diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile index 9bc898878e15..bb0889a362d5 100644 --- a/biology/iolib/Makefile +++ b/biology/iolib/Makefile @@ -1,28 +1,25 @@ 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 .include 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 @@ -1,10 +1,10 @@ ---- 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 #include #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 @@ -1,115 +1,126 @@ bin/append_sff bin/convert_trace bin/cram_dump bin/cram_filter bin/cram_index bin/cram_size bin/extract_fastq bin/extract_qual bin/extract_seq bin/get_comment bin/hash_exp bin/hash_extract bin/hash_list bin/hash_sff bin/hash_tar bin/index_tar bin/io_lib-config bin/makeSCF bin/scf_dump bin/scf_info bin/scf_update bin/scram_flagstat bin/scram_merge bin/scram_pileup bin/scram_test bin/scramble bin/srf2fasta bin/srf2fastq bin/srf_dump_all bin/srf_extract_hash bin/srf_extract_linear bin/srf_filter bin/srf_index_hash 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 include/io_lib/array.h include/io_lib/bam.h include/io_lib/bgzip.h 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 include/io_lib/cram_index.h include/io_lib/cram_io.h include/io_lib/cram_stats.h include/io_lib/cram_structs.h include/io_lib/deflate_interlaced.h include/io_lib/dstring.h 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 include/io_lib/md5.h include/io_lib/misc.h include/io_lib/open_trace_file.h include/io_lib/os.h include/io_lib/plain.h include/io_lib/pooled_alloc.h include/io_lib/sam_header.h include/io_lib/scf.h include/io_lib/scf_extras.h include/io_lib/scram.h include/io_lib/seqIOABI.h include/io_lib/sff.h include/io_lib/srf.h include/io_lib/stdio_hack.h include/io_lib/string_alloc.h 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 share/man/man1/srf_index_hash.1.gz share/man/man1/srf_info.1.gz share/man/man1/srf_list.1.gz share/man/man3/ExperimentFile.3.gz share/man/man3/exp2read.3.gz share/man/man3/fread_reading.3.gz share/man/man3/fread_scf.3.gz share/man/man3/fwrite_reading.3.gz share/man/man3/fwrite_scf.3.gz share/man/man3/read2exp.3.gz share/man/man3/read2scf.3.gz share/man/man3/read_allocate.3.gz share/man/man3/read_deallocate.3.gz share/man/man3/read_reading.3.gz share/man/man3/read_scf.3.gz share/man/man3/read_scf_header.3.gz share/man/man3/scf2read.3.gz share/man/man3/write_reading.3.gz share/man/man3/write_scf.3.gz share/man/man3/write_scf_header.3.gz share/man/man4/Read.4.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 @@ -1,21 +1,21 @@ PORTNAME= Bio-SCF PORTVERSION= 1.03 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= wen@FreeBSD.org COMMENT= Read and Update SCF Chromatographic Sequence Files WWW= https://metacpan.org/release/Bio-SCF LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= ${LOCALBASE}/include/io_lib/scf.h:biology/iolib USES= perl5 localbase:ldflags USE_PERL5= configure .include