv('QUIET_CURL'))
+
+level.message <- function(...)
+ message('[ ', arg.level, ' ] ', ...)
+
+warning.message <- function(...)
+ level.message('WARNING: ', ...)
+
+R_version <- function()
+{
+ info <- R.Version()
+ version <- paste0(info[['major']],'.',info[['minor']])
+ version
+}
+
+set.locale <- function() { invisible(Sys.setlocale('LC_ALL','C')) }
+
+trim.space <- function(s) gsub('[[:space:]]','',s)
+trim.blank <- function(s) gsub('[[:blank:]]','',s)
+one.space <- function(s) gsub('[[:blank:]]+',' ',s)
+one.line <- function(s) gsub('\n',' ',s)
+pkg.vers <- function(s) gsub('_','.',s)
+field <- function(key,value) paste(key,'=\t',value,sep='')
+
+# The list of "recommended packages which are to be included in all
+# binary distributions of R." (R FAQ 5.1.2 2018-10-18)
+#
+base.packages.FAQ.5.1.2 <- c(
+ 'KernSmooth',
+ 'MASS',
+ 'Matrix',
+ 'boot',
+ 'class',
+ 'cluster',
+ 'codetools',
+ 'foreign',
+ 'lattice',
+ 'mgcv',
+ 'nlme',
+ 'nnet',
+ 'rpart',
+ 'spatial',
+ 'survival')
+
+# Other R packages that appear in dependency lists but are included in
+# the R package.
+#
+base.packages.other <- c(
+ 'grDevices',
+ 'graphics',
+ 'grid',
+ 'methods',
+ 'parallel',
+ 'splines',
+ 'stats',
+ 'tools',
+ 'utils')
+base.packages <- c('R',base.packages.FAQ.5.1.2,base.packages.other)
+
+licenses <- list()
+licenses[['ACM']] <- 'acm-license'
+licenses[['ACM | file LICENSE']] <- 'acm-license # OR file LICENSE'
+licenses[['APACHE']] <- 'apache-1.1 OR apache-2.0'
+licenses[['Apache License 2.0']] <- 'apache-2.0'
+licenses[['Apache License (== 2.0)']] <- 'apache-2.0'
+licenses[['Apache License (== 2.0) | file LICENSE']] <- 'apache-2.0 # OR file LICENSE'
+licenses[['ARTISTIC']] <- 'artistic OR artistic-2.0'
+licenses[['Artistic-2.0']] <- 'artistic-2.0'
+licenses[['BSD']] <- '2-clause-bsd OR modified-bsd OR original-bsd'
+licenses[['BSD-2']] <- '2-clause-bsd'
+licenses[['BSD_2_clause + file LICENSE']] <- '2-clause-bsd # + file LICENSE'
+licenses[['BSD 3 clause']] <- 'modified-bsd'
+licenses[['BSD 3 clause + file LICENSE']] <- 'modified-bsd # + file LICENSE'
+licenses[['BSD_3_clause + file LICENSE']] <- 'modified-bsd # + file LICENSE'
+licenses[['BSL-1.0']] <- 'boost-license'
+licenses[['CC0']] <- 'cc0-1.0-universal'
+licenses[['GPL']] <- 'gnu-gpl-v1 OR gnu-gpl-v2 OR gnu-gpl-v3'
+licenses[['GPL-1']] <- 'gnu-gpl-v1'
+licenses[['GPL-2']] <- 'gnu-gpl-v2'
+licenses[['GPL-2 | file LICENSE']] <- 'gnu-gpl-v2 # OR file LICENSE'
+licenses[['GPL-3']] <- 'gnu-gpl-v3'
+licenses[['GPL-2 | GPL-3']] <- 'gnu-gpl-v2 OR gnu-gpl-v3'
+licenses[['GPL (>= 2)']] <- 'gnu-gpl-v2 OR gnu-gpl-v3'
+licenses[['GPL (>= 2.0)']] <- 'gnu-gpl-v2 OR gnu-gpl-v3'
+licenses[['GPL (>= 2) | file LICENSE']] <- 'gnu-gpl-v2 OR gnu-gpl-v3 # OR file LICENSE'
+licenses[['GPL (>= 3)']] <- 'gnu-gpl-v3'
+licenses[['LGPL']] <- 'gnu-lgpl-v2 OR gnu-lgpl-v2.1 OR gnu-lgpl-v3'
+licenses[['LGPL-2']] <- 'gnu-lgpl-v2'
+licenses[['LGPL-2.1']] <- 'gnu-lgpl-v2.1'
+licenses[['LGPL-3']] <- 'gnu-lgpl-v3'
+licenses[['LGPL-3 + file LICENSE']] <- 'gnu-lgpl-v3 # + file LICENSE'
+licenses[['LGPL-2 | LGPL-3']] <- 'gnu-lgpl-v2 OR gnu-lgpl-v3'
+licenses[['LGPL (>= 2)']] <- 'gnu-lgpl-v2 OR gnu-lgpl-v2.1 OR gnu-lgpl-v3'
+licenses[['LUCENT']] <- 'lucent'
+licenses[['Lucent Public License']] <- 'lucent'
+licenses[['MIT']] <- 'mit'
+licenses[['MIT + file LICENSE']] <- 'mit # + file LICENSE'
+licenses[['MIT + file LICENSE | Unlimited']] <- 'mit # + file LICENSE OR unlimited'
+licenses[['MPL-1.0']] <- 'mpl-1.0'
+licenses[['MPL-1.1']] <- 'mpl-1.1'
+licenses[['MPL-2.0']] <- 'mpl-2.0'
+licenses[['MPL-2.0 | file LICENSE']] <- 'mpl-2.0 # OR file LICENSE'
+licenses[['POSTGRESQL']] <- 'postgresql-license'
+
+adjacent.duplicates <- function(x)
+{
+ a <- x[-length(x)]
+ b <- x[-1]
+ dups <- a == b
+ dups <- c(FALSE,dups)
+ dups
+}
+
+paste2 <- function(s1,s2)
+{
+ if (is.na(s1) && is.na(s2)) return ('')
+ if (is.na(s1) && !is.na(s2)) return (s2)
+ if (!is.na(s1) && is.na(s2)) return (s1)
+ if (!is.na(s1) && !is.na(s2)) return (paste(s1,s2))
+}
+
+end.paragraph <- function(l,l1=l,l2=list())
+{
+ if (length(l1) > 0 || length(l2) > 0)
+ l <- append(l,'')
+ l
+}
+
+as.sorted.list <- function(df)
+{
+ l <- list()
+ df <- df[!duplicated(df),]
+ if (nrow(df) > 0)
+ {
+ key <- as.vector(df[,1])
+ value <- as.vector(df[,2])
+ key <- order(key,value)
+ l <- as.list(value[key])
+ }
+ l
+}
+
+read.file.as.dataframe <- function(filename)
+{
+ # message('===> read.file.as.dataframe(',filename,')')
+ contents <- as.list(readLines(filename))
+ df <- data.frame()
+ for (line in contents)
+ {
+ # str(line)
+ df <- rbind(df,data.frame(line=line,stringsAsFactors=FALSE))
+ }
+ df
+}
+
+categorize.key_value <- function(df,line='line')
+{
+ re.skip_blank <- '[[:blank:]]*'
+ re.blank <- '[[:blank:]]+'
+ re.anything <- '.*'
+
+ re.key <- '[^+=[:blank:]]+'
+ re.operator <- '[+=]+'
+ re.delimiter <- re.skip_blank
+ re.value <- re.anything
+ re.optional_TODO <- '(#[[:blank:]]*TODO[[:blank:]]*:[[:blank:]]*)*'
+
+ re.match_key_value_line <- paste0('^',
+ re.skip_blank,
+ re.optional_TODO,
+ re.key,
+ re.skip_blank,
+ re.operator,
+ re.delimiter,
+ re.value,
+ '$')
+
+ re.match_key <- paste0('^',
+ re.skip_blank,
+ re.optional_TODO,
+ '(',re.key,')',
+ re.skip_blank,
+ re.operator,
+ re.delimiter,
+ re.value,
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