[Genabel-commits] r1936 - in pkg/DatABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 30 13:26:54 CEST 2015
Author: lckarssen
Date: 2015-03-30 13:26:54 +0200 (Mon, 30 Mar 2015)
New Revision: 1936
Removed:
pkg/DatABEL/R/checkPackageVersionOnCRAN.R
pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd
Modified:
pkg/DatABEL/ChangeLog
pkg/DatABEL/DESCRIPTION
pkg/DatABEL/NAMESPACE
pkg/DatABEL/R/zzz.R
Log:
DatABEL: Preparing for CRAN upload of minor update.
- Make myself maintainer instead of Yurii
- Remove the CRAN package version check at the request of Prof. Ripley (inappropriate use of CRAN, wrongly implemented (i.e. we took the Amsterdam mirror by default)).
Modified: pkg/DatABEL/ChangeLog
===================================================================
--- pkg/DatABEL/ChangeLog 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/ChangeLog 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,5 +1,14 @@
-**** v. 0.9-5 (2013.09.11)
+**** v. 0.9-6 (2015.03.30)
+- Removed the check for the current version of DatABEL on CRAN at the
+ request of Prof. Ripley.
+- Added missing Roxygen documentation for a few variables that R CMD check
+ was complaining about.
+- Converted inst/unitTests/Makefile to Unix format (LF line endings)
+ because R CMD check gave a warning about the CR or CRLF line endings.
+
+**** v. 0.9-5 (2014.01.05)
+
- Converted documentation to roxygen2 format (Lennart)
- Fixed bug #5793: impute2DatABEL gives several errors (Maksim)
- Fixed bug #1126: Using mach2databel() or impute2mach() to convert files
Modified: pkg/DatABEL/DESCRIPTION
===================================================================
--- pkg/DatABEL/DESCRIPTION 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/DESCRIPTION 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,11 +1,11 @@
Package: DatABEL
Type: Package
Title: file-based access to large matrices stored on HDD in binary format
-Version: 0.9-5
-Date: 2014-07-28
+Version: 0.9-6
+Date: 2015-03-30
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim
- Struchalin
-Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
+ Struchalin, Lennart C. Karssen
+Maintainer: Lennart Karssen <lennart at karssen.org>
Depends:
R (>= 2.4.0),
methods,
Modified: pkg/DatABEL/NAMESPACE
===================================================================
--- pkg/DatABEL/NAMESPACE 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/NAMESPACE 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2 (4.1.0): do not edit by hand
S3method(as.double,databel)
export("cachesizeMb<-")
Deleted: pkg/DatABEL/R/checkPackageVersionOnCRAN.R
===================================================================
--- pkg/DatABEL/R/checkPackageVersionOnCRAN.R 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/R/checkPackageVersionOnCRAN.R 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,94 +0,0 @@
-#' checks what is the version of package on CRAN
-#'
-#' Checks what is the version of package on CRAN.
-#' The CRAN page (baseUrlCRAN+packageName) is checked
-#' and parsed extracting the line with
-#' "Package source: packageName_Version.tar.gz"
-#' e.g.
-#' "Package source: GenABEL_1.6-9.tar.gz"
-#' and then the 'Version' is returned.
-#' Otherwise, NULL is returned.
-#'
-#' @return string containing CRAN version
-#' of the package
-#'
-#' @param packageName name of the package to check
-#'
-#' @examples
-#' library(GenABEL)
-#' packageVersion("GenABEL")
-#' checkPackageVersionOnCRAN("GenABEL")
-#'
-#' @author Yurii Aulchenko
-#'
-checkPackageVersionOnCRAN <- function(packageName)
-{
-
-
-mirror_df <- getCRANmirrors(all = FALSE, local.only = FALSE)
-mirror <- mirror_df$URL[mirror_df$Country == "Netherlands" & mirror_df$City == "Amsterdam"]
-
-
-CRAN_mirror_ref <- paste(mirror, "/src/contrib", sep="")
-
-all_cran_packs <- available.packages(contriburl=CRAN_mirror_ref)
-all_cran_packs_df <- as.data.frame(all_cran_packs)
-
-databel_info <- all_cran_packs_df[all_cran_packs_df$Package == "DatABEL",]
-cranVersion <- as.character(databel_info$Version)
-
-return(cranVersion)
-
-
-
-# Below is an old verion which depends on CRAN site content that is unreliable.
-
-# # change default timout
-# svtmo <- options("timeout")
-# options("timeout"=timeout)
-# # page to check is
-# pageAddress <- paste(baseUrlCRAN,packageName,sep="/")
-# # establish connection to the CRAN page of the package
-# suppressWarnings(
-# conn <- try( url(pageAddress) , silent=TRUE )
-# )
-# # if connection ok, read full page, store the results in pageContent; if failed, pageContent <- "try-error"
-# if ( all( class(conn) != "try-error") ) {
-# suppressWarnings(
-# pageContent <- try( readLines(conn) , silent=TRUE )
-# )
-# close(conn)
-# } else {
-# pageContent <- "try-error"
-# class(pageContent) <- "try-error"
-# }
-# # restore default timeout
-# options("timeout"=svtmo)
-# # if failed in reading (pageContent is "try-error"), return NULL
-# if (class(pageContent) == "try-error") return(NULL)
-# # parse the page and get string starting with "Package source:"
-# targetLine <- pageContent[grep("source:",pageContent)]
-# # split the string at "Package_" and ".tar.gz"; the element before the last will contain the version
-# splitPattern <- paste(packageName,"_|.tar.gz",sep="")
-# stringSplit <- strsplit(targetLine,splitPattern)
-# cranVersion <- stringSplit[[1]][length(stringSplit[[1]])-1]
-# # return version
-# return(cranVersion)
-
-
-
-# Below is a patch received from Marco De Simone <marco.desimone at cbm.fvg.it>. This version is, however, use content if CRAN that is aso unreliable.
-#
-#options("timeout"=svtmo)
-## if failed in reading (pageContent is "try-error"), return NULL
-#if (class(pageContent) == "try-error") return(NULL)
-## parse the table inside the page for the cell with the content "Version:" and select the following cell that contains the version"
-#targetLine <- pageContent[grep("Version:",pageContent)+1]
-## Strip the html tags <td> and </td> and get the content value of version
-#splitPattern <- paste("<td>|</td>",sep="")
-#
-#cranVersion <- stringSplit[[1]][length(stringSplit[[1]])]
-## return version
-#return(cranVersion)
-
-}
Modified: pkg/DatABEL/R/zzz.R
===================================================================
--- pkg/DatABEL/R/zzz.R 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/R/zzz.R 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,24 +1,7 @@
.onAttach <- function(lib, pkg) {
- pkgVersion <- "0.9-5"
- pkgDate <- "July 28 2014"
- welcomeMessage <- paste(pkg, " v.", pkgVersion,
- " (", pkgDate, ") loaded\n", sep="")
+ pkgVersion <- "0.9-6"
+ welcomeMessage <- paste0(pkg, " v.", pkgVersion," loaded\n")
- ## check if CRAN version is the same as loaded
- cranVersion <- try( checkPackageVersionOnCRAN(pkg) )
- if (!is.null(cranVersion) & !( class(cranVersion) == "try-error") & length(cranVersion) != 0)
- if (pkgVersion != cranVersion) {
- welcomeMessage <- paste(welcomeMessage,
- "\nInstalled ",pkg," version (",
- pkgVersion, ") is not the same as stable\n",
- "version available from CRAN (",
- cranVersion, "). Unless used intentionally,\n",
- "consider updating to the latest CRAN version. For that, use\n",
- "'install.packages(\"", pkg,
- "\")', or ask your system administrator\n",
- "to update the package.\n\n", sep="")
- }
-
## check for news
address <- c(
"http://genabel.r-forge.r-project.org/version_and_news.html",
Deleted: pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd
===================================================================
--- pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd 2015-03-30 11:23:25 UTC (rev 1935)
+++ pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd 2015-03-30 11:26:54 UTC (rev 1936)
@@ -1,33 +0,0 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{checkPackageVersionOnCRAN}
-\alias{checkPackageVersionOnCRAN}
-\title{checks what is the version of package on CRAN}
-\usage{
-checkPackageVersionOnCRAN(packageName)
-}
-\arguments{
-\item{packageName}{name of the package to check}
-}
-\value{
-string containing CRAN version
-of the package
-}
-\description{
-Checks what is the version of package on CRAN.
-The CRAN page (baseUrlCRAN+packageName) is checked
-and parsed extracting the line with
-"Package source: packageName_Version.tar.gz"
-e.g.
-"Package source: GenABEL_1.6-9.tar.gz"
-and then the 'Version' is returned.
-Otherwise, NULL is returned.
-}
-\examples{
-library(GenABEL)
-packageVersion("GenABEL")
-checkPackageVersionOnCRAN("GenABEL")
-}
-\author{
-Yurii Aulchenko
-}
-
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