Binary files /tmp/tmppj3EAe/TRzydHyLgM/r-bioc-cner-1.22.0+dfsg/build/vignette.rds and /tmp/tmppj3EAe/WX63racosH/r-bioc-cner-1.24.0+dfsg/build/vignette.rds differ diff -Nru r-bioc-cner-1.22.0+dfsg/debian/changelog r-bioc-cner-1.24.0+dfsg/debian/changelog --- r-bioc-cner-1.22.0+dfsg/debian/changelog 2019-11-12 06:26:24.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/changelog 2020-05-31 06:06:23.000000000 +0000 @@ -1,3 +1,26 @@ +r-bioc-cner (1.24.0+dfsg-1build1) groovy; urgency=medium + + * No-change rebuild against r-api-4.0 + + -- Steve Langasek Sun, 31 May 2020 06:06:23 +0000 + +r-bioc-cner (1.24.0+dfsg-1) unstable; urgency=medium + + * Team upload. + * New upstream version + + -- Dylan Aïssi Wed, 20 May 2020 18:14:18 +0200 + +r-bioc-cner (1.22.0+dfsg-2) unstable; urgency=medium + + * Team upload. + * Add patch to fix autopkgtest. + * Standards-Version: 4.5.0 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Dylan Aïssi Sun, 15 Mar 2020 08:16:09 +0100 + r-bioc-cner (1.22.0+dfsg-1) unstable; urgency=medium * Team upload. diff -Nru r-bioc-cner-1.22.0+dfsg/debian/control r-bioc-cner-1.24.0+dfsg/debian/control --- r-bioc-cner-1.22.0+dfsg/debian/control 2019-11-12 06:26:24.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/control 2020-05-31 06:06:23.000000000 +0000 @@ -1,5 +1,6 @@ Source: r-bioc-cner -Maintainer: Debian R Packages Maintainers +Maintainer: Ubuntu Developers +XSBC-Original-Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Section: gnu-r Testsuite: autopkgtest-pkg-r @@ -26,10 +27,11 @@ r-bioc-go.db, r-cran-r.utils, r-bioc-keggrest -Standards-Version: 4.4.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-cner Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-cner.git Homepage: https://bioconductor.org/packages/CNEr/ +Rules-Requires-Root: no Package: r-bioc-cner Architecture: any diff -Nru r-bioc-cner-1.22.0+dfsg/debian/docs r-bioc-cner-1.24.0+dfsg/debian/docs --- r-bioc-cner-1.22.0+dfsg/debian/docs 2019-11-12 06:26:24.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/docs 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -debian/tests/run-unit-test -tests diff -Nru r-bioc-cner-1.22.0+dfsg/debian/patches/Fix_autopkgtest.patch r-bioc-cner-1.24.0+dfsg/debian/patches/Fix_autopkgtest.patch --- r-bioc-cner-1.22.0+dfsg/debian/patches/Fix_autopkgtest.patch 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/patches/Fix_autopkgtest.patch 2020-05-20 16:14:18.000000000 +0000 @@ -0,0 +1,79 @@ +Description: Skip tests if required packages are not yet available in Debian. +Forwarded: TODO +Author: Dylan Aïssi + +--- a/tests/testthat/test_Axt.R ++++ b/tests/testthat/test_Axt.R +@@ -69,6 +69,8 @@ + test_that("test_subAxt", { + library(GenomicRanges) + library(rtracklayer) ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + tAssemblyFn <- file.path(system.file("extdata", + package="BSgenome.Hsapiens.UCSC.hg38"), + "single_sequences.2bit") +@@ -104,6 +106,8 @@ + # ) + + test_that("test_fixCoordinates", { ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"), + "danRer10.hg38.net.axt") + qAssemblyFn <- file.path(system.file("extdata", +@@ -130,6 +134,8 @@ + ) + + test_that("test_subAxt", { ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + tAssemblyFn <- file.path(system.file("extdata", + package="BSgenome.Drerio.UCSC.danRer10"), + "single_sequences.2bit") +@@ -156,6 +162,8 @@ + ) + + test_that("test_makeAxtTracks", { ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + tAssemblyFn <- file.path(system.file("extdata", + package="BSgenome.Drerio.UCSC.danRer10"), + "single_sequences.2bit") +--- a/tests/testthat/test_ceScan.R ++++ b/tests/testthat/test_ceScan.R +@@ -11,6 +11,9 @@ + bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"), + "filter_regions.danRer10.bed") + bedDanRer10 <- readBed(bedDanRer10Fn) ++ ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + library(BSgenome.Drerio.UCSC.danRer10) + library(BSgenome.Hsapiens.UCSC.hg38) + qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38) +@@ -49,4 +52,4 @@ + cigar=c("65M", "66M", "51M", "218M1D190M")) + expect_identical(mcols(CNEHg38DanRer10[["45_50"]]), mcolsCNEs) + } +-) +\ No newline at end of file ++) +--- a/tests/testthat/test_CNE.R ++++ b/tests/testthat/test_CNE.R +@@ -26,6 +26,8 @@ + 146653221)), + strand="+") + ) ++ skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38") ++ skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10") + assembly1Fn <- file.path(system.file("extdata", + package="BSgenome.Drerio.UCSC.danRer10"), + "single_sequences.2bit") +@@ -63,4 +65,4 @@ + expect_identical(CNEMerged(cne), CNE12) + expect_identical(CNEFinal(cne), CNE12) + } +-) +\ No newline at end of file ++) diff -Nru r-bioc-cner-1.22.0+dfsg/debian/patches/series r-bioc-cner-1.24.0+dfsg/debian/patches/series --- r-bioc-cner-1.22.0+dfsg/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/patches/series 2020-05-20 16:14:18.000000000 +0000 @@ -0,0 +1 @@ +Fix_autopkgtest.patch diff -Nru r-bioc-cner-1.22.0+dfsg/debian/salsa-ci.yml r-bioc-cner-1.24.0+dfsg/debian/salsa-ci.yml --- r-bioc-cner-1.22.0+dfsg/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/salsa-ci.yml 2020-05-20 16:14:18.000000000 +0000 @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff -Nru r-bioc-cner-1.22.0+dfsg/debian/tests/control_ r-bioc-cner-1.24.0+dfsg/debian/tests/control_ --- r-bioc-cner-1.22.0+dfsg/debian/tests/control_ 2019-11-12 06:26:24.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/tests/control_ 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -## Deactivated since the needed data packages are not available -Tests: run-unit-test -Depends: @, r-cran-testthat, -Restrictions: allow-stderr - - diff -Nru r-bioc-cner-1.22.0+dfsg/debian/tests/run-unit-test r-bioc-cner-1.24.0+dfsg/debian/tests/run-unit-test --- r-bioc-cner-1.22.0+dfsg/debian/tests/run-unit-test 2019-11-12 06:26:24.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/debian/tests/run-unit-test 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -#!/bin/sh -e - -pkgname=CNEr -debname=r-bioc-cner - -if [ "$AUTOPKGTEST_TMP" = "" ] ; then - AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX` - trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM -fi -cd $AUTOPKGTEST_TMP -cp -a /usr/share/doc/$debname/tests/* $AUTOPKGTEST_TMP -gunzip -r * -for testfile in *.R; do - echo "BEGIN TEST $testfile" - LC_ALL=C R --no-save < $testfile -done - diff -Nru r-bioc-cner-1.22.0+dfsg/DESCRIPTION r-bioc-cner-1.24.0+dfsg/DESCRIPTION --- r-bioc-cner-1.22.0+dfsg/DESCRIPTION 2019-10-30 00:50:58.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/DESCRIPTION 2020-04-28 01:06:39.000000000 +0000 @@ -1,5 +1,5 @@ Package: CNEr -Version: 1.22.0 +Version: 1.24.0 Date: 2019-09-12 Title: CNE Detection and Visualization Description: Large-scale identification and advanced visualization @@ -35,8 +35,8 @@ DB.R AssemblyStats.R GRB.R WholeGenomeAlignment.R Ancora.R CNE-methods.R GO.R KEGG.R git_url: https://git.bioconductor.org/packages/CNEr -git_branch: RELEASE_3_10 -git_last_commit: fcde299 -git_last_commit_date: 2019-10-29 -Date/Publication: 2019-10-29 -Packaged: 2019-10-30 00:50:58 UTC; biocbuild +git_branch: RELEASE_3_11 +git_last_commit: 4d2a728 +git_last_commit_date: 2020-04-27 +Date/Publication: 2020-04-27 +Packaged: 2020-04-28 01:06:39 UTC; biocbuild diff -Nru r-bioc-cner-1.22.0+dfsg/inst/doc/CNEr.R r-bioc-cner-1.24.0+dfsg/inst/doc/CNEr.R --- r-bioc-cner-1.22.0+dfsg/inst/doc/CNEr.R 2019-10-30 00:50:56.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/inst/doc/CNEr.R 2020-04-28 01:06:34.000000000 +0000 @@ -1,15 +1,15 @@ -## ----code, echo = FALSE---------------------------------------------------- +## ----code, echo = FALSE------------------------------------------------------- date = "`r doc_date()`" pkg = "`r pkg_ver('CNEr')`" -## ----global_options, echo=FALSE-------------------------------------------- +## ----global_options, echo=FALSE----------------------------------------------- short=TRUE #if short==TRUE, do not echo code chunks debug=FALSE knitr::opts_chunk$set(echo=!short, warning=debug, message=debug, error=FALSE, cache.path = "cache/", fig.path = "figures/") -## ----Axt, eval=TRUE, echo=TRUE--------------------------------------------- +## ----Axt, eval=TRUE, echo=TRUE------------------------------------------------ library(CNEr) ## These axt files are specially prepared for the region ## (chr6:24,000,000..27,000,000) @@ -18,21 +18,21 @@ axtFilesDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"), "danRer10.hg38.net.axt") -## ----readAxt, eval=TRUE, echo=TRUE----------------------------------------- +## ----readAxt, eval=TRUE, echo=TRUE-------------------------------------------- axtHg38DanRer10 <- readAxt(axtFilesHg38DanRer10) axtDanRer10Hg38 <- readAxt(axtFilesDanRer10Hg38) -## ----showAxt, eval=TRUE, echo=TRUE----------------------------------------- +## ----showAxt, eval=TRUE, echo=TRUE-------------------------------------------- ## Axt class is shown in UCSC axt format axtHg38DanRer10 axtDanRer10Hg38 -## ----matchDistribution, eval=TRUE, echo=TRUE------------------------------- +## ----matchDistribution, eval=TRUE, echo=TRUE---------------------------------- ## Distribution of matched alignments; Given an Axt alignment, plot a heatmap with percentage of each matched alignment matchDistribution(axtHg38DanRer10) matchDistribution(axtDanRer10Hg38) -## ----syntenyDotplot, eval=TRUE, echo=TRUE---------------------------------- +## ----syntenyDotplot, eval=TRUE, echo=TRUE------------------------------------- ## Example of chr4 on hg19 and galGal3 ## The synteny of human and zebrafish is not quite obvious on the dotplot. library(BSgenome.Hsapiens.UCSC.hg19) @@ -49,7 +49,7 @@ library(GenomeInfoDb) syntenicDotplot(axt, firstChrs=c("chr4"), secondChrs="chr4", type="dot") -## ----UCSC, eval=FALSE, echo=TRUE------------------------------------------- +## ----UCSC, eval=FALSE, echo=TRUE---------------------------------------------- # ## To fetch rmsk table from UCSC # library(rtracklayer) # mySession <- browserSession("UCSC") @@ -80,7 +80,7 @@ # library(TxDb.Hsapiens.UCSC.hg38.knownGene) # exonsRanges <- exons(TxDb.Hsapiens.UCSC.hg38.knownGene) -## ----Bed, eval=TRUE, echo=TRUE--------------------------------------------- +## ----Bed, eval=TRUE, echo=TRUE------------------------------------------------ ## Existing bed file for chr6:24,000,000..27,000,000 of Zebrafish danRer10 bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"), "filter_regions.danRer10.bed") @@ -94,7 +94,7 @@ hg38Filter <- readBed(bedHg38Fn) hg38Filter -## ----CNE, eval=TRUE, echo=TRUE--------------------------------------------- +## ----CNE, eval=TRUE, echo=TRUE------------------------------------------------ ## Here we have the twoBit files from Bioconductor package ## BSgenome.Drerio.UCSC.danRer10 and BSgenome.Hsapiens.UCSC.hg38 cneDanRer10Hg38 <- CNE( @@ -108,7 +108,7 @@ cutoffs1=8L, cutoffs2=4L) cneDanRer10Hg38 -## ----CNEScan, eval=TRUE, echo=TRUE----------------------------------------- +## ----CNEScan, eval=TRUE, echo=TRUE-------------------------------------------- identities <- c(45L, 48L, 49L) windows <- c(50L, 50L, 50L) ## Here danRer10Filter is tFilter since danRer10 is assembly1 @@ -116,19 +116,19 @@ qFilter=hg38Filter, window=windows, identity=identities) -## ----CNEScanHead, eval=TRUE, echo=TRUE------------------------------------- +## ----CNEScanHead, eval=TRUE, echo=TRUE---------------------------------------- ## CNEs from the alignments with danRer10 as reference CNE12(cneListDanRer10Hg38[["45_50"]]) ## CNEs from the alignments with hg38 as reference CNE21(cneListDanRer10Hg38[["45_50"]]) -## ----CNEMerge, eval=TRUE, echo=TRUE---------------------------------------- +## ----CNEMerge, eval=TRUE, echo=TRUE------------------------------------------- cneMergedListDanRer10Hg38 <- lapply(cneListDanRer10Hg38, cneMerge) -## ----CNERealignment, eval=FALSE, echo=TRUE--------------------------------- +## ----CNERealignment, eval=FALSE, echo=TRUE------------------------------------ # cneFinalListDanRer10Hg38 <- lapply(cneMergedListDanRer10Hg38, blatCNE) -## ----saveCNE, eval=TRUE, echo=TRUE----------------------------------------- +## ----saveCNE, eval=TRUE, echo=TRUE-------------------------------------------- ## on individual tables dbName <- tempfile() data(cneFinalListDanRer10Hg38) @@ -139,7 +139,7 @@ overwrite=TRUE) } -## ----queryCNE, eval=TRUE, echo=TRUE---------------------------------------- +## ----queryCNE, eval=TRUE, echo=TRUE------------------------------------------- chr <- "chr6" start <- 24000000L end <- 27000000L @@ -150,7 +150,7 @@ minLength=minLength) fetchedCNERanges -## ----CNEWidthDistribution, eval=TRUE, echo=TRUE---------------------------- +## ----CNEWidthDistribution, eval=TRUE, echo=TRUE------------------------------- dbName <- file.path(system.file("extdata", package="CNEr"), "danRer10CNE.sqlite") tAssemblyFn <- file.path(system.file("extdata", @@ -165,13 +165,13 @@ qAssemblyFn=qAssemblyFn) plotCNEWidth(cneGRangePairs) -## ----plotCNEDistribution, eval=TRUE, echo=TRUE----------------------------- +## ----plotCNEDistribution, eval=TRUE, echo=TRUE-------------------------------- plotCNEDistribution(first(cneGRangePairs)) -## ----outputBedBW, eval=FALSE, echo=TRUE------------------------------------ +## ----outputBedBW, eval=FALSE, echo=TRUE--------------------------------------- # makeCNEDensity(cneGRangePairs[1:1000]) -## ----queryUCSC, eval=FALSE, echo=TRUE, cache=TRUE-------------------------- +## ----queryUCSC, eval=FALSE, echo=TRUE, cache=TRUE----------------------------- # library(Gviz) # library(biomaRt) # genome <- "danRer10" @@ -197,18 +197,18 @@ # biomart=ensembl, # start=start , end=end, name="Ensembl Genes") -## ----loadAnnotation, eval=TRUE, echo=FALSE--------------------------------- +## ----loadAnnotation, eval=TRUE, echo=FALSE------------------------------------ data(axisTrack) data(cpgIslands) data(refGenes) -## ----plotAnnotation, eval=TRUE, echo=TRUE, fig.height=5, fig.width=7------- +## ----plotAnnotation, eval=TRUE, echo=TRUE, fig.height=5, fig.width=7---------- library(Gviz) plotTracks(list(axisTrack, cpgIslands, refGenes), collapseTranscripts=TRUE, shape="arrow", transcriptAnnotation="symbol") -## ----CNEDensity, eval=TRUE, echo=TRUE-------------------------------------- +## ----CNEDensity, eval=TRUE, echo=TRUE----------------------------------------- dbName <- file.path(system.file("extdata", package="CNEr"), "danRer10CNE.sqlite") genome <- "danRer10" @@ -245,7 +245,7 @@ end=end, windowSize=windowSize, minLength=minLength) -## ----GvizDataTrack, eval=TRUE, echo=TRUE----------------------------------- +## ----GvizDataTrack, eval=TRUE, echo=TRUE-------------------------------------- dTrack1 <- DataTrack(range=cneDanRer10Hg38_21_30, genome=genome, type="horiz", horizon.scale=max(cneDanRer10Hg38_21_30$score)/3, @@ -277,7 +277,7 @@ "yellow", "orange", "red"), name="grass carp 75/75", background.title="brown") -## ----plotCNE, eval=TRUE, echo=TRUE, fig.height=10, fig.width=8------------- +## ----plotCNE, eval=TRUE, echo=TRUE, fig.height=10, fig.width=8---------------- ht <- HighlightTrack(trackList=list(refGenes, dTrack5, dTrack4, dTrack1, dTrack2, dTrack3), start=c(24200000, 25200000, 26200000), @@ -288,6 +288,6 @@ transcriptAnnotation="symbol", from=24000000, to=27000000) -## ----sessionInfo, eval=TRUE, echo=TRUE------------------------------------- +## ----sessionInfo, eval=TRUE, echo=TRUE---------------------------------------- sessionInfo() diff -Nru r-bioc-cner-1.22.0+dfsg/inst/doc/PairwiseWholeGenomeAlignment.R r-bioc-cner-1.24.0+dfsg/inst/doc/PairwiseWholeGenomeAlignment.R --- r-bioc-cner-1.22.0+dfsg/inst/doc/PairwiseWholeGenomeAlignment.R 2019-10-30 00:50:58.000000000 +0000 +++ r-bioc-cner-1.24.0+dfsg/inst/doc/PairwiseWholeGenomeAlignment.R 2020-04-28 01:06:37.000000000 +0000 @@ -1,4 +1,4 @@ -## ----code, echo = FALSE---------------------------------------------------- +## ----code, echo = FALSE------------------------------------------------------- code <- function(...) { cat(paste(..., sep = "\n")) } @@ -6,7 +6,7 @@ date = "`r doc_date()`" pkg = "`r pkg_ver('BiocStyle')`" -## ----lastz, eval=FALSE, echo=TRUE------------------------------------------ +## ----lastz, eval=FALSE, echo=TRUE--------------------------------------------- # ## lastz aligner # assemblyDir <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit" # axtDir <- "/Users/gtan/OneDrive/Project/CSC/CNEr/axt" @@ -25,7 +25,7 @@ # ## lav files to psl files conversion # psls <- lavToPsl(lavs, removeLav=FALSE, binary="lavToPsl") -## ----last, eval=FALSE, echo=TRUE------------------------------------------- +## ----last, eval=FALSE, echo=TRUE---------------------------------------------- # ## Build the lastdb index # system2(command="lastdb", args=c("-c", file.path(assemblyDir, "danRer10"), # file.path(assemblyDir, "danRer10.fa"))) @@ -42,7 +42,7 @@ # file.path(axtDir, "danRer10.hg38.maf"), # ">", psls)) -## ----chain, eval=FALSE, echo=TRUE------------------------------------------ +## ----chain, eval=FALSE, echo=TRUE--------------------------------------------- # ## Join close alignments # chains <- axtChain(psls, assemblyTarget=assemblyTarget, # assemblyQuery=assemblyQuery, distance="far", @@ -57,7 +57,7 @@ # ignore.case=TRUE), ".all.chain")), # removeChains=FALSE, binary="chainMergeSort") -## ----netting, eval=FALSE, echo=TRUE---------------------------------------- +## ----netting, eval=FALSE, echo=TRUE------------------------------------------- # ## Filtering out chains # allPreChain <- chainPreNet(allChain, assemblyTarget, assemblyQuery, # allPreChain=file.path(axtDir, @@ -82,7 +82,7 @@ # ".noClass.net")), # binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic") -## ----axtNet, eval=FALSE, echo=TRUE----------------------------------------- +## ----axtNet, eval=FALSE, echo=TRUE-------------------------------------------- # netToAxt(netSyntenicFile, allPreChain, assemblyTarget, assemblyQuery, # axtFile=file.path(axtDir, # paste0(sub("\\.2bit$", "", @@ -96,6 +96,6 @@ # binaryNetToAxt="netToAxt", binaryAxtSort="axtSort") # -## ----sessionInfo, echo=FALSE----------------------------------------------- +## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()