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charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: alven X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 6620ae9fa686febb2f2344ec86f0dfe072b4f7c3 Auto-Submitted: auto-generated Date: Tue, 20 Jan 2026 12:52:14 +0000 Message-Id: <696f7a7e.438e5.288d844a@gitrepo.freebsd.org> The branch main has been updated by alven: URL: https://cgit.FreeBSD.org/ports/commit/?id=6620ae9fa686febb2f2344ec86f0dfe072b4f7c3 commit 6620ae9fa686febb2f2344ec86f0dfe072b4f7c3 Author: Älven AuthorDate: 2026-01-07 01:13:53 +0000 Commit: Älven CommitDate: 2026-01-20 12:51:34 +0000 biology/iolib: Update 1.14.10 => 1.15.1, take maintainership Changelogs: * https://github.com/jkbonfield/io_lib/blob/io_lib-1-15-1/CHANGES * https://github.com/jkbonfield/io_lib/compare/io_lib-1-15-0...io_lib-1-15-1 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-15...io_lib-1-15-0 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-14...io_lib-1-14-15 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-13...io_lib-1-14-14 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-12...io_lib-1-14-13 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-11...io_lib-1-14-12 * https://github.com/jkbonfield/io_lib/compare/io_lib-1-14-10...io_lib-1-14-11 * Use release tarball * Add WWW for source code repository * Pet portclippy(1) and portfmt(1) * Re-generate patches via `make makepatch` to ensure proper patch format Approved by: yuri@ (Mentor) Differential Revision: https://reviews.freebsd.org/D54568 --- biology/iolib/Makefile | 19 ++++++++----------- biology/iolib/distinfo | 6 +++--- biology/iolib/files/patch-io__lib_c__range__coder.h | 11 ----------- biology/iolib/files/patch-io__lib_tokenise__name3.c | 18 ------------------ biology/iolib/files/patch-progs-scram__merge.c | 7 ------- biology/iolib/files/patch-progs-scramble.c | 7 ------- biology/iolib/files/patch-progs__scram_test.c | 10 ---------- ..._scram_flgstat.c => patch-progs_scram__flagstat.c} | 4 ++-- biology/iolib/files/patch-progs_scram__merge.c | 10 ++++++++++ biology/iolib/files/patch-progs_scram__test.c | 10 ++++++++++ biology/iolib/files/patch-progs_scramble.c | 10 ++++++++++ biology/iolib/pkg-plist | 17 ++++++++++++++--- biology/p5-Bio-SCF/Makefile | 2 +- 13 files changed, 58 insertions(+), 73 deletions(-) diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile index 9bc898878e15..bb0889a362d5 100644 --- a/biology/iolib/Makefile +++ b/biology/iolib/Makefile @@ -1,27 +1,24 @@ PORTNAME= io_lib -DISTVERSIONPREFIX= ${PORTNAME}- -DISTVERSION= 1-14-10 -PORTREVISION= 1 +DISTVERSION= 1-15-1 CATEGORIES= biology +MASTER_SITES= https://github.com/jkbonfield/${PORTNAME}/releases/download/${DISTNAME:S/./-/g}/ +DISTNAME= ${PORTNAME}-${PORTVERSION} -MAINTAINER= ports@FreeBSD.org +MAINTAINER= alven@FreeBSD.org COMMENT= General purpose trace file (and Experiment File) reading interface -WWW= https://staden.sourceforge.net/ +WWW= https://staden.sourceforge.net/ \ + https://github.com/jkbonfield/io_lib/ LICENSE= BSD3CLAUSE LIB_DEPENDS= libcurl.so:ftp/curl USES= autoreconf gmake libtool - -USE_GITHUB= yes -GH_ACCOUNT= jkbonfield +USE_LDCONFIG= yes GNU_CONFIGURE= yes -GNU_CONFIGURE_MANPREFIX=${PREFIX}/share -USE_LDCONFIG= yes + INSTALL_TARGET= install-strip -LDFLAGS+= -lpthread CONFLICTS_INSTALL= filters scramble # bin/scramble diff --git a/biology/iolib/distinfo b/biology/iolib/distinfo index e6cd8974208d..b7542b459186 100644 --- a/biology/iolib/distinfo +++ b/biology/iolib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1538157628 -SHA256 (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 4bd576e52bb7e6be6c2efe42db2764b713c8b61b44a025ad0567dba052b6db1c -SIZE (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 3391479 +TIMESTAMP = 1767736222 +SHA256 (io_lib-1.15.1.tar.gz) = 4e6f08265bee63211bb20feb4dc03993e57b447b90dc84a4c272cf1aed954e4f +SIZE (io_lib-1.15.1.tar.gz) = 7357740 diff --git a/biology/iolib/files/patch-io__lib_c__range__coder.h b/biology/iolib/files/patch-io__lib_c__range__coder.h deleted file mode 100644 index 889cd0d3b75e..000000000000 --- a/biology/iolib/files/patch-io__lib_c__range__coder.h +++ /dev/null @@ -1,11 +0,0 @@ ---- io_lib/c_range_coder.h.orig 2018-10-18 16:44:55 UTC -+++ io_lib/c_range_coder.h -@@ -14,8 +14,6 @@ - #define DO(n) int _;for (_=0; _ - #include - #include - #include diff --git a/biology/iolib/files/patch-progs-scramble.c b/biology/iolib/files/patch-progs-scramble.c deleted file mode 100644 index ce81737b6117..000000000000 --- a/biology/iolib/files/patch-progs-scramble.c +++ /dev/null @@ -1,7 +0,0 @@ ---- progs/scramble.c.orig 2013-04-30 08:28:30.000000000 -0400 -+++ progs/scramble.c 2013-04-30 08:28:43.000000000 -0400 -@@ -1,3 +1,4 @@ -+#include - #include - #include - #include diff --git a/biology/iolib/files/patch-progs__scram_test.c b/biology/iolib/files/patch-progs__scram_test.c deleted file mode 100644 index cfcb52696bb8..000000000000 --- a/biology/iolib/files/patch-progs__scram_test.c +++ /dev/null @@ -1,10 +0,0 @@ ---- ./progs/scram_test.c.orig 2014-05-31 14:25:16.000000000 -0300 -+++ ./progs/scram_test.c 2014-05-31 14:25:27.000000000 -0300 -@@ -44,6 +44,7 @@ - #include - #include - #include -+#include - - #if defined(__MINGW32__) - # include diff --git a/biology/iolib/files/patch-progs__scram_flgstat.c b/biology/iolib/files/patch-progs_scram__flagstat.c similarity index 54% rename from biology/iolib/files/patch-progs__scram_flgstat.c rename to biology/iolib/files/patch-progs_scram__flagstat.c index 4b3919d2f3b4..08ee37887ac6 100644 --- a/biology/iolib/files/patch-progs__scram_flgstat.c +++ b/biology/iolib/files/patch-progs_scram__flagstat.c @@ -1,4 +1,4 @@ ---- progs/scram_flagstat.c.orig +--- progs/scram_flagstat.c.orig 2025-07-14 08:18:28 UTC +++ progs/scram_flagstat.c @@ -44,6 +44,7 @@ #include @@ -6,5 +6,5 @@ #include +#include - #if defined(__MINGW32__) + #if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__) # include diff --git a/biology/iolib/files/patch-progs_scram__merge.c b/biology/iolib/files/patch-progs_scram__merge.c new file mode 100644 index 000000000000..d3453fa7ba79 --- /dev/null +++ b/biology/iolib/files/patch-progs_scram__merge.c @@ -0,0 +1,10 @@ +--- progs/scram_merge.c.orig 2025-07-14 08:18:28 UTC ++++ progs/scram_merge.c +@@ -39,6 +39,7 @@ + #include "io_lib_config.h" + #endif + ++#include + #include + #include + #include diff --git a/biology/iolib/files/patch-progs_scram__test.c b/biology/iolib/files/patch-progs_scram__test.c new file mode 100644 index 000000000000..560563edc188 --- /dev/null +++ b/biology/iolib/files/patch-progs_scram__test.c @@ -0,0 +1,10 @@ +--- progs/scram_test.c.orig 2025-07-14 08:18:28 UTC ++++ progs/scram_test.c +@@ -48,6 +48,7 @@ + #include + #include + #include ++#include + + #if defined(__MINGW32__) || defined(__FreeBSD__) || defined(__APPLE__) + # include diff --git a/biology/iolib/files/patch-progs_scramble.c b/biology/iolib/files/patch-progs_scramble.c new file mode 100644 index 000000000000..01be1557fc48 --- /dev/null +++ b/biology/iolib/files/patch-progs_scramble.c @@ -0,0 +1,10 @@ +--- progs/scramble.c.orig 2025-07-14 08:18:28 UTC ++++ progs/scramble.c +@@ -39,6 +39,7 @@ + #include "io_lib_config.h" + #endif + ++#include + #include + #include + #include diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist index e38239a9a97d..96dd5ca7cd49 100644 --- a/biology/iolib/pkg-plist +++ b/biology/iolib/pkg-plist @@ -35,6 +35,15 @@ bin/srf_info bin/srf_list bin/trace_dump bin/ztr_dump +include/htscodecs/arith_dynamic.h +include/htscodecs/fqzcomp_qual.h +include/htscodecs/htscodecs.h +include/htscodecs/pack.h +include/htscodecs/rANS_static.h +include/htscodecs/rANS_static4x16.h +include/htscodecs/rle.h +include/htscodecs/tokenise_name3.h +include/htscodecs/varint.h include/io_lib/Read.h include/io_lib/abi.h include/io_lib/alf.h @@ -45,6 +54,7 @@ include/io_lib/binning.h include/io_lib/compress.h include/io_lib/compression.h include/io_lib/cram.h +include/io_lib/cram_bambam.h include/io_lib/cram_codecs.h include/io_lib/cram_decode.h include/io_lib/cram_encode.h @@ -58,7 +68,6 @@ include/io_lib/error.h include/io_lib/expFileIO.h include/io_lib/fpoint.h include/io_lib/hash_table.h -include/io_lib/io_lib_config.h include/io_lib/jenkins_lookup3.h include/io_lib/mFILE.h include/io_lib/mach-io.h @@ -81,14 +90,16 @@ include/io_lib/tar_format.h include/io_lib/thread_pool.h include/io_lib/traceType.h include/io_lib/translate.h +include/io_lib/version.h include/io_lib/vlen.h include/io_lib/xalloc.h include/io_lib/zfio.h include/io_lib/ztr.h +lib/libhtscodecs.a lib/libstaden-read.a lib/libstaden-read.so -lib/libstaden-read.so.13 -lib/libstaden-read.so.13.0.0 +lib/libstaden-read.so.14 +lib/libstaden-read.so.14.1.4 share/man/man1/scramble.1.gz share/man/man1/srf2fasta.1.gz share/man/man1/srf2fastq.1.gz diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile index 88685f19c21b..b56264f8a8cb 100644 --- a/biology/p5-Bio-SCF/Makefile +++ b/biology/p5-Bio-SCF/Makefile @@ -1,6 +1,6 @@ PORTNAME= Bio-SCF PORTVERSION= 1.03 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5-