Binary files /tmp/tmpljz5K0/yrzjHvyVqc/r-bioc-shortread-1.44.3/build/vignette.rds and /tmp/tmpljz5K0/7KZnUASyHv/r-bioc-shortread-1.46.0/build/vignette.rds differ diff -Nru r-bioc-shortread-1.44.3/debian/changelog r-bioc-shortread-1.46.0/debian/changelog --- r-bioc-shortread-1.44.3/debian/changelog 2020-02-07 19:50:24.000000000 +0000 +++ r-bioc-shortread-1.46.0/debian/changelog 2020-05-31 06:10:18.000000000 +0000 @@ -1,3 +1,19 @@ +r-bioc-shortread (1.46.0-1build1) groovy; urgency=medium + + * No-change rebuild against r-api-4.0 + + -- Steve Langasek Sun, 31 May 2020 06:10:18 +0000 + +r-bioc-shortread (1.46.0-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Testsuite: autopkgtest-pkg-r (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Dylan Aïssi Wed, 20 May 2020 14:28:26 +0200 + r-bioc-shortread (1.44.3-1) unstable; urgency=medium * Team upload. diff -Nru r-bioc-shortread-1.44.3/debian/control r-bioc-shortread-1.46.0/debian/control --- r-bioc-shortread-1.44.3/debian/control 2020-02-07 19:50:24.000000000 +0000 +++ r-bioc-shortread-1.46.0/debian/control 2020-05-31 06:10:18.000000000 +0000 @@ -1,7 +1,9 @@ Source: r-bioc-shortread -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 Priority: optional Build-Depends: debhelper-compat (= 12), dh-r, @@ -25,6 +27,7 @@ Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-shortread Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git Homepage: https://bioconductor.org/packages/ShortRead/ +Rules-Requires-Root: no Package: r-bioc-shortread Architecture: any diff -Nru r-bioc-shortread-1.44.3/debian/salsa-ci.yml r-bioc-shortread-1.46.0/debian/salsa-ci.yml --- r-bioc-shortread-1.44.3/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-shortread-1.46.0/debian/salsa-ci.yml 2020-05-20 12:28:26.000000000 +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-shortread-1.44.3/DESCRIPTION r-bioc-shortread-1.46.0/DESCRIPTION --- r-bioc-shortread-1.44.3/DESCRIPTION 2020-02-04 00:38:49.000000000 +0000 +++ r-bioc-shortread-1.46.0/DESCRIPTION 2020-04-27 23:59:18.000000000 +0000 @@ -1,7 +1,7 @@ Package: ShortRead Type: Package Title: FASTQ input and manipulation -Version: 1.44.3 +Version: 1.46.0 Author: Martin Morgan, Michael Lawrence, Simon Anders Maintainer: Bioconductor Package Maintainer @@ -23,9 +23,9 @@ LinkingTo: S4Vectors, IRanges, XVector, Biostrings biocViews: DataImport, Sequencing, QualityControl git_url: https://git.bioconductor.org/packages/ShortRead -git_branch: RELEASE_3_10 -git_last_commit: d97933c -git_last_commit_date: 2020-02-03 -Date/Publication: 2020-02-03 +git_branch: RELEASE_3_11 +git_last_commit: 7b25d95 +git_last_commit_date: 2020-04-27 +Date/Publication: 2020-04-27 NeedsCompilation: yes -Packaged: 2020-02-04 00:38:49 UTC; biocbuild +Packaged: 2020-04-27 23:59:18 UTC; biocbuild Binary files /tmp/tmpljz5K0/yrzjHvyVqc/r-bioc-shortread-1.44.3/inst/doc/Overview.pdf and /tmp/tmpljz5K0/7KZnUASyHv/r-bioc-shortread-1.46.0/inst/doc/Overview.pdf differ diff -Nru r-bioc-shortread-1.44.3/inst/unitTests/test_AlignedRead.R r-bioc-shortread-1.46.0/inst/unitTests/test_AlignedRead.R --- r-bioc-shortread-1.44.3/inst/unitTests/test_AlignedRead.R 2019-10-29 20:13:34.000000000 +0000 +++ r-bioc-shortread-1.46.0/inst/unitTests/test_AlignedRead.R 2020-04-27 20:22:34.000000000 +0000 @@ -223,7 +223,8 @@ fl <- "s_1_results_head.txt" src <- system.file("unitTests", "cases", package="ShortRead") tbl <- read.table(file.path(src, fl), fill=TRUE, - col.names=paste("V", 1:12, sep="")) + col.names=paste("V", 1:12, sep=""), + stringsAsFactors = TRUE) aln <- readAligned(src, fl, "SolexaResult") checkIdentical(as.character(tbl[[2]]), as.character(sread(aln))) @@ -239,8 +240,8 @@ checkIdentical(tbl[[6]], ad[[4]]) checkIdentical(tbl[[10]], ad[[5]]) - checkIdentical(tbl[[11]], ad[[6]]) - checkIdentical(tbl[[12]], ad[[7]]) + checkIdentical(as.character(tbl[[11]]), ad[[6]]) + checkIdentical(as.character(tbl[[12]]), ad[[7]]) } test_AlignedRead_constructor <- function() diff -Nru r-bioc-shortread-1.44.3/R/methods-SolexaIntensity.R r-bioc-shortread-1.46.0/R/methods-SolexaIntensity.R --- r-bioc-shortread-1.44.3/R/methods-SolexaIntensity.R 2019-10-29 20:13:34.000000000 +0000 +++ r-bioc-shortread-1.46.0/R/methods-SolexaIntensity.R 2020-04-27 20:22:34.000000000 +0000 @@ -187,7 +187,7 @@ verbose=verbose) ## lane, tile, x, y - lanes <- sub("s_([0-9]+)_.*", "\\1", basename(posFiles)) + lanes <- factor(sub("s_([0-9]+)_.*", "\\1", basename(posFiles))) tiles <- as.integer(sub("s_[0-9]+_([0-9]+)_.*", "\\1", basename(posFiles))) pos <- do.call(rbind, mapply(function(fl, lane, tile) { cbind(lane=lane, tile=tile, read.table(fl))