From noreply at r-forge.r-project.org Mon Feb 11 22:07:56 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 11 Feb 2013 22:07:56 +0100 (CET) Subject: [Sciviews-commits] r527 - komodo/SciViews-K/defaults pkg/svKomodo pkg/svKomodo/R pkg/svKomodo/inst pkg/svKomodo/man Message-ID: <20130211210756.EE027184639@r-forge.r-project.org> Author: phgrosjean Date: 2013-02-11 22:07:56 +0100 (Mon, 11 Feb 2013) New Revision: 527 Modified: komodo/SciViews-K/defaults/svStart.R pkg/svKomodo/DESCRIPTION pkg/svKomodo/NEWS pkg/svKomodo/R/svKomodo-internal.R pkg/svKomodo/inst/NEWS.Rd pkg/svKomodo/man/svKomodo-package.Rd Log: svStart() and .onAttach() in svKomodo adapted for better handling of locate in Mac OS X Modified: komodo/SciViews-K/defaults/svStart.R =================================================================== --- komodo/SciViews-K/defaults/svStart.R 2013-01-30 15:02:47 UTC (rev 526) +++ komodo/SciViews-K/defaults/svStart.R 2013-02-11 21:07:56 UTC (rev 527) @@ -8,6 +8,7 @@ ## Version 0.9.25, 2011-12-28 modified by Ph. Grosjean ## Version 0.9.27, 2012-04-22 modified by Ph. Grosjean ## Version 0.9.28, 2012-12-17 modified by Ph. Grosjean +## Version 0.9.29, 2013-02-08 modified by Ph. Grosjean (don't use locate on the Mac) ## TODO: also use value in koDebug to debug server from within R! ## TODO: use the mechanism of startHttpServer() to retrieve default config @@ -441,11 +442,22 @@ debugMsg("which", "returned", Komodo) } + isMac <- function () (grepl("^mac", .Platform$pkgType)) if (length(Komodo) == 0 || Komodo == "") { - Komodo <- system(paste("locate --basename -e --regex ^komodo$", - "| grep -vF 'INSTALLDIR' | grep -F 'bin/komodo'", - "| tail --lines=1"), intern = TRUE, ignore.stderr = TRUE) - debugMsg("locate komodo", "returned", Komodo) + if (!isMac()) { + isLocate <- suppressWarnings(length(system('which locate', + intern = TRUE)) > 0) + if (!isLocate) { # locate is not there + Komodo <- NULL + } else { + Komodo <- try(suppressWarnings(system(paste( + "locate --basename -e --regex ^komodo$", + "| grep -vF 'INSTALLDIR' | grep -F 'bin/komodo'", + "| tail --lines=1"), intern = TRUE, ignore.stderr = TRUE)), + silent = TRUE) + debugMsg("locate komodo", "returned", Komodo) + } + } else Komodo <- NULL } } else { # Windows @@ -468,7 +480,7 @@ key <- "Applications\\komodo.exe\\shell\\open\\command" Komodo <- tryCatch(readRegistry(key, hive = "HCR")[["(Default)"]], - error = err.null) + error = err.null) if (!is.null(Komodo)) Komodo <- sub(" *\\\"%[1-9\\*].*$", "", Komodo) } @@ -493,34 +505,59 @@ debugMsg("Komodo path is:", Komodo) } - if (!is.null(Komodo) && Komodo != "" && file.exists(Komodo)) { + if (length(Komodo) && Komodo != "" && file.exists(Komodo)) { ## Change the editor and the pager to Komodo + options(pager2 = getOption("pager")) ## A custom pager consists in displaying the file in Komodo svPager <- function (files, header, title, delete.file) { require(svKomodo) files <- gsub("\\", "\\\\", files[1], fixed = TRUE) - koCmd(sprintf('sv.r.pager("%s", "%s")', files, title)) - if (delete.file) { - cmd <- paste('window.setTimeout("try { ', - 'sv.tools.file.getfile(\\"%s\\").remove(false); } ', - 'catch(e) {}", 10000);', sep = "") - koCmd(sprintf(cmd, files)); + res <- tryCatch(koCmd(sprintf('sv.r.pager("%s", "%s")', files, title)), + error = function (e) return(FALSE)) + if (res == FALSE) { + ## Try using pager2 instead + pager2 <- getOption("pager2") + if (is.null(pager2)) { + stop("You must start Komodo Edit for displaying this file!") + } else if (is.function(pager2)) { + pager2(files = files, header = header, title = title, + delete.file = delete.file) + } else { + ## Replacement for the following line of code to avoid + ## using .Internal() + #.Internal(file.show(files, header, title, delete.file, pager2)) + file.show(files, header = header, title = title, + delete.file = delete.file, pager = pager2) + } + } else { + if (delete.file) { + cmd <- paste('window.setTimeout("try { ', + 'sv.tools.file.getfile(\\"%s\\").remove(false); } ', + 'catch(e) {}", 10000);', sep = "") + koCmd(sprintf(cmd, files)) + } } } + options(browser2 = getOption("browser")) svBrowser <- function (url) { require(svKomodo) url <- gsub("\\", "\\\\", url, fixed = TRUE) ## If the URL starts with '/', I could safely assume a file path ## on Unix or Mac and prepend 'file://' url <- sub("^/", "file:///", url) - koCmd(sprintf("sv.command.openHelp(\"%s\")", url)) + res <- tryCatch(koCmd(sprintf("sv.command.openHelp(\"%s\")", url)), + error = function (e) return(FALSE)) + if (res == FALSE) { + ## Try using browser2 instead + browser2 <- getOption("browser2") + if (is.null(browser2)) { + stop("You must start Komodo Edit for browsing files") + } else browseURL(url, browser = browser2) + } } - ## The current SciViews-K help window in Komodo is buggy - ## it let's Komodo crash on closing, and probably causes - ## other problems => for now, just use the default browser! - #options(editor = Komodo, browser = svBrowser, pager = svPager) - options(editor = Komodo) + option(editor2 = getOption("editor")) + options(editor = Komodo, browser = svBrowser, pager = svPager) } else { Komodo <- NULL cat("R cannot find Komodo.", file = stderr()) @@ -590,7 +627,7 @@ } ## Change the working directory to the provided directory - setwd(getOption("R.initdir")) + try(setwd(getOption("R.initdir")), silent = TRUE) ## Create a .Last.sys function that clears some variables in .GlobalEnv ## and then, switch to R.initdir before closing R. The function is @@ -621,7 +658,7 @@ if (!"--vanilla" %in% args && !"--no-restore" %in% args && !"--no.restore-data" %in% args) { if (file.exists(".RData")) { - load(".RData") + load(".RData", envir = .GlobalEnv) msg2 <- append(msg2, "data loaded") } else { msg2 <- append(msg2, "no data") @@ -644,7 +681,7 @@ msg2 <- append(msg2, "data and history not loaded") } - cat(msg, " (", paste(msg2, collapse=", "), ")", "\n", + cat(msg, " (", paste(msg2, collapse = ", "), ")", "\n", sep = "", file = stderr()) ## Do we reactivate Komodo now? Modified: pkg/svKomodo/DESCRIPTION =================================================================== --- pkg/svKomodo/DESCRIPTION 2013-01-30 15:02:47 UTC (rev 526) +++ pkg/svKomodo/DESCRIPTION 2013-02-11 21:07:56 UTC (rev 527) @@ -1,7 +1,7 @@ Package: svKomodo Type: Package -Version: 0.9-59 -Date: 2013-01-27 +Version: 0.9-60 +Date: 2013-02-11 Title: SciViews GUI API - Functions to interface with Komodo Edit/IDE Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"), email = "phgrosjean at sciviews.org")) Modified: pkg/svKomodo/NEWS =================================================================== --- pkg/svKomodo/NEWS 2013-01-30 15:02:47 UTC (rev 526) +++ pkg/svKomodo/NEWS 2013-02-11 21:07:56 UTC (rev 527) @@ -1,7 +1,12 @@ = svKomodo News -== Change in svKomodo 0.9-59 +== Changes in svKomodo 0.9-60 +* .onAttach() is reworked for not issuing warning messages in Mac OS X. + + +== Changes in svKomodo 0.9-59 + * R is now configured to be used with SciViews Komodo (Komodo Edit + SciViews-K) when the package is attached. It was previously configured when it was loaded. Modified: pkg/svKomodo/R/svKomodo-internal.R =================================================================== --- pkg/svKomodo/R/svKomodo-internal.R 2013-01-30 15:02:47 UTC (rev 526) +++ pkg/svKomodo/R/svKomodo-internal.R 2013-02-11 21:07:56 UTC (rev 527) @@ -158,17 +158,19 @@ } if (length(Komodo) == 0 || Komodo == "") { - isLocate <- suppressWarnings(length(system('which locate', - intern = TRUE)) > 0) - if (!isLocate || isMac()) { # locate is not there or Mac OS X - Komodo <- NULL - } else { - Komodo <- try(suppressWarnings(system( - "locate --basename -e --regex ^komodo$ | grep -vF 'INSTALLDIR' | grep -F 'bin/komodo' | tail --lines=1", - intern = TRUE, ignore.stderr = TRUE)), silent = TRUE) - if (inherits(Komodo, "try-error")) Komodo <- NULL - #debugMsg("locate komodo", "returned", Komodo) - } + if (!isMac()) { + isLocate <- suppressWarnings(length(system('which locate', + intern = TRUE)) > 0) + if (!isLocate) { # locate is not there + Komodo <- NULL + } else { + Komodo <- try(suppressWarnings(system( + "locate --basename -e --regex ^komodo$ | grep -vF 'INSTALLDIR' | grep -F 'bin/komodo' | tail --lines=1", + intern = TRUE, ignore.stderr = TRUE)), silent = TRUE) + if (inherits(Komodo, "try-error")) Komodo <- NULL + #debugMsg("locate komodo", "returned", Komodo) + } + } else Komodo <- NULL } ## Just to avoid warnings while compiling outside of Windows... readRegistry <- function() return() Modified: pkg/svKomodo/inst/NEWS.Rd =================================================================== --- pkg/svKomodo/inst/NEWS.Rd 2013-01-30 15:02:47 UTC (rev 526) +++ pkg/svKomodo/inst/NEWS.Rd 2013-02-11 21:07:56 UTC (rev 527) @@ -1,8 +1,14 @@ \name{NEWS} \title{NEWS file for the svKomodo package} +\section{Changes in version 0.9-60}{ + \itemize{ + \item{ You must start Komodo Edit for browsing files. } + } +} + \section{Changes in version 0.9-59}{ - \itemize{ + \itemize{ \item{ R is now configured to be used with SciViews Komodo (Komodo Edit + SciViews-K) when the package is attached. It was previously configured when it was loaded. } @@ -15,21 +21,21 @@ } \section{Changes in version 0.9-58}{ - \itemize{ + \itemize{ \item{ The package was not loading correctly when not on \code{.libPaths}. Fixed. } } } \section{Changes in version 0.9-57}{ - \itemize{ + \itemize{ \item{ svKomodo creates now at loading a \code{.Last.sys()} function in - \code{SciViews:TempEnv} indicating to Komodo Edit that R has quit. This - is required to update R menus there. } + \code{SciViews:TempEnv} indicating to Komodo Edit that R has quit. This + is required to update R menus there. } - \item{ The SciViews-K configuration file is not saved from here anymore - (CRAN now does not accept packages that write files elsewhere than in R - temp dir). This configuration file is now created by the SciViews-K Komodo - plugin, in \preformatted{svStart.R}. } + \item{ The SciViews-K configuration file is not saved from here anymore + (CRAN now does not accept packages that write files elsewhere than in R + temp dir). This configuration file is now created by the SciViews-K Komodo + plugin, in \preformatted{svStart.R}. } } } Modified: pkg/svKomodo/man/svKomodo-package.Rd =================================================================== --- pkg/svKomodo/man/svKomodo-package.Rd 2013-01-30 15:02:47 UTC (rev 526) +++ pkg/svKomodo/man/svKomodo-package.Rd 2013-02-11 21:07:56 UTC (rev 527) @@ -13,8 +13,8 @@ \tabular{ll}{ Package: \tab svKomodo\cr Type: \tab Package\cr - Version: \tab 0.9-58\cr - Date: \tab 2012-06-22\cr + Version: \tab 0.9-60\cr + Date: \tab 2013-02-11\cr License: \tab GPL 2 or above, at your convenience\cr } % TODO: add description of main functions here. Also add examples From noreply at r-forge.r-project.org Mon Feb 11 23:54:15 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 11 Feb 2013 23:54:15 +0100 (CET) Subject: [Sciviews-commits] r528 - komodo/SciViews-K/defaults Message-ID: <20130211225415.A38A1184860@r-forge.r-project.org> Author: phgrosjean Date: 2013-02-11 23:54:15 +0100 (Mon, 11 Feb 2013) New Revision: 528 Added: komodo/SciViews-K/defaults/R reference (0.9.30).kpz komodo/SciViews-K/defaults/ascii_2.1.tar.gz komodo/SciViews-K/defaults/ascii_2.1.zip komodo/SciViews-K/defaults/svDoc_0.9-7.tar.gz komodo/SciViews-K/defaults/svDoc_0.9-7.zip komodo/SciViews-K/defaults/svKomodo_0.9-60.tar.gz komodo/SciViews-K/defaults/svKomodo_0.9-60.zip komodo/SciViews-K/defaults/svMisc_0.9-68.tar.gz komodo/SciViews-K/defaults/svMisc_0.9-68.zip komodo/SciViews-K/defaults/svSocket_0.9-55.tar.gz komodo/SciViews-K/defaults/svSocket_0.9-55.zip Removed: komodo/SciViews-K/defaults/R reference (0.9.29).kpz komodo/SciViews-K/defaults/svKomodo_0.9-58.tar.gz komodo/SciViews-K/defaults/svKomodo_0.9-58.zip komodo/SciViews-K/defaults/svMisc_0.9-67.tar.gz komodo/SciViews-K/defaults/svMisc_0.9-67.zip komodo/SciViews-K/defaults/svSocket_0.9-53.tar.gz komodo/SciViews-K/defaults/svSocket_0.9-53.zip Modified: komodo/SciViews-K/defaults/.DS_Store komodo/SciViews-K/defaults/SciViews_0.9-10.zip komodo/SciViews-K/defaults/svHttp_0.9-54.tar.gz komodo/SciViews-K/defaults/svHttp_0.9-54.zip komodo/SciViews-K/defaults/svStart.R komodo/SciViews-K/defaults/svTools_0.9-3.tar.gz komodo/SciViews-K/defaults/svTools_0.9-3.zip komodo/SciViews-K/defaults/toolbox.zip Log: Slight change in svStart.R + update of R packages in SciViews-K + addition of ascii and svDoc Modified: komodo/SciViews-K/defaults/.DS_Store =================================================================== (Binary files differ) Deleted: komodo/SciViews-K/defaults/R reference (0.9.29).kpz 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differ) Property changes on: komodo/SciViews-K/defaults/svKomodo_0.9-60.zip ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Deleted: komodo/SciViews-K/defaults/svMisc_0.9-67.tar.gz =================================================================== (Binary files differ) Deleted: komodo/SciViews-K/defaults/svMisc_0.9-67.zip =================================================================== (Binary files differ) Added: komodo/SciViews-K/defaults/svMisc_0.9-68.tar.gz =================================================================== (Binary files differ) Property changes on: komodo/SciViews-K/defaults/svMisc_0.9-68.tar.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: komodo/SciViews-K/defaults/svMisc_0.9-68.zip =================================================================== (Binary files differ) Property changes on: komodo/SciViews-K/defaults/svMisc_0.9-68.zip ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Deleted: komodo/SciViews-K/defaults/svSocket_0.9-53.tar.gz =================================================================== (Binary files differ) Deleted: komodo/SciViews-K/defaults/svSocket_0.9-53.zip =================================================================== (Binary files differ) Added: komodo/SciViews-K/defaults/svSocket_0.9-55.tar.gz =================================================================== (Binary files differ) Property changes on: komodo/SciViews-K/defaults/svSocket_0.9-55.tar.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: komodo/SciViews-K/defaults/svSocket_0.9-55.zip =================================================================== (Binary files differ) Property changes on: komodo/SciViews-K/defaults/svSocket_0.9-55.zip ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: komodo/SciViews-K/defaults/svStart.R =================================================================== --- komodo/SciViews-K/defaults/svStart.R 2013-02-11 21:07:56 UTC (rev 527) +++ komodo/SciViews-K/defaults/svStart.R 2013-02-11 22:54:15 UTC (rev 528) @@ -556,7 +556,7 @@ } else browseURL(url, browser = browser2) } } - option(editor2 = getOption("editor")) + options(editor2 = getOption("editor")) options(editor = Komodo, browser = svBrowser, pager = svPager) } else { Komodo <- NULL Modified: komodo/SciViews-K/defaults/svTools_0.9-3.tar.gz =================================================================== (Binary files differ) Modified: komodo/SciViews-K/defaults/svTools_0.9-3.zip =================================================================== (Binary files differ) Modified: komodo/SciViews-K/defaults/toolbox.zip =================================================================== (Binary files differ)