--- /srv/rebuilderd/tmp/rebuilderdSrF9cZ/inputs/r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb +++ /srv/rebuilderd/tmp/rebuilderdSrF9cZ/out/r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-01-13 20:12:39.000000 debian-binary │ --rw-r--r-- 0 0 0 2396 2025-01-13 20:12:39.000000 control.tar.xz │ --rw-r--r-- 0 0 0 927044 2025-01-13 20:12:39.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2356 2025-01-13 20:12:39.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 927076 2025-01-13 20:12:39.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-01-13 20:12:39.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1421 2025-01-13 20:12:39.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 1308 2025-01-13 20:12:39.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 4507 2025-01-13 20:12:39.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-genomicfeatures │ │ │ Version: 1.58.0+dfsg-2 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ Installed-Size: 1485 │ │ │ Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-biocgenerics (>= 0.51.2), r-bioc-s4vectors (>= 0.17.29), r-bioc-iranges (>= 2.37.1), r-bioc-genomeinfodb (>= 1.35.8), r-bioc-genomicranges (>= 1.55.2), r-bioc-annotationdbi (>= 1.41.4), r-cran-dbi, r-bioc-xvector, r-bioc-biostrings, r-bioc-rtracklayer │ │ │ -Suggests: r-bioc-txdbmaker, r-bioc-org.hs.eg.db, r-bioc-bsgenome, r-bioc-rsamtools, r-bioc-genomicalignments (>= 1.15.7), r-bioc-ensembldb, r-bioc-annotationfilter, r-cran-runit, r-bioc-biocstyle, r-cran-knitr, r-cran-markdown │ │ │ +Suggests: r-bioc-rsamtools, r-bioc-genomicalignments (>= 1.15.7), r-bioc-biocstyle, r-cran-knitr, r-cran-markdown │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/GenomicFeatures/ │ │ │ Description: GNU R tools for making and manipulating transcript centric annotations │ │ │ A set of tools and methods for making and manipulating transcript │ │ │ centric annotations. With these tools the user can easily download the │ │ │ genomic locations of the transcripts, exons and cds of a given organism, │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -20,16 +20,16 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/R/GenomicFeatures │ │ │ -rw-r--r-- 0 root (0) root (0) 881041 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/R/GenomicFeatures.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 6886 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/R/GenomicFeatures.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3968 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.R │ │ │ -rw-r--r-- 0 root (0) root (0) 13287 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 26187 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.html │ │ │ --rw-r--r-- 0 root (0) root (0) 18060 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.md │ │ │ +-rw-r--r-- 0 root (0) root (0) 26186 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 18059 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.md │ │ │ -rw-r--r-- 0 root (0) root (0) 1786 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 45056 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/Biomart_Ensembl_sample.sqlite │ │ │ -rw-r--r-- 0 root (0) root (0) 34816 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/FeatureDb.sqlite │ │ │ -rw-r--r-- 0 root (0) root (0) 9684 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/ITAG4.1_gene_models.subset.gff │ │ │ -rw-r--r-- 0 root (0) root (0) 111616 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/hg19_knownGene_sample.sqlite │ │ │ -rw-r--r-- 0 root (0) root (0) 6490 2025-01-13 20:12:39.000000 ./usr/lib/R/site-library/GenomicFeatures/extdata/sample_ranges.rds │ │ ├── ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.html │ │ │ @@ -142,15 +142,15 @@ │ │ │
│ │ │

Obtaining and Utilizing TxDb Objects

│ │ │

list(name = “Marc Carlson”) │ │ │ list(name = “Patrick Aboyoun”) │ │ │ list(name = “Hervé Pagès”) │ │ │ list(name = “Seth Falcon”) │ │ │ list(name = “Martin Morgan”)

│ │ │ -

Monday, January 13, 2025

│ │ │ +

Thursday, July 24, 2025

│ │ │
│ │ │
│ │ │

Introduction

│ │ │

The GenomicFeatures package implements the TxDb container for │ │ │ storing transcript metadata for a given organism. A TxDb object │ │ │ stores the genomic positions of the 5’ and 3’ untranslated regions │ │ │ (UTRs), protein coding sequences (CDSs), and exons for a set of mRNA │ │ │ ├── html2text {} │ │ │ │ @@ -1,11 +1,11 @@ │ │ │ │ ************ OObbttaaiinniinngg aanndd UUttiilliizziinngg TTxxDDbb OObbjjeeccttss ************ │ │ │ │ ********** lliisstt((nnaammee == ?“MMaarrcc CCaarrllssoonn?”)) lliisstt((nnaammee == ?“PPaattrriicckk AAbbooyyoouunn?”)) lliisstt((nnaammee == │ │ │ │ ?“HHeerrvv?é PPaagg?èss?”)) lliisstt((nnaammee == ?“SSeetthh FFaallccoonn?”)) lliisstt((nnaammee == ?“MMaarrttiinn MMoorrggaann?”)) ********** │ │ │ │ -******** MMoonnddaayy,, JJaannuuaarryy 1133,, 22002255 ******** │ │ │ │ +******** TThhuurrssddaayy,, JJuullyy 2244,, 22002255 ******** │ │ │ │ ************ IInnttrroodduuccttiioonn ************ │ │ │ │ The GenomicFeatures package implements the TxDb container for storing │ │ │ │ transcript metadata for a given organism. A TxDb object stores the genomic │ │ │ │ positions of the 5’ and 3’ untranslated regions (UTRs), protein coding │ │ │ │ sequences (CDSs), and exons for a set of mRNA transcripts. The genomic │ │ │ │ positions are stored and reported with respect to a given genome assembly. TxDb │ │ │ │ objects have numerous accessors functions to allow such features to be │ │ ├── ./usr/lib/R/site-library/GenomicFeatures/doc/GenomicFeatures.md │ │ │ @@ -2,15 +2,15 @@ │ │ │ title: "Obtaining and Utilizing TxDb Objects" │ │ │ author: │ │ │ - name: Marc Carlson │ │ │ - name: Patrick Aboyoun │ │ │ - name: Hervé Pagès │ │ │ - name: Seth Falcon │ │ │ - name: Martin Morgan │ │ │ -date: "Monday, January 13, 2025" │ │ │ +date: "Thursday, July 24, 2025" │ │ │ package: GenomicFeatures │ │ │ vignette: | │ │ │ %\VignetteIndexEntry{Obtaining and Utilizing TxDb Objects} │ │ │ %\VignetteEngine{knitr::rmarkdown} │ │ │ %\VignetteEncoding{UTF-8} │ │ │ %\VignetteDepends{GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19} │ │ │ %\VignetteKeywords{annotation, database}