Binary files /tmp/tmpeinvx12n/rEeIL_Dqyk/r-bioc-bsgenome-1.62.0/build/vignette.rds and /tmp/tmpeinvx12n/9wXeBdyYVd/r-bioc-bsgenome-1.64.0/build/vignette.rds differ diff -Nru r-bioc-bsgenome-1.62.0/debian/changelog r-bioc-bsgenome-1.64.0/debian/changelog --- r-bioc-bsgenome-1.62.0/debian/changelog 2021-11-25 19:37:08.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/debian/changelog 2022-05-16 09:59:25.000000000 +0000 @@ -1,3 +1,11 @@ +r-bioc-bsgenome (1.64.0-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.6.1 (routine-update) + * dh-update-R to update Build-Depends (routine-update) + + -- Andreas Tille Mon, 16 May 2022 11:59:25 +0200 + r-bioc-bsgenome (1.62.0-1) unstable; urgency=medium * New upstream version diff -Nru r-bioc-bsgenome-1.62.0/debian/control r-bioc-bsgenome-1.64.0/debian/control --- r-bioc-bsgenome-1.62.0/debian/control 2021-11-25 19:37:08.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/debian/control 2022-05-16 09:59:25.000000000 +0000 @@ -10,14 +10,14 @@ r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, - r-bioc-genomeinfodb, + r-bioc-genomeinfodb (>= 1.25.6), r-bioc-genomicranges, r-bioc-biostrings, r-bioc-rtracklayer, r-cran-matrixstats, - r-bioc-xvector, + r-bioc-xvector (>= 0.29.3), r-bioc-rsamtools -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-bsgenome Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-bsgenome.git Homepage: https://bioconductor.org/packages/BSgenome/ diff -Nru r-bioc-bsgenome-1.62.0/DESCRIPTION r-bioc-bsgenome-1.64.0/DESCRIPTION --- r-bioc-bsgenome-1.62.0/DESCRIPTION 2021-10-26 21:00:07.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/DESCRIPTION 2022-04-26 20:10:33.000000000 +0000 @@ -7,7 +7,7 @@ SequenceMatching, Annotation, SNP URL: https://bioconductor.org/packages/BSgenome BugReports: https://github.com/Bioconductor/BSgenome/issues -Version: 1.62.0 +Version: 1.64.0 License: Artistic-2.0 Encoding: UTF-8 Author: Hervé Pagès @@ -38,9 +38,9 @@ extractAt-methods.R bsapply.R BSgenomeViews-class.R BSgenome-utils.R export-methods.R BSgenomeForge.R git_url: https://git.bioconductor.org/packages/BSgenome -git_branch: RELEASE_3_14 -git_last_commit: 9b1859e -git_last_commit_date: 2021-10-26 -Date/Publication: 2021-10-26 +git_branch: RELEASE_3_15 +git_last_commit: 59cdebd +git_last_commit_date: 2022-04-26 +Date/Publication: 2022-04-26 NeedsCompilation: no -Packaged: 2021-10-26 21:00:07 UTC; biocbuild +Packaged: 2022-04-26 20:10:33 UTC; biocbuild Binary files /tmp/tmpeinvx12n/rEeIL_Dqyk/r-bioc-bsgenome-1.62.0/inst/doc/BSgenomeForge.pdf and /tmp/tmpeinvx12n/9wXeBdyYVd/r-bioc-bsgenome-1.64.0/inst/doc/BSgenomeForge.pdf differ Binary files /tmp/tmpeinvx12n/rEeIL_Dqyk/r-bioc-bsgenome-1.62.0/inst/doc/GenomeSearching.pdf and /tmp/tmpeinvx12n/9wXeBdyYVd/r-bioc-bsgenome-1.64.0/inst/doc/GenomeSearching.pdf differ diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau9.masked-seed r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau9.masked-seed --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau9.masked-seed 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Btaurus.UCSC.bosTau9.masked-seed 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,18 @@ +Package: BSgenome.Btaurus.UCSC.bosTau9.masked +Title: Full masked genome sequences for Bos taurus (UCSC version bosTau9) +Description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. +Version: 1.4.4 +RefPkgname: BSgenome.Btaurus.UCSC.bosTau9 +source_url: https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/ +organism_biocview: Bos_taurus +nmask_per_seq: 4 +SrcDataFiles: AGAPS masks: gap.txt.gz, downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/ on March 23, 2022 + RM masks: bosTau9.fa.out.gz, downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/ on March 23, 2022 + TRF masks: bosTau9.trf.bed.gz, downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/ on March 23, 2022 +PkgExamples: genome$chr1 # a MaskedDNAString object! + ## To get rid of the masks altogether: + unmasked(genome$chr1) # same as BSgenome.Btaurus.UCSC.bosTau9$chr1 +masks_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Btaurus.UCSC.bosTau9/masks +AGAPSfiles_name: gap.txt.gz +RMfiles_name: bosTau9.fa.out.gz +TRFfiles_name: bosTau9.trf.bed.gz diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Cjacchus.UCSC.calJac4-seed r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Cjacchus.UCSC.calJac4-seed --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Cjacchus.UCSC.calJac4-seed 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Cjacchus.UCSC.calJac4-seed 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,16 @@ +Package: BSgenome.Cjacchus.UCSC.calJac4 +Title: Full genome sequences for Callithrix jacchus (UCSC version calJac4) +Description: Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object. +Version: 1.5.0 +organism: Callithrix jacchus +common_name: Marmoset +genome: calJac4 +provider: UCSC +release_date: May 2020 +source_url: http://hgdownload.cse.ucsc.edu/goldenPath/calJac4/bigZips/ +organism_biocview: Callithrix_jacchus +BSgenomeObjname: Cjacchus +SrcDataFiles: calJac4.2bit from http://hgdownload.cse.ucsc.edu/goldenPath/calJac4/bigZips/ +PkgExamples: genome$chr1 # same as genome[["chr1"]] +seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Cjacchus.UCSC.calJac4/seqs +seqfile_name: calJac4.2bit diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-seed r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-seed --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-seed 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-seed 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,16 @@ +Package: BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 +Title: T2T-CHM13v2.0 assembly (Homo sapiens) wrapped in a BSgenome object +Description: The T2T-CHM13v2.0 assembly (accession GCA_009914755.4), as submitted to NCBI by the T2T Consortium, and wrapped in a BSgenome object. Companion paper: "The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022. +Version: 1.5.0 +organism: Homo sapiens +common_name: Human +genome: T2T-CHM13v2.0 +provider: NCBI +release_date: 2022/01/24 +source_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_009914755.4 +organism_biocview: Homo_sapiens +BSgenomeObjname: Hsapiens +SrcDataFiles: GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/ +PkgExamples: genome[["1"]] +seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0/seqs +seqfile_name: T2T-CHM13v2.0.sorted.2bit diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-tools/fasta_to_sorted_2bit.R r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-tools/fasta_to_sorted_2bit.R --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-tools/fasta_to_sorted_2bit.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0-tools/fasta_to_sorted_2bit.R 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,24 @@ +### +library(Biostrings) + +### Download GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz from +### https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/ +dna <- readDNAStringSet("GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz") + +### Check seqnames. +current_GenBankAccn <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L)) +library(GenomeInfoDb) +chrominfo <- getChromInfoFromNCBI("GCA_009914755.4") +expected_GenBankAccn <- chrominfo[ , "GenBankAccn"] +stopifnot(setequal(expected_GenBankAccn, current_GenBankAccn)) + +### Reorder sequences. +dna <- dna[match(expected_GenBankAccn, current_GenBankAccn)] + +### Rename sequences. +names(dna) <- chrominfo[ , "SequenceName"] + +### Export as 2bit. +library(rtracklayer) +export.2bit(dna, "T2T-CHM13v2.0.sorted.2bit") + diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-seed r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-seed --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-seed 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-seed 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,16 @@ +Package: BSgenome.Mfascicularis.NCBI.6.0 +Title: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_6.0) +Description: Full genome sequences for Macaca fascicularis (Crab-eating macaque) as provided by NCBI (assembly Macaca_fascicularis_6.0, assembly accession GCA_011100615.1) and stored in Biostrings objects. +Version: 1.5.0 +organism: Macaca fascicularis +common_name: Crab-eating macaque +genome: Macaca_fascicularis_6.0 +provider: NCBI +release_date: 2020/03/10 +source_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_011100615.1 +organism_biocview: Macaca_fascicularis +BSgenomeObjname: Mfascicularis +SrcDataFiles: GCA_011100615.1_Macaca_fascicularis_6.0_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/ +PkgExamples: genome[["1"]] +seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Mfascicularis.NCBI.6.0/seqs +seqfile_name: Macaca_fascicularis_6.0.sorted.2bit diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-tools/fasta_to_sorted_2bit.R r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-tools/fasta_to_sorted_2bit.R --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-tools/fasta_to_sorted_2bit.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/BSgenome.Mfascicularis.NCBI.6.0-tools/fasta_to_sorted_2bit.R 2022-04-26 17:57:47.000000000 +0000 @@ -0,0 +1,24 @@ +### +library(Biostrings) + +### Download GCA_011100615.1_Macaca_fascicularis_6.0_genomic.fna.gz from +### https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/ +dna <- readDNAStringSet("GCA_011100615.1_Macaca_fascicularis_6.0_genomic.fna.gz") + +### Check seqnames. +current_GenBankAccn <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L)) +library(GenomeInfoDb) +chrominfo <- getChromInfoFromNCBI("GCA_011100615.1") +expected_GenBankAccn <- chrominfo[ , "GenBankAccn"] +stopifnot(setequal(expected_GenBankAccn, current_GenBankAccn)) + +### Reorder sequences. +dna <- dna[match(expected_GenBankAccn, current_GenBankAccn)] + +### Rename sequences. +names(dna) <- chrominfo[ , "SequenceName"] + +### Export as 2bit. +library(rtracklayer) +export.2bit(dna, "Macaca_fascicularis_6.0.sorted.2bit") + diff -Nru r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/ForgeAll.R r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/ForgeAll.R --- r-bioc-bsgenome-1.62.0/inst/extdata/GentlemanLab/ForgeAll.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/inst/extdata/GentlemanLab/ForgeAll.R 2022-04-26 17:57:47.000000000 +0000 @@ -26,6 +26,7 @@ "BSgenome.Cfamiliaris.UCSC.canFam2", "BSgenome.Cfamiliaris.UCSC.canFam3", "BSgenome.Cjacchus.UCSC.calJac3", + "BSgenome.Cjacchus.UCSC.calJac4", "BSgenome.Creinhardtii.JGI.v5.6", "BSgenome.Dmelanogaster.UCSC.dm2", "BSgenome.Dmelanogaster.UCSC.dm3", @@ -48,8 +49,10 @@ "BSgenome.Hsapiens.UCSC.hg19", "BSgenome.Hsapiens.NCBI.GRCh38", "BSgenome.Hsapiens.UCSC.hg38", + "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0", "BSgenome.Mdomestica.UCSC.monDom5", "BSgenome.Mfascicularis.NCBI.5.0", + "BSgenome.Mfascicularis.NCBI.6.0", "BSgenome.Mfuro.UCSC.musFur1", "BSgenome.Mmulatta.UCSC.rheMac2", "BSgenome.Mmulatta.UCSC.rheMac3", @@ -93,6 +96,7 @@ "BSgenome.Btaurus.UCSC.bosTau3.masked", "BSgenome.Btaurus.UCSC.bosTau4.masked", "BSgenome.Btaurus.UCSC.bosTau6.masked", + "BSgenome.Btaurus.UCSC.bosTau9.masked", "BSgenome.Cfamiliaris.UCSC.canFam2.masked", "BSgenome.Cfamiliaris.UCSC.canFam3.masked", "BSgenome.Dmelanogaster.UCSC.dm2.masked", diff -Nru r-bioc-bsgenome-1.62.0/man/SNPlocs-class.Rd r-bioc-bsgenome-1.64.0/man/SNPlocs-class.Rd --- r-bioc-bsgenome-1.62.0/man/SNPlocs-class.Rd 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/man/SNPlocs-class.Rd 2022-04-26 17:57:47.000000000 +0000 @@ -58,7 +58,7 @@ \alias{inferRefAndAltAlleles} -% Old SNPlocs extractors (deprecated) +% Old SNPlocs extractors (defunct) \alias{snpid2loc} \alias{snpid2loc,SNPlocs-method} \alias{snpid2loc,OldFashionSNPlocs-method} diff -Nru r-bioc-bsgenome-1.62.0/R/BSgenome-class.R r-bioc-bsgenome-1.64.0/R/BSgenome-class.R --- r-bioc-bsgenome-1.62.0/R/BSgenome-class.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/R/BSgenome-class.R 2022-04-26 17:57:47.000000000 +0000 @@ -160,11 +160,9 @@ setMethod("releaseName", "BSgenome", function(x) { - msg <- c("Starting with Bioconductor 3.12, BSgenome objects no ", - "longer have a \"release name\". As a consequence of ", - "this change calling releaseName() on a BSgenome object ", - "now always returns NA and is deprecated.") - .Deprecated(msg=c(" ", wmsg(msg))) + msg <- c("starting with Bioconductor 3.15, calling releaseName() ", + "on a BSgenome object is defunct") + .Defunct(msg=c(" ", wmsg(msg))) NA_character_ } ) diff -Nru r-bioc-bsgenome-1.62.0/R/BSgenomeForge.R r-bioc-bsgenome-1.64.0/R/BSgenomeForge.R --- r-bioc-bsgenome-1.62.0/R/BSgenomeForge.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/R/BSgenomeForge.R 2022-04-26 17:57:47.000000000 +0000 @@ -82,10 +82,21 @@ { srcpaths <- getSeqSrcpaths(seqnames, prefix=prefix, suffix=suffix, seqs_srcdir=seqs_srcdir) - ans <- vapply(seqnames, - function(seqname) { + ans <- vapply(setNames(seq_along(seqnames), seqnames), + function(i) { + seqname <- seqnames[[i]] srcpath <- srcpaths[[seqname]] ans <- fasta.seqlengths(srcpath) + if (i %% 200L == 0L) { + ## Unfortunately, the files opened by fasta.seqlengths() only + ## get closed at garbage collection time! So if we don't + ## explicitly call gc() every once in a while in this loop, + ## we run into the risk of reaching the maximum number of + ## files that can be opened simultaneously on the system (this + ## is OS-dependent). This is a huge drawback of using + ## XVector::open_input_files() internally to open the files! + gc() + } if (length(ans) == 0L) stop("In file '", srcpath, "': no sequence found") if (length(ans) > 1L) @@ -736,7 +747,7 @@ ondisk_seq_format="2bit", citation_file=NA_character_ ) -) +) setClass("MaskedBSgenomeDataPkgSeed", representation( @@ -787,7 +798,7 @@ TRFfiles_prefix="", TRFfiles_suffix=".bed" ) -) +) ### Generic transformation of a named list into an S4 object with automatic ### coercion of the list elements to the required types. @@ -857,16 +868,16 @@ } else { .seqnames <- NULL } - seqnames <- deparse(.seqnames) - } + } + seqnames <- deparse1(.seqnames) circ_seqs <- x@circ_seqs if (!is.na(circ_seqs)) { .circ_seqs <- eval(parse(text=circ_seqs)) } else { si <- Seqinfo(genome=x@genome) - .circ_seqs <- seqlevels(si)[isCircular(si)] - circ_seqs <- deparse(.circ_seqs) + .circ_seqs <- seqlevels(si)[isCircular(si)] } + circ_seqs <- deparse1(.circ_seqs) symvals <- list( PKGTITLE=x@Title, PKGDESCRIPTION=x@Description, diff -Nru r-bioc-bsgenome-1.62.0/R/OldFashionSNPlocs-class.R r-bioc-bsgenome-1.64.0/R/OldFashionSNPlocs-class.R --- r-bioc-bsgenome-1.62.0/R/OldFashionSNPlocs-class.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/R/OldFashionSNPlocs-class.R 2022-04-26 17:57:47.000000000 +0000 @@ -239,7 +239,7 @@ ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -### Old SNPlocs extractors (deprecated in BioC 3.5): +### Old SNPlocs extractors (deprecated in BioC 3.5, defunct in BioC 3.15): ### snpid2loc() ### snpid2alleles() ### snpid2grange() @@ -350,8 +350,8 @@ setMethod("snpid2loc", "OldFashionSNPlocs", function(x, snpid, caching=TRUE) { - .Deprecated(msg=wmsg("snpid2loc() is deprecated. ", - "Please use snpsById() instead.")) + .Defunct(msg=wmsg("snpid2loc() is defunct. ", + "Please use snpsById() instead.")) snpid <- .normarg_snpid(snpid) if (!isTRUEorFALSE(caching)) stop("'caching' must be TRUE or FALSE") @@ -381,8 +381,8 @@ setMethod("snpid2alleles", "OldFashionSNPlocs", function(x, snpid, caching=TRUE) { - .Deprecated(msg=wmsg("snpid2alleles() is deprecated. ", - "Please use snpsById() instead.")) + .Defunct(msg=wmsg("snpid2alleles() is defunct. ", + "Please use snpsById() instead.")) snpid <- .normarg_snpid(snpid) if (!isTRUEorFALSE(caching)) stop("'caching' must be TRUE or FALSE") @@ -407,8 +407,8 @@ setMethod("snpid2grange", "OldFashionSNPlocs", function(x, snpid, caching=TRUE) { - .Deprecated(msg=wmsg("snpid2grange() is deprecated. ", - "Please use snpsById() instead.")) + .Defunct(msg=wmsg("snpid2grange() is defunct. ", + "Please use snpsById() instead.")) .snpid2grange_OldFashionSNPlocs(x, snpid, caching=caching) } ) diff -Nru r-bioc-bsgenome-1.62.0/R/OnDiskLongTable-class.R r-bioc-bsgenome-1.64.0/R/OnDiskLongTable-class.R --- r-bioc-bsgenome-1.62.0/R/OnDiskLongTable-class.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/R/OnDiskLongTable-class.R 2022-04-26 17:57:47.000000000 +0000 @@ -621,7 +621,7 @@ listData <- c(list(seqnames=seqnames), listData) if (!is.null(rowids)) listData <- c(list(rowids=rowids), listData) - new("DataFrame", listData=listData, nrows=nrows) + S4Vectors:::new_DataFrame(listData, nrows=nrows) } ### batchidx: integer vector of batch indices. diff -Nru r-bioc-bsgenome-1.62.0/R/OnDiskLongTable_old-class.R r-bioc-bsgenome-1.64.0/R/OnDiskLongTable_old-class.R --- r-bioc-bsgenome-1.62.0/R/OnDiskLongTable_old-class.R 2021-10-26 18:52:56.000000000 +0000 +++ r-bioc-bsgenome-1.64.0/R/OnDiskLongTable_old-class.R 2022-04-26 17:57:47.000000000 +0000 @@ -467,9 +467,9 @@ ## vector. if (!is.null(ans_rowids)) ans_rowids <- as.character(ans_rowids) - ans <- new("DataFrame", listData=ans_listData, - nrows=sum(ans_blocksizes), - rownames=ans_rowids) + ans <- new("DFrame", listData=ans_listData, + nrows=sum(ans_blocksizes), + rownames=ans_rowids) } ans } @@ -559,8 +559,7 @@ if (as.data.frame) { ans <- data.frame(ans_listData, stringsAsFactors=FALSE) } else { - ans <- new("DataFrame", listData=ans_listData, - nrows=length(rowidx)) + ans <- S4Vectors:::new_DataFrame(ans_listData, nrows=length(rowidx)) } ans }