commit: ec69f56bc3a7550b3c5018017b762e109ff19e5a Author: Ionen Wolkens <ionen <AT> gentoo <DOT> org> AuthorDate: Wed Oct 19 08:57:37 2022 +0000 Commit: Ionen Wolkens <ionen <AT> gentoo <DOT> org> CommitDate: Wed Oct 19 09:21:44 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec69f56b
sci-biology/trnascan-se: fix build w/ clang16, pass -std=gnu89 Closes: https://bugs.gentoo.org/874477 Signed-off-by: Ionen Wolkens <ionen <AT> gentoo.org> .../files/trnascan-se-1.31-clang16.patch | 62 ++++++++++++++++++++++ ...e-1.31-r2.ebuild => trnascan-se-1.31-r3.ebuild} | 4 +- 2 files changed, 65 insertions(+), 1 deletion(-) diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch new file mode 100644 index 000000000000..33889c90cf69 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch @@ -0,0 +1,62 @@ +https://bugs.gentoo.org/874477 +--- a/eufind_main.c ++++ b/eufind_main.c +@@ -23,4 +23,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include "squid.h" + #include "sqfuncs.h" +@@ -47,4 +48,14 @@ + -i <integer> : start nucleotide numbering at <integer> (def=1)\n\n"; + ++int GetBbox(float*, int*, char*, int, int, int); ++int GetBestABox(TRNA_TYPE*, char*, char*, int, int, int, int, int); ++int GetBestTrxTerm(TRNA_TYPE*, char*, int, float); ++int GetSecABox(TRNA_TYPE*, char*); ++void Get_tRNA_stats(TRNA_TYPE*, char*, int, int); ++int Init_tRNA(TRNA_TYPE*); ++int IntEncodeSeq(char*, char*, int); ++void Save_tRNA(TRNA_TYPE*, SQINFO*, char*, int, int, long int); ++int tRNAOverlap(TRNA_TYPE*, TRNA_TYPE*, int); ++ + int + main (int argc, char **argv) +--- a/scan_main.c ++++ b/scan_main.c +@@ -8,4 +8,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/score_main.c ++++ b/score_main.c +@@ -10,4 +10,5 @@ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <time.h> + #include <math.h> +--- a/trnascan.c ++++ b/trnascan.c +@@ -69,4 +69,5 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <unistd.h> + #include <ctype.h> + +@@ -333,5 +334,5 @@ + ); + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + /* pointers to the different files fpi=input file, fpo=output file, +@@ -1419,5 +1420,5 @@ + /* Calls to this function eliminated for efficiency T. Lowe 11/95 */ + +-myindex (char *s, char *t) ++int myindex (char *s, char *t) + { + int i, j, k; diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild similarity index 84% rename from sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild rename to sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild index f35c31b22798..f43243921f2f 100644 --- a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild +++ b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit perl-functions toolchain-funcs +inherit flag-o-matic perl-functions toolchain-funcs DESCRIPTION="tRNA detection in large-scale genome sequences" HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"; @@ -20,10 +20,12 @@ BDEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${P}-makefile.patch "${FILESDIR}"/${P}-portable-perl-shebangs.patch + "${FILESDIR}"/${P}-clang16.patch ) src_configure() { tc-export CC + append-cflags -std=gnu89 # mid-migration from K&R C, incompatible with c2x } src_test() {
