diff -Nru r-bioc-xvector-0.20.0/debian/changelog r-bioc-xvector-0.22.0/debian/changelog --- r-bioc-xvector-0.20.0/debian/changelog 2018-06-01 18:46:45.000000000 +0000 +++ r-bioc-xvector-0.22.0/debian/changelog 2018-11-08 21:23:38.000000000 +0000 @@ -1,8 +1,10 @@ -r-bioc-xvector (0.20.0-2build1) cosmic; urgency=medium +r-bioc-xvector (0.22.0-1) unstable; urgency=medium - * No-change rebuild against r-api-3.5 + * Team upload. + * New upstream version + * Standards-Version: 4.2.1 - -- Graham Inggs Fri, 01 Jun 2018 18:46:45 +0000 + -- Dylan Aïssi Thu, 08 Nov 2018 22:23:38 +0100 r-bioc-xvector (0.20.0-2) unstable; urgency=medium diff -Nru r-bioc-xvector-0.20.0/debian/control r-bioc-xvector-0.22.0/debian/control --- r-bioc-xvector-0.20.0/debian/control 2018-05-06 06:16:34.000000000 +0000 +++ r-bioc-xvector-0.22.0/debian/control 2018-11-08 21:23:38.000000000 +0000 @@ -7,12 +7,9 @@ dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.19.2), - r-bioc-s4vectors (>= 0.17.24), - r-bioc-iranges (>= 2.13.16), - r-bioc-biocgenerics, - r-bioc-s4vectors, - r-bioc-iranges -Standards-Version: 4.1.4 + r-bioc-s4vectors (>= 0.19.15), + r-bioc-iranges (>= 2.15.12) +Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-xvector Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-xvector.git Homepage: https://bioconductor.org/packages/XVector/ diff -Nru r-bioc-xvector-0.20.0/debian/patches/use_debian_packaged_zlib.patch r-bioc-xvector-0.22.0/debian/patches/use_debian_packaged_zlib.patch --- r-bioc-xvector-0.20.0/debian/patches/use_debian_packaged_zlib.patch 2018-05-06 06:16:34.000000000 +0000 +++ r-bioc-xvector-0.22.0/debian/patches/use_debian_packaged_zlib.patch 2018-11-08 21:23:38.000000000 +0000 @@ -5,10 +5,10 @@ --- a/DESCRIPTION +++ b/DESCRIPTION -@@ -9,7 +9,7 @@ Maintainer: Hervé Pagès = 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= - 0.17.24), IRanges (>= 2.13.16) + 0.19.15), IRanges (>= 2.15.12) -Imports: methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges +Imports: methods, utils, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges @@ -16,7 +16,7 @@ License: Artistic-2.0 --- a/NAMESPACE +++ b/NAMESPACE -@@ -2,7 +2,6 @@ useDynLib(XVector) +@@ -2,7 +2,6 @@ import(methods) importFrom(utils, download.file) diff -Nru r-bioc-xvector-0.20.0/DESCRIPTION r-bioc-xvector-0.22.0/DESCRIPTION --- r-bioc-xvector-0.20.0/DESCRIPTION 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/DESCRIPTION 2018-10-30 23:52:16.000000000 +0000 @@ -2,13 +2,13 @@ Title: Representation and manipulation of external sequences Description: Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk). -Version: 0.20.0 +Version: 0.22.0 Encoding: UTF-8 Author: Hervé Pagès and Patrick Aboyoun Maintainer: Hervé Pagès biocViews: Infrastructure, DataRepresentation Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= - 0.17.24), IRanges (>= 2.13.16) + 0.19.15), IRanges (>= 2.15.12) Imports: methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit @@ -21,5 +21,10 @@ RdaCollection-class.R intra-range-methods.R compact-methods.R reverse-methods.R slice-methods.R view-summarization-methods.R updateObject-methods.R zzz.R +git_url: https://git.bioconductor.org/packages/XVector +git_branch: RELEASE_3_8 +git_last_commit: b5e107a +git_last_commit_date: 2018-10-30 +Date/Publication: 2018-10-30 NeedsCompilation: yes -Packaged: 2018-04-30 23:45:51 UTC; biocbuild +Packaged: 2018-10-30 23:52:16 UTC; biocbuild diff -Nru r-bioc-xvector-0.20.0/inst/include/XVector_interface.h r-bioc-xvector-0.22.0/inst/include/XVector_interface.h --- r-bioc-xvector-0.20.0/inst/include/XVector_interface.h 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/inst/include/XVector_interface.h 2018-10-30 19:41:27.000000000 +0000 @@ -29,6 +29,8 @@ int *EOL_in_buf ); +long long int filexp_tell(SEXP filexp); + void filexp_seek( SEXP filexp, long long int offset, diff -Nru r-bioc-xvector-0.20.0/inst/include/_XVector_stubs.c r-bioc-xvector-0.22.0/inst/include/_XVector_stubs.c --- r-bioc-xvector-0.20.0/inst/include/_XVector_stubs.c 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/inst/include/_XVector_stubs.c 2018-10-30 19:41:27.000000000 +0000 @@ -41,6 +41,11 @@ ( filexp, buf, buf_size, EOL_in_buf) ) +DEFINE_CCALLABLE_STUB(long long int, filexp_tell, + (SEXP filexp), + ( filexp) +) + DEFINE_NOVALUE_CCALLABLE_STUB(filexp_seek, (SEXP filexp, long long int offset, int whence), ( filexp, offset, whence) diff -Nru r-bioc-xvector-0.20.0/man/XVector-class.Rd r-bioc-xvector-0.22.0/man/XVector-class.Rd --- r-bioc-xvector-0.20.0/man/XVector-class.Rd 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/man/XVector-class.Rd 2018-10-30 19:41:27.000000000 +0000 @@ -7,7 +7,7 @@ \alias{XVector} \alias{length,XVector-method} -\alias{concatenateObjects,XVector-method} +\alias{bindROWS,XVector-method} \alias{subseq} \alias{subseq<-} \alias{subseq,XVector-method} diff -Nru r-bioc-xvector-0.20.0/man/XVectorList-class.Rd r-bioc-xvector-0.22.0/man/XVectorList-class.Rd --- r-bioc-xvector-0.20.0/man/XVectorList-class.Rd 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/man/XVectorList-class.Rd 2018-10-30 19:41:27.000000000 +0000 @@ -21,7 +21,7 @@ \alias{names<-,XVectorList-method} \alias{[,XVectorList-method} \alias{subseq,XVectorList-method} -\alias{concatenateObjects,XVectorList-method} +\alias{bindROWS,XVectorList-method} \alias{showAsCell,XVectorList-method} diff -Nru r-bioc-xvector-0.20.0/NAMESPACE r-bioc-xvector-0.22.0/NAMESPACE --- r-bioc-xvector-0.20.0/NAMESPACE 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/NAMESPACE 2018-10-30 19:41:27.000000000 +0000 @@ -60,7 +60,7 @@ ## Methods for generics defined in the S4Vectors package: showAsCell, - concatenateObjects, + bindROWS, parallelSlotNames, pcompare, elementNROWS, @@ -82,6 +82,7 @@ ### export( + open_input_files, SharedVector.compare, SharedVector.copy, SharedRaw, diff -Nru r-bioc-xvector-0.20.0/R/io-utils.R r-bioc-xvector-0.22.0/R/io-utils.R --- r-bioc-xvector-0.20.0/R/io-utils.R 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/R/io-utils.R 2018-10-30 19:41:27.000000000 +0000 @@ -24,9 +24,9 @@ PACKAGE="XVector") } -finalize_filexp <- function(filexp) +close_filexp <- function(filexp) { - .Call2("finalize_filexp", filexp, PACKAGE="XVector") + .Call2("close_filexp", filexp, PACKAGE="XVector") } .normarg_input_filepath <- function(filepath) @@ -71,7 +71,7 @@ function(fp) { filexp <- new_input_filexp(fp) - reg.finalizer(filexp, finalize_filexp, onexit=TRUE) + reg.finalizer(filexp, close_filexp, onexit=TRUE) filexp }) names(ans) <- filepath @@ -124,7 +124,7 @@ filepath2 <- path.expand(filepath) filexp <- new_output_filexp(filepath2, append, compress, compression_level) - reg.finalizer(filexp, finalize_filexp, onexit=TRUE) + reg.finalizer(filexp, close_filexp, onexit=TRUE) ans <- list(filexp) names(ans) <- filepath ans diff -Nru r-bioc-xvector-0.20.0/R/XVector-class.R r-bioc-xvector-0.22.0/R/XVector-class.R --- r-bioc-xvector-0.20.0/R/XVector-class.R 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/R/XVector-class.R 2018-10-30 19:41:27.000000000 +0000 @@ -67,7 +67,7 @@ start, end, width) x@offset <- x@offset + start(solved_SEW) - 1L x@length <- width(solved_SEW) - mcols(x) <- extractROWS(mcols(x), solved_SEW) + mcols(x) <- extractROWS(mcols(x, use.names=FALSE), solved_SEW) x } ) @@ -124,7 +124,7 @@ .concatenate_XVector_objects <- function(x, objects=list(), use.names=TRUE, ignore.mcols=FALSE, check=TRUE) { - objects <- S4Vectors:::prepare_objects_to_concatenate(x, objects) + objects <- S4Vectors:::prepare_objects_to_bind(x, objects) all_objects <- c(list(x), objects) ans_len <- suppressWarnings(sum(lengths(all_objects))) @@ -166,7 +166,7 @@ check=check) } -setMethod("concatenateObjects", "XVector", .concatenate_XVector_objects) +setMethod("bindROWS", "XVector", .concatenate_XVector_objects) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -Nru r-bioc-xvector-0.20.0/R/XVectorList-class.R r-bioc-xvector-0.22.0/R/XVectorList-class.R --- r-bioc-xvector-0.20.0/R/XVectorList-class.R 2018-04-30 17:31:28.000000000 +0000 +++ r-bioc-xvector-0.22.0/R/XVectorList-class.R 2018-10-30 19:41:27.000000000 +0000 @@ -279,7 +279,7 @@ .concatenate_XVectorList_objects <- function(x, objects=list(), use.names=TRUE, ignore.mcols=FALSE, check=TRUE) { - objects <- S4Vectors:::prepare_objects_to_concatenate(x, objects) + objects <- S4Vectors:::prepare_objects_to_bind(x, objects) all_objects <- c(list(x), objects) ## Call method for Vector objects to concatenate all the parallel slots @@ -312,9 +312,7 @@ .dropDuplicatedPoolElts(ans) } -setMethod("concatenateObjects", "XVectorList", - .concatenate_XVectorList_objects -) +setMethod("bindROWS", "XVectorList", .concatenate_XVectorList_objects) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -Nru r-bioc-xvector-0.20.0/src/io_utils.c r-bioc-xvector-0.22.0/src/io_utils.c --- r-bioc-xvector-0.20.0/src/io_utils.c 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/src/io_utils.c 2018-10-30 23:52:16.000000000 +0000 @@ -193,6 +193,26 @@ return *EOL_in_buf ? 2 : 1; } +static long long int iZFile_tell(ZFile *zfile) +{ + int ztype; + void *file; + long long int offset; + + ztype = zfile->ztype; + file = zfile->file; + switch (ztype) { + case UNCOMPRESSED: + case GZ_TYPE: + offset = gztell((gzFile) file); + break; + default: + error(INTERNAL_ERR_IN "iZFile_tell(): " + "invalid ztype value %d", ztype); + } + return offset; +} + static void iZFile_seek(ZFile *zfile, long long int offset, int whence) { int ztype; @@ -487,6 +507,12 @@ buf, buf_size, EOL_in_buf); } +long long int _filexp_tell(SEXP filexp) +{ + CHECK_USER_INTERRUPT(100); + return iZFile_tell(R_ExternalPtrAddr(filexp)); +} + void _filexp_seek(SEXP filexp, long long int offset, int whence) { CHECK_USER_INTERRUPT(100); @@ -546,7 +572,7 @@ * From R: * x <- .Call("new_input_filexp", "path/to/some/file", PACKAGE="XVector") * reg.finalizer(x, - * function(e) .Call("finalize_filexp", e, PACKAGE="XVector"), + * function(e) .Call("close_filexp", e, PACKAGE="XVector"), * onexit=TRUE) */ SEXP new_input_filexp(SEXP filepath) @@ -579,7 +605,7 @@ /* --- .Call ENTRY POINT --- * Closes the file pointed to by 'filexp'. */ -SEXP finalize_filexp(SEXP filexp) +SEXP close_filexp(SEXP filexp) { ZFile *zfile; diff -Nru r-bioc-xvector-0.20.0/src/R_init_XVector.c r-bioc-xvector-0.22.0/src/R_init_XVector.c --- r-bioc-xvector-0.20.0/src/R_init_XVector.c 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/src/R_init_XVector.c 2018-10-30 23:52:16.000000000 +0000 @@ -11,7 +11,7 @@ CALLMETHOD_DEF(new_input_filexp, 1), CALLMETHOD_DEF(rewind_filexp, 1), CALLMETHOD_DEF(new_output_filexp, 4), - CALLMETHOD_DEF(finalize_filexp, 1), + CALLMETHOD_DEF(close_filexp, 1), /* RDS_random_access.c */ CALLMETHOD_DEF(RDS_read_file, 3), @@ -101,6 +101,7 @@ /* io_utils.c */ REGISTER_CCALLABLE(_filexp_read); REGISTER_CCALLABLE(_filexp_gets); + REGISTER_CCALLABLE(_filexp_tell); REGISTER_CCALLABLE(_filexp_seek); REGISTER_CCALLABLE(_filexp_rewind); REGISTER_CCALLABLE(_filexp_puts); diff -Nru r-bioc-xvector-0.20.0/src/vector_copy.c r-bioc-xvector-0.22.0/src/vector_copy.c --- r-bioc-xvector-0.20.0/src/vector_copy.c 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/src/vector_copy.c 2018-10-30 23:52:16.000000000 +0000 @@ -29,7 +29,9 @@ size_t blocksize = 0; /* gcc -Wall */ if (lkup == R_NilValue && reverse == 0 && Omode == 0) { - copy_vector_block(out, out_offset, in, in_offset, nelt); + copy_vector_block(out, (long long int) out_offset, + in, (long long int) in_offset, + (long long int) nelt); return; } if (Omode >= 0) { diff -Nru r-bioc-xvector-0.20.0/src/XVector.h r-bioc-xvector-0.22.0/src/XVector.h --- r-bioc-xvector-0.20.0/src/XVector.h 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/src/XVector.h 2018-10-30 23:52:16.000000000 +0000 @@ -25,6 +25,8 @@ int *EOL_in_buf ); +long long int _filexp_tell(SEXP filexp); + void _filexp_seek( SEXP filexp, long long int offset, @@ -54,7 +56,7 @@ SEXP compression_level ); -SEXP finalize_filexp(SEXP filexp); +SEXP close_filexp(SEXP filexp); int _delete_trailing_LF_or_CRLF( const char *buf, diff -Nru r-bioc-xvector-0.20.0/src/XVectorList_class.c r-bioc-xvector-0.22.0/src/XVectorList_class.c --- r-bioc-xvector-0.20.0/src/XVectorList_class.c 2018-04-30 23:45:51.000000000 +0000 +++ r-bioc-xvector-0.22.0/src/XVectorList_class.c 2018-10-30 23:52:16.000000000 +0000 @@ -338,7 +338,7 @@ SEXP width) { int ans_length, tag_length, new_tag_length, i, nelt; - SEXP start, group, ranges, tags, tag, ans; + SEXP start, group, names, ranges, tags, tag, ans; IntAE *tag_lengths; ans_length = LENGTH(width); @@ -363,7 +363,12 @@ IntAE_insert_at(tag_lengths, IntAE_get_nelt(tag_lengths), tag_length); } - PROTECT(ranges = new_IRanges("IRanges", start, width, NULL)); + names = GET_NAMES(width); + if (names != R_NilValue) { + PROTECT(width = duplicate(width)); + SET_NAMES(width, R_NilValue); + } + PROTECT(ranges = new_IRanges("IRanges", start, width, names)); nelt = IntAE_get_nelt(tag_lengths); PROTECT(tags = NEW_LIST(nelt)); if (strcmp(tag_type, "raw") == 0) { @@ -395,6 +400,8 @@ error("IRanges internal error in alloc_XVectorList(): " "%s: invalid 'tag_type'", tag_type); } + if (names != R_NilValue) + UNPROTECT(1); UNPROTECT(5); return ans; }