[med-svn] [r-bioc-biobase] 04/06: Imported Upstream version 2.26.0
Andreas Tille
tille at debian.org
Thu Oct 16 16:59:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-biobase.
commit c879a2e0bc8bc52ca42a1fd6d106d520b0d6fcb8
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 16 16:43:11 2014 +0200
Imported Upstream version 2.26.0
---
DESCRIPTION | 4 +-
build/vignette.rds | Bin 481 -> 344 bytes
inst/doc/BiobaseDevelopment.pdf | Bin 246481 -> 246497 bytes
inst/doc/Bioconductor.R | 8 --
inst/doc/Bioconductor.pdf | Bin 71100 -> 0 bytes
inst/doc/ExpressionSetIntroduction.pdf | Bin 174953 -> 174973 bytes
inst/doc/HowTo.R | 8 --
inst/doc/HowTo.pdf | Bin 54524 -> 0 bytes
inst/doc/Qviews.R | 120 ----------------
inst/doc/Qviews.pdf | Bin 77433 -> 0 bytes
inst/doc/esApply.pdf | Bin 93274 -> 93273 bytes
vignettes/Bioconductor.Rnw | 96 -------------
vignettes/HowTo.Rnw | 91 ------------
vignettes/Qviews.Rnw | 176 ------------------------
{inst/doc => vignettes/legacy}/Bioconductor.Rnw | 0
{inst/doc => vignettes/legacy}/HowTo.Rnw | 0
{inst/doc => vignettes/legacy}/Qviews.Rnw | 0
17 files changed, 2 insertions(+), 501 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 408a9b1..53702b3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: Biobase
Title: Biobase: Base functions for Bioconductor
-Version: 2.24.0
+Version: 2.26.0
Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
Description: Functions that are needed by many other packages or which
replace R functions.
@@ -21,4 +21,4 @@ Collate: tools.R strings.R environment.R vignettes.R packages.R
updateObjectTo.R methods-ScalarObject.R zzz.R
LazyLoad: yes
biocViews: Infrastructure
-Packaged: 2014-04-12 05:10:37 UTC; biocbuild
+Packaged: 2014-10-14 00:25:57 UTC; biocbuild
diff --git a/build/vignette.rds b/build/vignette.rds
index e8cce3d..0cf9324 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/BiobaseDevelopment.pdf b/inst/doc/BiobaseDevelopment.pdf
index 57ad635..98ec3c9 100644
Binary files a/inst/doc/BiobaseDevelopment.pdf and b/inst/doc/BiobaseDevelopment.pdf differ
diff --git a/inst/doc/Bioconductor.R b/inst/doc/Bioconductor.R
deleted file mode 100644
index f9d667b..0000000
--- a/inst/doc/Bioconductor.R
+++ /dev/null
@@ -1,8 +0,0 @@
-### R code from vignette source 'Bioconductor.Rnw'
-
-###################################################
-### code chunk number 1: Bioconductor.Rnw:91-92
-###################################################
-sessionInfo()
-
-
diff --git a/inst/doc/Bioconductor.pdf b/inst/doc/Bioconductor.pdf
deleted file mode 100644
index 0d6bdf8..0000000
Binary files a/inst/doc/Bioconductor.pdf and /dev/null differ
diff --git a/inst/doc/ExpressionSetIntroduction.pdf b/inst/doc/ExpressionSetIntroduction.pdf
index 0556913..7ebbb9e 100644
Binary files a/inst/doc/ExpressionSetIntroduction.pdf and b/inst/doc/ExpressionSetIntroduction.pdf differ
diff --git a/inst/doc/HowTo.R b/inst/doc/HowTo.R
deleted file mode 100644
index 14ba6ce..0000000
--- a/inst/doc/HowTo.R
+++ /dev/null
@@ -1,8 +0,0 @@
-### R code from vignette source 'HowTo.Rnw'
-
-###################################################
-### code chunk number 1: HowTo.Rnw:86-87
-###################################################
-sessionInfo()
-
-
diff --git a/inst/doc/HowTo.pdf b/inst/doc/HowTo.pdf
deleted file mode 100644
index c0d25dc..0000000
Binary files a/inst/doc/HowTo.pdf and /dev/null differ
diff --git a/inst/doc/Qviews.R b/inst/doc/Qviews.R
deleted file mode 100644
index 40f4346..0000000
--- a/inst/doc/Qviews.R
+++ /dev/null
@@ -1,120 +0,0 @@
-### R code from vignette source 'Qviews.Rnw'
-
-###################################################
-### code chunk number 1: doa
-###################################################
-if (!("Biobase" %in% search())) library(Biobase)
-if (!("ALL" %in% search())) library(ALL)
-if (!("ALL" %in% objects())) data(ALL)
-
-
-###################################################
-### code chunk number 2: getaEF (eval = FALSE)
-###################################################
-## library(Biobase)
-## library(ALL)
-## data(ALL)
-## ALL
-
-
-###################################################
-### code chunk number 3: mkprov
-###################################################
-dataSource = function(dsn) {
- if (!is(dsn, "character")) dsn = try(deparse(substitute(dsn)))
- if (inherits(dsn, "try-error")) stop("can't parse dsn arg")
- dd = data()$results
- if (is.na(match(dsn, dd[,"Item"]))) return(NULL)
- paste("package:", dd[ dd[,"Item"] == dsn, "Package" ], sep="")
-}
-
-
-
-
-###################################################
-### code chunk number 4: newmeth
-###################################################
-setGeneric("peek", function(x,maxattr=10)standardGeneric("peek"))
-setMethod("peek", c("eSet", "numeric"), function(x,maxattr=10) {
- ds = dataSource(deparse(substitute(x)))
- if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="")
- else ds = ""
- cat(deparse(substitute(x)), ds, ":\n", sep="")
- cat("Platform annotation: ", annotation(x),"\n")
- cat("primary assay results are:\n")
- print(dim(x))
- cat("sample attributes are:\n")
- vn = rownames(varMetadata(x))
- ld = substr(varMetadata(x)$labelDescription,1,50)
- dd = data.frame("labelDescription[truncated]"=ld)
- rownames(dd) = vn
- if ((ndd <- nrow(dd)) <= maxattr) show(dd)
- else {
- cat("first", maxattr, "of", ndd, "attributes:\n")
- show(dd[1:maxattr,,drop=FALSE])
- }
- cat("----------\n")
- cat("use varTable to see values/freqs of all sample attributes\n")
- cat("----------\n")
-})
-setMethod("peek", c("eSet", "missing"), function(x,maxattr=10) {
- ds = dataSource(deparse(substitute(x)))
- if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="")
- else ds = ""
- cat(deparse(substitute(x)), ds, ":\n", sep="")
- cat("Platform annotation: ", annotation(x),"\n")
- cat("primary assay results are:\n")
- print(dim(x))
- cat("sample attributes are:\n")
- vn = rownames(varMetadata(x))
- ld = substr(varMetadata(x)$labelDescription,1,50)
- dd = data.frame("labelDescription[truncated]"=ld)
- rownames(dd) = vn
- if ((ndd <- nrow(dd)) <= maxattr) show(dd)
- else {
- cat("first", maxattr, "of", ndd, "attributes:\n")
- show(dd[1:maxattr,,drop=FALSE])
- }
- cat("----------\n")
- cat("use varTable to see values/freqs of all sample attributes\n")
- cat("----------\n")
-})
-setGeneric("varTable", function(x, full=FALSE, max=Inf) standardGeneric("varTable"))
-setMethod("varTable", c("eSet", "missing", "ANY"), function(x, full=FALSE, max=Inf) varTable(x, FALSE, max))
-setMethod("varTable", c("eSet", "logical", "ANY"), function(x, full=FALSE, max=Inf) {
- ans = lapply( names(pData(x)), function(z)table(x[[z]]) )
- tans = lapply(ans, names)
- kp = 1:min(max,length(tans))
- if (!full) ans = sapply(tans, selectSome, 3)[kp]
- else ans = tans[kp]
- names(ans) = names(pData(x))[kp]
- ans
-})
-setGeneric("varNames", function(x) standardGeneric("varNames"))
-setMethod("varNames", "eSet", function(x) names(pData(x)))
-
-
-###################################################
-### code chunk number 5: lka
-###################################################
-peek(ALL)
-
-
-###################################################
-### code chunk number 6: lkv
-###################################################
-varNames(ALL)
-
-
-###################################################
-### code chunk number 7: lkvn
-###################################################
-varTable(ALL, max=4)
-
-
-###################################################
-### code chunk number 8: lkvn
-###################################################
-varTable(ALL, full=TRUE, max=4)
-
-
diff --git a/inst/doc/Qviews.pdf b/inst/doc/Qviews.pdf
deleted file mode 100644
index 42d60b3..0000000
Binary files a/inst/doc/Qviews.pdf and /dev/null differ
diff --git a/inst/doc/esApply.pdf b/inst/doc/esApply.pdf
index b192161..56287aa 100644
Binary files a/inst/doc/esApply.pdf and b/inst/doc/esApply.pdf differ
diff --git a/vignettes/Bioconductor.Rnw b/vignettes/Bioconductor.Rnw
deleted file mode 100644
index daadd8a..0000000
--- a/vignettes/Bioconductor.Rnw
+++ /dev/null
@@ -1,96 +0,0 @@
-%
-% NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is
-% likely to be overwritten.
-%
-%\VignetteIndexEntry{Bioconductor Overview}
-%\VignetteDepends{}
-%\VignetteKeywords{Documentation}
-%\VignettePackage{Biobase}
-\documentclass[12pt]{article}
-
-\usepackage{times}
-\usepackage{hyperref}
-
-
-\textwidth=6.2in
-\textheight=8.5in
-%\parskip=.3cm
-\oddsidemargin=.1in
-\evensidemargin=.1in
-\headheight=-.3in
-
-\newcommand{\scscst}{\scriptscriptstyle}
-\newcommand{\scst}{\scriptstyle}
-
-\bibliographystyle{plainnat}
-
-\begin{document}
-
-\title{What is Bioconductor}
-\maketitle
-
-\section*{Prequisites}
-
-Bioconductor is a project to develop innovative software tools for use
-in computational biology.
-It is based on the R language ({\url www.r-project.org}).
-You should already be quite familiar with R before using
-Bioconductor. There are several on--line resources that can help you
-get started using R. They can be found from the R website.
-Some users find this a very steep learning curve; your experience may
-be similar.
-
-Bioconductor packages provide flexible interactive tools for carrying
-out a number of different computational tasks. They are generally not
-as fast as other analysis tools (since they are interactive) and often
-reflect current ideas. Most can be improved and interested users should
-file bug reports and feature requests on the Bioconductor mailing list.
-
-
-Bioconductor welcome collaboration in many different forms. These
-include new packages, fixes or additions to existing packages and help
-on different projects that are currently underway.
-Please see the {\em Current Projects} web page to see if there are any
-projects that are intersting to you.
-
-\subsection*{How to report a bug}
-
-Please provide enough information for us to help you. This typically
-includes the platform (windows, Unix, Macintosh) that you are using as
-well as version numbers for R and for the package that seems to be
-working incorrectly.
-
-Include a small complete example that can be run and demonstrates the
-problem. In some cases it is also important that you describe what you
-thought you should get.
-
-Please note:
-\begin{itemize}
-\item bugs in R should be reported to the R community
-\item missing features are not bugs -- they are feature requests.
-\end{itemize}
-
-\section{Bioconductor Design}
-
-Bioconductor relies on the R package system to distribute code and
-data. Most packages use S4 methods and classes (as described in {\em
- Programming with Data} by J. M. Chambers). This adherence to object
-oriented programming makes it easier to build component software and
-helps to deal with the complexity of the data.
-
-One of the important Bioconductor packages is {\em annotate}. This
-package provides access to various genomic annotation data.
-This package makes use of various web resources and precompiled data
-packages to provide tools for exploring biological data.
-
-\section{Session Information}
-
-The version number of R and packages loaded for generating the vignette were:
-
-\begin{verbatim}
-<<echo=FALSE,results=tex>>=
-sessionInfo()
-@
-\end{verbatim}
-
-\end{document}
diff --git a/vignettes/HowTo.Rnw b/vignettes/HowTo.Rnw
deleted file mode 100644
index 6d670a3..0000000
--- a/vignettes/HowTo.Rnw
+++ /dev/null
@@ -1,91 +0,0 @@
-%
-% NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is
-% likely to be overwritten.
-%
-% \VignetteIndexEntry{Notes for writing introductory 'how to' documents}
-%\VignetteDepends{}
-%\VignetteKeywords{Expression Analysis}
-%\VignettePackage{Biobase}
-\documentclass[12pt]{article}
-
-\usepackage{times}
-\usepackage{hyperref}
-
-\newcommand{\Rfunction}[1]{{\texttt{#1}}}
-\newcommand{\Robject}[1]{{\texttt{#1}}}
-\newcommand{\Rpackage}[1]{{\textit{#1}}}
-\newcommand{\Rmethod}[1]{{\texttt{#1}}}
-\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
-\newcommand{\Rclass}[1]{{\textit{#1}}}
-
-\textwidth=6.2in
-\textheight=8.5in
-%\parskip=.3cm
-\oddsidemargin=.1in
-\evensidemargin=.1in
-\headheight=-.3in
-
-\newcommand{\scscst}{\scriptscriptstyle}
-\newcommand{\scst}{\scriptstyle}
-
-\bibliographystyle{plainnat}
-
-\begin{document}
-
-\section*{How to write a HowTo}
-
-One of the goals of the Bioconductor project is to produce (and
-encourage others to produce) documentation on how to perform various
-tasks. Our main interest is in tasks associated with computational
-biology. However, we hope to produce HowTo documents for a wide
-variety of tasks.
-
-R has a very good mechanism for documenting individual functions,
-methods and classes. However, there are many situations where the task
-that we want to perform requires the use of many components. In other
-cases we would like to document the overall purpose of an R package
-rather than the individual functions. In this document we provide some
-advice on how to construct a document to describe how to perform a task.
-
-In most cases HowTo's will be written using \Rfunction{Sweave} in the
-\Rpackage{tools} package.
-In this document we give some general advice on how to write a HowTo.
-Of courese there is no \textit{right} way to do this but we feel that we
-can provide a few design principles that will help authors write
-better HowTo's.
-
-
-These design principles are listed below:
-\begin{itemize}
-\item It should be short (2 pages at most) and explicit.
-\item It should be about a single topic.
-\item It should contain runnable code and rely on data that are
- available in R or the libraries needed to carry out the task being
- documented.
-\item HowTo's should not be about single functions. The function
- documentation is the right place to document that. HowTo's should
- document a process or task and will typically involve several functions.
-
-\item To paraphrase Paul Halmos, you should imagine that you are
- writing a document for a friend who is as smart and has the same
- general level of knowledge as you but who does
- not know how to do the specific task at hand.
-
-\item Make use of the indexing system. The title of the document should
-be included in the \verb+% \VignetteIndexEntry+.
-It should
-contain the word \verb+HowTo+ to easily allow for programmatic
-manipulation and sorting of the HowTo's.
-\end{itemize}
-
-\section{Session Information}
-
-The version number of R and packages loaded for generating the vignette were:
-
-\begin{verbatim}
-<<echo=FALSE,results=tex>>=
-sessionInfo()
-@
-\end{verbatim}
-
-\end{document}
diff --git a/vignettes/Qviews.Rnw b/vignettes/Qviews.Rnw
deleted file mode 100644
index f2bfbd9..0000000
--- a/vignettes/Qviews.Rnw
+++ /dev/null
@@ -1,176 +0,0 @@
-%\VignetteIndexEntry{quick views of eSet instances}
-%\VignetteDepends{Biobase, ALL}
-%\VignetteKeywords{Data representation, Analysis}
-%\VignettePackage{Biobase}
-
-
-%
-% NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is
-% likely to be overwritten.
-%
-\documentclass[12pt]{article}
-\usepackage{amsmath,fullpage}
-\usepackage[authoryear,round]{natbib}
-\usepackage{hyperref}
-
-
-\textwidth=6.2in
-\textheight=8.5in
-%\parskip=.3cm
-\oddsidemargin=.1in
-\evensidemargin=.1in
-\headheight=-.3in
-
-\newcommand{\scscst}{\scriptscriptstyle}
-\newcommand{\scst}{\scriptstyle}
-
-
-\newcommand{\Rfunction}[1]{{\texttt{#1}}}
-\newcommand{\Robject}[1]{{\texttt{#1}}}
-\newcommand{\Rpackage}[1]{{\textit{#1}}}
-\newcommand{\Rmethod}[1]{{\texttt{#1}}}
-\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
-\newcommand{\Rclass}[1]{{\textit{#1}}}
-
-\textwidth=6.2in
-
-\bibliographystyle{plainnat}
-
-\begin{document}
-%\setkeys{Gin}{width=0.55\textwidth}
-
-\title{quick view tools for eSets}
-\author{VJ Carey}
-
-\maketitle
-\tableofcontents
-
-\section{Introduction}
-
-In teaching a course where a large number of datasets are
-introduced over a short period of time, the relationship
-between data content and software infrastructure can
-be hard to master. This document introduces a number of
-experimental approaches to getting rapid access to key
-elements of eSet derivatives.
-
-
-
-We will work with the ALL data for demonstration.
-<<doa,echo=FALSE,results=hide>>=
-if (!("Biobase" %in% search())) library(Biobase)
-if (!("ALL" %in% search())) library(ALL)
-if (!("ALL" %in% objects())) data(ALL)
-<<getaEF,eval=FALSE>>=
-library(Biobase)
-library(ALL)
-data(ALL)
-ALL
-@
-
-\section{An alternative to the current show method}
-
-It could be nice to tell the package from which the dataset
-was loaded.
-
-<<mkprov>>=
-dataSource = function(dsn) {
- if (!is(dsn, "character")) dsn = try(deparse(substitute(dsn)))
- if (inherits(dsn, "try-error")) stop("can't parse dsn arg")
- dd = data()$results
- if (is.na(match(dsn, dd[,"Item"]))) return(NULL)
- paste("package:", dd[ dd[,"Item"] == dsn, "Package" ], sep="")
-}
-
-
-<<newmeth,echo=FALSE,results=hide>>=
-setGeneric("peek", function(x,maxattr=10)standardGeneric("peek"))
-setMethod("peek", c("eSet", "numeric"), function(x,maxattr=10) {
- ds = dataSource(deparse(substitute(x)))
- if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="")
- else ds = ""
- cat(deparse(substitute(x)), ds, ":\n", sep="")
- cat("Platform annotation: ", annotation(x),"\n")
- cat("primary assay results are:\n")
- print(dim(x))
- cat("sample attributes are:\n")
- vn = rownames(varMetadata(x))
- ld = substr(varMetadata(x)$labelDescription,1,50)
- dd = data.frame("labelDescription[truncated]"=ld)
- rownames(dd) = vn
- if ((ndd <- nrow(dd)) <= maxattr) show(dd)
- else {
- cat("first", maxattr, "of", ndd, "attributes:\n")
- show(dd[1:maxattr,,drop=FALSE])
- }
- cat("----------\n")
- cat("use varTable to see values/freqs of all sample attributes\n")
- cat("----------\n")
-})
-setMethod("peek", c("eSet", "missing"), function(x,maxattr=10) {
- ds = dataSource(deparse(substitute(x)))
- if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="")
- else ds = ""
- cat(deparse(substitute(x)), ds, ":\n", sep="")
- cat("Platform annotation: ", annotation(x),"\n")
- cat("primary assay results are:\n")
- print(dim(x))
- cat("sample attributes are:\n")
- vn = rownames(varMetadata(x))
- ld = substr(varMetadata(x)$labelDescription,1,50)
- dd = data.frame("labelDescription[truncated]"=ld)
- rownames(dd) = vn
- if ((ndd <- nrow(dd)) <= maxattr) show(dd)
- else {
- cat("first", maxattr, "of", ndd, "attributes:\n")
- show(dd[1:maxattr,,drop=FALSE])
- }
- cat("----------\n")
- cat("use varTable to see values/freqs of all sample attributes\n")
- cat("----------\n")
-})
-setGeneric("varTable", function(x, full=FALSE, max=Inf) standardGeneric("varTable"))
-setMethod("varTable", c("eSet", "missing", "ANY"), function(x, full=FALSE, max=Inf) varTable(x, FALSE, max))
-setMethod("varTable", c("eSet", "logical", "ANY"), function(x, full=FALSE, max=Inf) {
- ans = lapply( names(pData(x)), function(z)table(x[[z]]) )
- tans = lapply(ans, names)
- kp = 1:min(max,length(tans))
- if (!full) ans = sapply(tans, selectSome, 3)[kp]
- else ans = tans[kp]
- names(ans) = names(pData(x))[kp]
- ans
-})
-setGeneric("varNames", function(x) standardGeneric("varNames"))
-setMethod("varNames", "eSet", function(x) names(pData(x)))
-@
-
-We use \texttt{peek} to get a concise view:
-<<lka>>=
-peek(ALL)
-@
-
-
-\section{Sample characterization}
-
-Getting a handle on sample characterization requires survey
-of variable names.
-<<lkv>>=
-varNames(ALL)
-@
-
-In addition, we need to know values taken. This can be very
-cumbersome. We have a few parameters on how much detail
-is provided.
-<<lkvn>>=
-varTable(ALL, max=4)
-@
-In the above, we are only showing 4 attributes. By default
-all attributes would be shown. Note
-that the report on range of values is truncated and is character
-mode. We can show the full range of values using the
-\texttt{full} parameter.
-<<lkvn>>=
-varTable(ALL, full=TRUE, max=4)
-@
-
-\end{document}
diff --git a/inst/doc/Bioconductor.Rnw b/vignettes/legacy/Bioconductor.Rnw
similarity index 100%
rename from inst/doc/Bioconductor.Rnw
rename to vignettes/legacy/Bioconductor.Rnw
diff --git a/inst/doc/HowTo.Rnw b/vignettes/legacy/HowTo.Rnw
similarity index 100%
rename from inst/doc/HowTo.Rnw
rename to vignettes/legacy/HowTo.Rnw
diff --git a/inst/doc/Qviews.Rnw b/vignettes/legacy/Qviews.Rnw
similarity index 100%
rename from inst/doc/Qviews.Rnw
rename to vignettes/legacy/Qviews.Rnw
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