Binary files /tmp/tmplavyvq_c/v8XyTQJ5SB/r-bioc-annotationhub-3.4.0+dfsg/build/vignette.rds and /tmp/tmplavyvq_c/gKwB7R7K8_/r-bioc-annotationhub-3.6.0+dfsg/build/vignette.rds differ diff -Nru r-bioc-annotationhub-3.4.0+dfsg/debian/changelog r-bioc-annotationhub-3.6.0+dfsg/debian/changelog --- r-bioc-annotationhub-3.4.0+dfsg/debian/changelog 2022-05-16 04:52:39.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/debian/changelog 2022-11-22 06:41:51.000000000 +0000 @@ -1,3 +1,10 @@ +r-bioc-annotationhub (3.6.0+dfsg-1) unstable; urgency=medium + + * New upstream version + * Reduce piuparts noise in transitions (routine-update) + + -- Andreas Tille Tue, 22 Nov 2022 07:41:51 +0100 + r-bioc-annotationhub (3.4.0+dfsg-1) unstable; urgency=medium * Team upload. diff -Nru r-bioc-annotationhub-3.4.0+dfsg/debian/salsa-ci.yml r-bioc-annotationhub-3.6.0+dfsg/debian/salsa-ci.yml --- r-bioc-annotationhub-3.4.0+dfsg/debian/salsa-ci.yml 2021-10-18 20:26:27.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/debian/salsa-ci.yml 2022-11-22 06:41:51.000000000 +0000 @@ -7,3 +7,7 @@ # Thus reprotest is disabled here variables: SALSA_CI_DISABLE_REPROTEST: 1 + +# Reduce piuparts noise in transitions +piuparts: + allow_failure: true diff -Nru r-bioc-annotationhub-3.4.0+dfsg/DESCRIPTION r-bioc-annotationhub-3.6.0+dfsg/DESCRIPTION --- r-bioc-annotationhub-3.4.0+dfsg/DESCRIPTION 2022-04-26 20:00:06.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/DESCRIPTION 2022-11-01 20:50:28.000000000 +0000 @@ -1,7 +1,7 @@ Package: AnnotationHub Type: Package Title: Client to access AnnotationHub resources -Version: 3.4.0 +Version: 3.6.0 Authors@R: c(person("Bioconductor Package", "Maintainer", email="maintainer@bioconductor.org", role="cre"), @@ -42,11 +42,11 @@ BugReports: https://github.com/Bioconductor/AnnotationHub/issues NeedsCompilation: yes git_url: https://git.bioconductor.org/packages/AnnotationHub -git_branch: RELEASE_3_15 -git_last_commit: e74e54c -git_last_commit_date: 2022-04-26 -Date/Publication: 2022-04-26 -Packaged: 2022-04-26 20:00:06 UTC; biocbuild +git_branch: RELEASE_3_16 +git_last_commit: 3315a73 +git_last_commit_date: 2022-11-01 +Date/Publication: 2022-11-01 +Packaged: 2022-11-01 20:50:28 UTC; biocbuild Author: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Marc Carlson [ctb], diff -Nru r-bioc-annotationhub-3.4.0+dfsg/NEWS r-bioc-annotationhub-3.6.0+dfsg/NEWS --- r-bioc-annotationhub-3.4.0+dfsg/NEWS 2022-04-26 18:04:50.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/NEWS 2022-11-01 18:49:05.000000000 +0000 @@ -1,3 +1,12 @@ +CHANGES IN VERSION 3.5.0 +------------------------- + +NEW FEATURES + + o (3.5.2) Add dcf dispatchclass + o (3.5.1) Add CompDb dispatchclass + + CHANGES IN VERSION 3.3.0 ------------------------- diff -Nru r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubResource-class.R r-bioc-annotationhub-3.6.0+dfsg/R/AnnotationHubResource-class.R --- r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubResource-class.R 2022-04-26 18:04:50.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/R/AnnotationHubResource-class.R 2022-11-01 18:49:05.000000000 +0000 @@ -342,6 +342,17 @@ cache(getHub(x)) }) +## CompoundDb +setClass("CompDbResource", contains = "AnnotationHubResource") + +setMethod(".get1", "CompDbResource", + function(x, ...) +{ + .require("CompoundDb") + yy <- cache(getHub(x)) + dat <- CompoundDb::CompDb(yy) +}) + ## FilePathResource - to download raw file and return path setClass("FilePathResource", contains = "AnnotationHubResource") @@ -350,3 +361,12 @@ { cache(getHub(x)) }) + +## DCF +setClass("dcfResource", contains = "AnnotationHubResource") + +setMethod(".get1", "dcfResource", function(x, ...) { + dcf <- cache(getHub(x)) + read.dcf(dcf, ...) +}) + diff -Nru r-bioc-annotationhub-3.4.0+dfsg/R/utilities.R r-bioc-annotationhub-3.6.0+dfsg/R/utilities.R --- r-bioc-annotationhub-3.4.0+dfsg/R/utilities.R 2022-04-26 18:04:50.000000000 +0000 +++ r-bioc-annotationhub-3.6.0+dfsg/R/utilities.R 2022-11-01 18:49:05.000000000 +0000 @@ -169,6 +169,7 @@ "RDS", "readRDS()", "Rda", "get(load())", "data.frame", "get(load())", + "dcf", "read.dcf()", "GRanges", "get(load()); requires GenomicRanges", "VCF", "get(load()); requires VariantAnnotation", "ChainFile", @@ -210,6 +211,7 @@ "mzRpwiz", "mzR::openMSfile(); require mzR", "mzRident", "mzR::openIDfile(); require mzR", "MSnSet", "get(load()); require MSnbase", - "AAStringSet", "Biostrings::readAAStringSet(); require Biostrings" + "AAStringSet", "Biostrings::readAAStringSet(); require Biostrings", + "CompDb", "CompoundDb::Compdb(); requires CompoundDb" ), ncol=2, byrow=TRUE) }