[Sciviews-commits] r548 - in pkg: svKomodo svKomodo/R svKomodo/inst svMisc svMisc/R svMisc/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 2 08:06:56 CET 2014
Author: phgrosjean
Date: 2014-03-02 08:06:51 +0100 (Sun, 02 Mar 2014)
New Revision: 548
Modified:
pkg/svKomodo/NAMESPACE
pkg/svKomodo/NEWS
pkg/svKomodo/R/svKomodo-internal.R
pkg/svKomodo/inst/NEWS.Rd
pkg/svMisc/DESCRIPTION
pkg/svMisc/NEWS
pkg/svMisc/R/completion.R
pkg/svMisc/R/descFun.R
pkg/svMisc/R/isHelp.R
pkg/svMisc/R/pkgMan.R
pkg/svMisc/man/svMisc-package.Rd
Log:
svMisc reworked to eliminate use of :::. IN svKomodo, utils::rc.settings() set on attaching and reset when unloading
Modified: pkg/svKomodo/NAMESPACE
===================================================================
--- pkg/svKomodo/NAMESPACE 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svKomodo/NAMESPACE 2014-03-02 07:06:51 UTC (rev 548)
@@ -1,4 +1,4 @@
-importFrom(utils, capture.output)
+importFrom(utils, capture.output, rc.settings)
import(svMisc)
export(koInstall,
Modified: pkg/svKomodo/NEWS
===================================================================
--- pkg/svKomodo/NEWS 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svKomodo/NEWS 2014-03-02 07:06:51 UTC (rev 548)
@@ -6,7 +6,9 @@
* .onAttach() reworked to eliminate ::: (not allowed by CRAN)
+* utils::rc.settings are adjusted in .onAttach() and restored in .onUnload()
+
== Changes in svKomodo 0.9-61
* Simplification of internal code to get Komodo location. It does not require
Modified: pkg/svKomodo/R/svKomodo-internal.R
===================================================================
--- pkg/svKomodo/R/svKomodo-internal.R 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svKomodo/R/svKomodo-internal.R 2014-03-02 07:06:51 UTC (rev 548)
@@ -114,6 +114,10 @@
## Make sure config is OK
.loadSvOptions()
+ ## Check that usually inactivated rc.settings are set
+ assignTemp(".old.rc.settings", rc.settings())
+ rc.settings(ipck = TRUE)
+
## Create our SciViews task callback manager
## Should eliminate this???
## PhG: inactivated for now, because it makes problems in R!!!
@@ -466,6 +470,11 @@
## Remove the SciViews task callback manager
try(removeTaskCallback("SV-taskCallbackManager"), silent = TRUE)
try(rmTemp(".svTaskCallbackManager"), silent = TRUE)
+
+ ## Restore rc.settings
+ settings <- getTemp(".old.rc.settings", rc.settings())
+ do.call("rc.settings", as.list(settings))
+ rmTemp(".old.rc.settings")
}
.packageName <- "svKomodo"
Modified: pkg/svKomodo/inst/NEWS.Rd
===================================================================
--- pkg/svKomodo/inst/NEWS.Rd 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svKomodo/inst/NEWS.Rd 2014-03-02 07:06:51 UTC (rev 548)
@@ -5,6 +5,8 @@
\itemize{
\item{ Author field rebuild in DESCRIPTION file }
\item{ \code{.onAttach()} reworked to eliminate \code{:::} (not allowed by CRAN) }
+ \item{ \code{utils::rc.settings} are adjusted in \code{.onAttach()} and
+ restored in \code{.onUnload()} }
}
}
Modified: pkg/svMisc/DESCRIPTION
===================================================================
--- pkg/svMisc/DESCRIPTION 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/DESCRIPTION 2014-03-02 07:06:51 UTC (rev 548)
@@ -1,7 +1,7 @@
Package: svMisc
Type: Package
Version: 0.9-70
-Date: 2013-11-30
+Date: 2014-03-01
Title: SciViews GUI API - Miscellaneous functions
Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"),
email = "phgrosjean at sciviews.org"),
Modified: pkg/svMisc/NEWS
===================================================================
--- pkg/svMisc/NEWS 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/NEWS 2014-03-02 07:06:51 UTC (rev 548)
@@ -8,7 +8,9 @@
* Function pkg() is renamed package().
+* Reworked code that was using :::.
+
== Changes in svMisc 0.9-69
* On Mac OS X >= 10.7, the package could not load because of a warning
Modified: pkg/svMisc/R/completion.R
===================================================================
--- pkg/svMisc/R/completion.R 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/R/completion.R 2014-03-02 07:06:51 UTC (rev 548)
@@ -1,4 +1,3 @@
-## TODO: activate rc.settings(ipck = TRUE) and rc.settings(files = TRUE)
completion <- function (code, pos = nchar(code), min.length = 2,
print = FALSE, types = c("default", "scintilla"), addition = FALSE, sort = TRUE,
what = c("arguments", "functions", "packages"), description = FALSE,
@@ -40,8 +39,7 @@
## Deal with argument completions (ending with " = ")
if (length(test.arg <- grep(" = ", completions))) {
- ## TODO: avoid using ::: here!
- fun <- utils:::.CompletionEnv[["fguess"]]
+ fun <- getNamespace("utils")$.CompletionEnv[["fguess"]]
ret[test.arg, "context"] <- fun
ret[test.arg, "desc"] <- descArgs(fun,
sub(" = $", "", completions[test.arg]))
@@ -126,10 +124,8 @@
ret$context, sep = field.sep), sep = sep)
}
if (sep != "\n") cat("\n")
- return(invisible(ret))
- } else {
- return(ret)
- }
+ invisible(ret)
+ } else ret
}
## Do we return the type of the entry, and if yes, in which format?
@@ -172,8 +168,8 @@
} else dblBrackets <- FALSE
## Save funarg.suffix and use " = " locally
- ## TODO: do not use ::: here!
- ComplEnv <- utils:::.CompletionEnv
+ utilsNS <- getNamespace("utils")
+ ComplEnv <- utilsNS$.CompletionEnv
opts <- ComplEnv$options
funarg.suffix <- opts$funarg.suffix
on.exit({
@@ -184,14 +180,12 @@
ComplEnv$options <- opts
## Calculate completion with standard R completion tools
- ## TODO: do not use ::: here!
- utils:::.assignLinebuffer(code)
- utils:::.assignEnd(pos)
- utils:::.guessTokenFromLine()
+ utilsNS$.assignLinebuffer(code)
+ utilsNS$.assignEnd(pos)
+ utilsNS$.guessTokenFromLine()
## The standard utils:::.completeToken() is replaced by our own version:
.completeTokenExt()
- ## TODO: do not use ::: here!
- completions <- utils:::.retrieveCompletions()
+ completions <- utilsNS$.retrieveCompletions()
triggerPos <- pos - ComplEnv[["start"]]
token <- ComplEnv[["token"]]
@@ -274,11 +268,13 @@
## (checked equivalent with R 2.11.1)
## Only difference: it also gets current arguments list (if applicable).
## They are assigned to utils:::.CompletionEnv$funargs
-## TODO: avoid using ::: in the code of a package!
.inFunctionExt <-
-function (line = utils:::.CompletionEnv[["linebuffer"]],
-cursor = utils:::.CompletionEnv[["start"]])
+function (line, cursor)
{
+ utilsNS <- getNamespace("utils")
+ if (missing(line)) line <- utilsNS$.CompletionEnv[["linebuffer"]]
+ if (missing(cursor)) cursor <- utilsNS$.CompletionEnv[["start"]]
+
parens <- sapply(c("(", ")"), function(s)
gregexpr(s, substr(line, 1L, cursor), fixed = TRUE)[[1L]],
simplify = FALSE)
@@ -295,7 +291,7 @@
suffix <- substr(line, index + 1L, cursor + 1L)
if ((length(grep("=", suffix, fixed = TRUE)) == 0L) &&
(length(grep(",", suffix, fixed = TRUE)) == 0L))
- utils:::setIsFirstArg(v = TRUE)
+ utilsNS$setIsFirstArg(v = TRUE)
if ((length(grep("=", suffix, fixed = TRUE))) && (length(grep(",",
substr(suffix, tail(gregexpr("=", suffix, fixed = TRUE)[[1L]],
1L), 1000000L), fixed = TRUE)) == 0L)) {
@@ -314,13 +310,13 @@
}
funargs <- strsplit(funargs, "\\s*,\\s*", perl=TRUE)[[1]]
funargs <- unname(sapply(funargs, sub, pattern = "\\s*=.*$",
- replacement = utils:::.CompletionEnv$options$funarg.suffix,
+ replacement = utilsNS$.CompletionEnv$options$funarg.suffix,
perl=TRUE))
- assign("funargs", funargs, utils:::.CompletionEnv)
+ assign("funargs", funargs, utilsNS$.CompletionEnv)
## TODO: how to take non named arguments into account too?
## ... addition ends here
- possible <- suppressWarnings(strsplit(prefix, utils:::breakRE,
+ possible <- suppressWarnings(strsplit(prefix, utilsNS$breakRE,
perl = TRUE))[[1L]]
possible <- possible[possible != ""]
if (length(possible)) {
@@ -339,24 +335,25 @@
## Main difference is that calls .inFunctionExt instead of utils:::inFunction
## and it also makes sure completion is for Complete in 'Complete("anova(", )'!
.completeTokenExt <- function () {
- ComplEnv <- utils:::.CompletionEnv
+ utilsNS <- getNamespace("utils")
+ ComplEnv <- utilsNS$.CompletionEnv
text <- ComplEnv$token
linebuffer <- ComplEnv$linebuffer
st <- ComplEnv$start
- if (utils:::isInsideQuotes()) {
+ if (utilsNS$isInsideQuotes()) {
probablyNotFilename <- (st > 2L &&
(substr(linebuffer, st - 1L, st - 1L) %in% c("[", ":", "$")))
if (ComplEnv$settings[["files"]]) {
if (probablyNotFilename) {
ComplEnv[["comps"]] <- character(0L)
} else {
- ComplEnv[["comps"]] <- utils:::fileCompletions(text)
+ ComplEnv[["comps"]] <- utilsNS$fileCompletions(text)
}
- utils:::.setFileComp(FALSE)
+ utilsNS$.setFileComp(FALSE)
} else {
ComplEnv[["comps"]] <- character(0L)
- utils:::.setFileComp(TRUE)
+ utilsNS$.setFileComp(TRUE)
}
} else {
@@ -375,8 +372,8 @@
}
## ... additions until here
- utils:::.setFileComp(FALSE)
- utils:::setIsFirstArg(FALSE)
+ utilsNS$.setFileComp(FALSE)
+ utilsNS$setIsFirstArg(FALSE)
guessedFunction <- ""
if (ComplEnv$settings[["args"]]) {
## Call of .inFunctionExt() instead of utils:::inFunction()
@@ -386,9 +383,9 @@
}
assign("fguess", guessedFunction, ComplEnv)
- fargComps <- utils:::functionArgs(guessedFunction, text)
+ fargComps <- utilsNS$functionArgs(guessedFunction, text)
- if (utils:::getIsFirstArg() && length(guessedFunction) &&
+ if (utilsNS$getIsFirstArg() && length(guessedFunction) &&
guessedFunction %in% c("library", "require", "data")) {
assign("comps", fargComps, ComplEnv)
return()
@@ -398,15 +395,15 @@
prefix <- substr(text, 1L, lastArithOp)
text <- substr(text, lastArithOp + 1L, 1000000L)
}
- spl <- utils:::specialOpLocs(text)
+ spl <- utilsNS$specialOpLocs(text)
if (length(spl)) {
- comps <- utils:::specialCompletions(text, spl)
+ comps <- utilsNS$specialCompletions(text, spl)
} else {
appendFunctionSuffix <- !any(guessedFunction %in%
c("help", "args", "formals", "example", "do.call",
"environment", "page", "apply", "sapply", "lapply",
"tapply", "mapply", "methods", "fix", "edit"))
- comps <- utils:::normalCompletions(text,
+ comps <- utilsNS$normalCompletions(text,
check.mode = appendFunctionSuffix)
}
if (haveArithOp && length(comps))
Modified: pkg/svMisc/R/descFun.R
===================================================================
--- pkg/svMisc/R/descFun.R 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/R/descFun.R 2014-03-02 07:06:51 UTC (rev 548)
@@ -20,8 +20,7 @@
file <- as.character(file)
if (length(file) > 0) {
## Read the Rd file and get the title section out of it
- ## TODO: avoid this!
- Rdoc <- utils:::.getHelpFile(file[1L])
+ Rdoc <- getNamespace("utils")$.getHelpFile(file[1L])
## Look for the \title tag
j <- 0
for (j in seq_along(Rdoc))
@@ -54,8 +53,7 @@
if (!file.exists(paste(RdDB, "rdx", sep=".")))
return(character(length(args)))
- ## TODO: avoid this!
- rd <- tools:::fetchRdDB(RdDB, basename(file))
+ rd <- getNamespace("tools")$fetchRdDB(RdDB, basename(file))
## This is not exported from tools
RdTags <- function (Rd) {
Modified: pkg/svMisc/R/isHelp.R
===================================================================
--- pkg/svMisc/R/isHelp.R 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/R/isHelp.R 2014-03-02 07:06:51 UTC (rev 548)
@@ -5,8 +5,8 @@
if (!is.character(topic)) topic <- deparse(topic)[1L]
pkgpaths <- find.package(package, lib.loc, verbose = FALSE)
- ## TODO: avoid using :::
- file <- utils:::index.search(topic, pkgpaths, TRUE)
+ utilsNS <- getNamespace("utils")
+ file <- utilsNS$index.search(topic, pkgpaths, TRUE)
if (!length(file)) return(c(help = FALSE, example = FALSE))
packagePath <- dirname(dirname(file))
@@ -16,8 +16,7 @@
tf <- tempfile("Rex")
on.exit(unlink(tf))
encoding <- "UTF-8"
- ## TODO: avoid using :::
- tools::Rd2ex(utils:::.getHelpFile(file), tf)
+ tools::Rd2ex(utilsNS$.getHelpFile(file), tf)
if (!file.exists(tf)) {
c(help = TRUE, example = FALSE)
} else c(help = TRUE, example = TRUE)
Modified: pkg/svMisc/R/pkgMan.R
===================================================================
--- pkg/svMisc/R/pkgMan.R 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/R/pkgMan.R 2014-03-02 07:06:51 UTC (rev 548)
@@ -23,8 +23,8 @@
if (isTRUE(print.it)) {
write.dcf(as.data.frame.list(desc[!sapply(desc, is.na)],
optional = TRUE), width = Inf)
- return(invisible(desc))
- } else return(desc)
+ invisible(desc)
+ } else desc
}
pkgManGetMirrors <- function ()
@@ -93,7 +93,6 @@
imax <- nrow(avpkg.list)
idx <- seq(imax)
}
- #browser()
assignTemp('avpkg.pattern', pattern)
if (page == "next") {
@@ -133,8 +132,7 @@
pkgManInstall <- function (pkgs, install.deps = FALSE, ask = TRUE)
{
- ## TODO: avoid using ::: !
- dep <- suppressMessages(utils:::getDependencies(pkgs,
+ dep <- suppressMessages(getNamespace("utils")$getDependencies(pkgs,
available = getTemp('avpkg.list')))
msg <- status <- ""
if (!isTRUE(ask) && (isTRUE(install.deps) || all(dep %in% pkgs))) {
@@ -147,10 +145,8 @@
"This will install packages: %s and %s.",
), paste(sQuote(dep[-l]), collapse = ", "), sQuote(dep[l]))
status <- "question"
-
}
- return(list(packages = dep, message = msg, status = status))
- #return(invisible(dep))
+ list(packages = dep, message = msg, status = status)
}
pkgManRemove <- function (pkgName)
@@ -170,10 +166,10 @@
pkglib <- normalizePath(file.path(pkgpath, ".."))
if (file.access(pkglib, 2) == 0) {
remove.packages(pkgName, lib = pkglib)
- return(TRUE)
+ TRUE
} else {
#warning("No sufficient access rights to library", sQuote(pkglib))
- return(FALSE)
+ FALSE
}
}, simplify = FALSE)
}
@@ -192,7 +188,7 @@
if (packSearchName %in% search())
detach(packSearchName, character.only = TRUE, unload = TRUE)
if(pkgName %in% loadedNamespaces()) unloadNamespace(pkgName)
- return(TRUE)
+ TRUE
}, error = function(e) { conditionMessage(e) })
}, simplify = FALSE)
}
Modified: pkg/svMisc/man/svMisc-package.Rd
===================================================================
--- pkg/svMisc/man/svMisc-package.Rd 2014-03-01 21:01:00 UTC (rev 547)
+++ pkg/svMisc/man/svMisc-package.Rd 2014-03-02 07:06:51 UTC (rev 548)
@@ -13,7 +13,7 @@
Package: \tab svMisc\cr
Type: \tab Package\cr
Version: \tab 0.9-70\cr
- Date: \tab 2013-11-30\cr
+ Date: \tab 2014-03-01\cr
License: \tab GPL 2 or above, at your convenience\cr
}
% TODO: add description of main functions here. Also add examples
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