diff options
Diffstat (limited to 'biology/fastx-toolkit/patches')
3 files changed, 51 insertions, 0 deletions
diff --git a/biology/fastx-toolkit/patches/patch-m4_Makefile.am b/biology/fastx-toolkit/patches/patch-m4_Makefile.am new file mode 100644 index 00000000000..e85265c188a --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-m4_Makefile.am @@ -0,0 +1,14 @@ +$NetBSD: patch-m4_Makefile.am,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +Do not install unrelated m4 files. + +--- m4/Makefile.am.orig 2017-08-14 18:08:32.000000000 +0000 ++++ m4/Makefile.am +@@ -17,6 +17,6 @@ m4macros = ax_c_long_long.m4 \ + ax_cxx_header_stdcxx_tr1.m4 + + # The following is boilerplate +-m4data_DATA = $(m4macros) ++#m4data_DATA = $(m4macros) + EXTRA_DIST = $(m4data_DATA) + diff --git a/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp b/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp new file mode 100644 index 00000000000..e2a5756115f --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp @@ -0,0 +1,14 @@ +$NetBSD: patch-src_fasta__formatter_fasta__formatter.cpp,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +# Silence compile error + +--- src/fasta_formatter/fasta_formatter.cpp.orig 2022-04-03 12:45:51.295476843 +0000 ++++ src/fasta_formatter/fasta_formatter.cpp +@@ -103,6 +103,7 @@ void parse_command_line(int argc, char* + switch(opt) { + case 'h': + usage(); ++ break; + + case 'i': + input_filename = optarg; diff --git a/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h b/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h new file mode 100644 index 00000000000..0a25126f420 --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h @@ -0,0 +1,23 @@ +$NetBSD: patch-src_libfastx_fastx.h,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +# Limit packing to this one structure to avoid compatibility issues + +--- src/libfastx/fastx.h.orig 2018-05-16 14:50:08 UTC ++++ src/libfastx/fastx.h +@@ -58,7 +58,7 @@ typedef enum { + OUTPUT_SAME_AS_INPUT=3 + } OUTPUT_FILE_TYPE; + +-#pragma pack(1) ++#pragma pack(push,1) + typedef struct + { + /* Record data - common for FASTA/FASTQ */ +@@ -115,6 +115,7 @@ typedef struct + FILE* input; + FILE* output; + } FASTX ; ++#pragma pack(pop) + + + void fastx_init_reader(FASTX *pFASTX, const char* filename, |