Binary files /tmp/tmpYZmh5z/F4hXyAn7Yr/r-bioc-biobase-2.40.0/build/vignette.rds and /tmp/tmpYZmh5z/rVsyr_l9V_/r-bioc-biobase-2.42.0/build/vignette.rds differ diff -Nru r-bioc-biobase-2.40.0/debian/changelog r-bioc-biobase-2.42.0/debian/changelog --- r-bioc-biobase-2.40.0/debian/changelog 2018-05-31 14:32:44.000000000 +0000 +++ r-bioc-biobase-2.42.0/debian/changelog 2018-11-04 17:15:40.000000000 +0000 @@ -1,8 +1,10 @@ -r-bioc-biobase (2.40.0-2build1) cosmic; urgency=medium +r-bioc-biobase (2.42.0-1) unstable; urgency=medium - * No-change rebuild for the r-api change. + * Team upload. + * New upstream version + * Standards-Version: 4.2.1 - -- Matthias Klose Thu, 31 May 2018 14:32:44 +0000 + -- Dylan Aïssi Sun, 04 Nov 2018 18:15:40 +0100 r-bioc-biobase (2.40.0-2) unstable; urgency=medium @@ -77,7 +79,7 @@ r-bioc-biobase (2.24.0-1) unstable; urgency=low [ Charles Plessy ] - * debian/control: removed myself from Uploaders. + * debian/control: removed myself from Uploaders. [ Andreas Tille ] * New usptream version diff -Nru r-bioc-biobase-2.40.0/debian/control r-bioc-biobase-2.42.0/debian/control --- r-bioc-biobase-2.40.0/debian/control 2018-05-05 21:57:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/debian/control 2018-11-04 17:15:40.000000000 +0000 @@ -6,8 +6,8 @@ Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, - r-bioc-biocgenerics (>= 0.3.2) -Standards-Version: 4.1.4 + r-bioc-biocgenerics (>= 0.27.1) +Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-biobase Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-biobase.git Homepage: https://bioconductor.org/packages/Biobase/ diff -Nru r-bioc-biobase-2.40.0/debian/patches/exclude_testing_golubEsets.patch r-bioc-biobase-2.42.0/debian/patches/exclude_testing_golubEsets.patch --- r-bioc-biobase-2.40.0/debian/patches/exclude_testing_golubEsets.patch 2018-05-05 21:57:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/debian/patches/exclude_testing_golubEsets.patch 2018-11-04 17:15:40.000000000 +0000 @@ -10,7 +10,7 @@ --- a/inst/unitTests/test_EsetSubclasses.R +++ b/inst/unitTests/test_EsetSubclasses.R -@@ -427,20 +427,24 @@ testSetAs <- function() { +@@ -426,20 +426,24 @@ suppressMessages(e <- as(exprSet,"ExpressionSet")) checkNewAndOld(e,exprSet) diff -Nru r-bioc-biobase-2.40.0/DESCRIPTION r-bioc-biobase-2.42.0/DESCRIPTION --- r-bioc-biobase-2.40.0/DESCRIPTION 2018-04-30 22:43:42.000000000 +0000 +++ r-bioc-biobase-2.42.0/DESCRIPTION 2018-10-30 22:46:40.000000000 +0000 @@ -1,11 +1,11 @@ Package: Biobase Title: Biobase: Base functions for Bioconductor -Version: 2.40.0 +Version: 2.42.0 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Description: Functions that are needed by many other packages or which replace R functions. Suggests: tools, tkWidgets, ALL, RUnit, golubEsets -Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils +Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Maintainer: Bioconductor Package Maintainer @@ -21,5 +21,10 @@ updateObjectTo.R methods-ScalarObject.R zzz.R LazyLoad: yes biocViews: Infrastructure +git_url: https://git.bioconductor.org/packages/Biobase +git_branch: RELEASE_3_8 +git_last_commit: 3e5bd46 +git_last_commit_date: 2018-10-30 +Date/Publication: 2018-10-30 NeedsCompilation: yes -Packaged: 2018-04-30 22:43:42 UTC; biocbuild +Packaged: 2018-10-30 22:46:40 UTC; biocbuild Binary files /tmp/tmpYZmh5z/F4hXyAn7Yr/r-bioc-biobase-2.40.0/inst/doc/BiobaseDevelopment.pdf and /tmp/tmpYZmh5z/rVsyr_l9V_/r-bioc-biobase-2.42.0/inst/doc/BiobaseDevelopment.pdf differ Binary files /tmp/tmpYZmh5z/F4hXyAn7Yr/r-bioc-biobase-2.40.0/inst/doc/esApply.pdf and /tmp/tmpYZmh5z/rVsyr_l9V_/r-bioc-biobase-2.42.0/inst/doc/esApply.pdf differ Binary files /tmp/tmpYZmh5z/F4hXyAn7Yr/r-bioc-biobase-2.40.0/inst/doc/ExpressionSetIntroduction.pdf and /tmp/tmpYZmh5z/rVsyr_l9V_/r-bioc-biobase-2.42.0/inst/doc/ExpressionSetIntroduction.pdf differ diff -Nru r-bioc-biobase-2.40.0/inst/doc/ExpressionSetIntroduction.R r-bioc-biobase-2.42.0/inst/doc/ExpressionSetIntroduction.R --- r-bioc-biobase-2.40.0/inst/doc/ExpressionSetIntroduction.R 2018-04-30 22:43:41.000000000 +0000 +++ r-bioc-biobase-2.42.0/inst/doc/ExpressionSetIntroduction.R 2018-10-30 22:46:38.000000000 +0000 @@ -9,8 +9,9 @@ ################################################### ### code chunk number 2: install-pkg (eval = FALSE) ################################################### -## source("http://bioconductor.org/biocLite.R") -## biocLite(c("Biobase")) +## if (!require("BiocManager")) +## install.packages("BiocManager") +## BiocManager::install("Biobase") ################################################### @@ -211,7 +212,7 @@ ################################################### -### code chunk number 29: ExpressionSetIntroduction.Rnw:489-490 +### code chunk number 29: ExpressionSetIntroduction.Rnw:490-491 ################################################### toLatex(sessionInfo()) diff -Nru r-bioc-biobase-2.40.0/inst/doc/ExpressionSetIntroduction.Rnw r-bioc-biobase-2.42.0/inst/doc/ExpressionSetIntroduction.Rnw --- r-bioc-biobase-2.40.0/inst/doc/ExpressionSetIntroduction.Rnw 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/inst/doc/ExpressionSetIntroduction.Rnw 2018-10-30 19:29:22.000000000 +0000 @@ -95,8 +95,9 @@ one or more additional packages. The best way to do this is to start an \R{} session and evaluate commands like <>= -source("http://bioconductor.org/biocLite.R") -biocLite(c("Biobase")) +if (!require("BiocManager")) + install.packages("BiocManager") +BiocManager::install("Biobase") @ %% diff -Nru r-bioc-biobase-2.40.0/man/class.eSet.Rd r-bioc-biobase-2.42.0/man/class.eSet.Rd --- r-bioc-biobase-2.40.0/man/class.eSet.Rd 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/man/class.eSet.Rd 2018-10-30 19:29:22.000000000 +0000 @@ -27,6 +27,7 @@ \alias{dimnames,eSet-method} \alias{dimnames<-,eSet-method} \alias{dim,eSet-method} +\alias{dims} \alias{dims,eSet-method} \alias{experimentData,eSet-method} \alias{experimentData<-,eSet,MIAME-method} diff -Nru r-bioc-biobase-2.40.0/man/dims.Rd r-bioc-biobase-2.42.0/man/dims.Rd --- r-bioc-biobase-2.40.0/man/dims.Rd 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/man/dims.Rd 1970-01-01 00:00:00.000000000 +0000 @@ -1,23 +0,0 @@ -\name{dims} -\alias{dims} - -\title{Retrieve dimensions of all elements in a list or environment} -\description{ - This function returns the dimensions of element members in lists or - environments such as \code{AssayData-class}. -} -\usage{ -dims(object) -} -\arguments{ - \item{object}{List or environment object containing one or several matrices} -} -\value{ - matrix of row and column dimensions, (in rows) for each element in - \code{object} (columns). -} -\author{Biocore} - -\seealso{\code{\link{eSet-class}}} - -\keyword{manip} diff -Nru r-bioc-biobase-2.40.0/NAMESPACE r-bioc-biobase-2.42.0/NAMESPACE --- r-bioc-biobase-2.40.0/NAMESPACE 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/NAMESPACE 2018-10-30 19:29:22.000000000 +0000 @@ -3,6 +3,7 @@ import(methods) importFrom(BiocGenerics, + dims, combine, updateObject, updateObjectFromSlots, getObjectSlots, annotation, "annotation<-" diff -Nru r-bioc-biobase-2.40.0/R/AllGenerics.R r-bioc-biobase-2.42.0/R/AllGenerics.R --- r-bioc-biobase-2.40.0/R/AllGenerics.R 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/R/AllGenerics.R 2018-10-30 19:29:22.000000000 +0000 @@ -10,7 +10,6 @@ setGeneric("description", function(object, ...) standardGeneric("description")) setGeneric("description<-", function(object, value) standardGeneric("description<-")) -setGeneric("dims", function(object) standardGeneric("dims")) setGeneric("dimnames") setGeneric("dimnames<-") setGeneric("dimLabels", function(object) standardGeneric("dimLabels")) diff -Nru r-bioc-biobase-2.40.0/R/methods-eSet.R r-bioc-biobase-2.42.0/R/methods-eSet.R --- r-bioc-biobase-2.40.0/R/methods-eSet.R 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/R/methods-eSet.R 2018-10-30 19:29:22.000000000 +0000 @@ -349,7 +349,7 @@ setMethod("dim", "eSet", function(x) assayDataDim(assayData(x))) -setMethod("dims", "eSet", function(object) assayDataDims(assayData(object))) +setMethod("dims", "eSet", function(x) assayDataDims(assayData(x))) setMethod("[", "eSet", function(x, i, j, ..., drop = FALSE) { if (missing(drop)) diff -Nru r-bioc-biobase-2.40.0/vignettes/ExpressionSetIntroduction.Rnw r-bioc-biobase-2.42.0/vignettes/ExpressionSetIntroduction.Rnw --- r-bioc-biobase-2.40.0/vignettes/ExpressionSetIntroduction.Rnw 2018-04-30 17:20:13.000000000 +0000 +++ r-bioc-biobase-2.42.0/vignettes/ExpressionSetIntroduction.Rnw 2018-10-30 19:29:22.000000000 +0000 @@ -95,8 +95,9 @@ one or more additional packages. The best way to do this is to start an \R{} session and evaluate commands like <>= -source("http://bioconductor.org/biocLite.R") -biocLite(c("Biobase")) +if (!require("BiocManager")) + install.packages("BiocManager") +BiocManager::install("Biobase") @ %%