diff options
Diffstat (limited to 'sci-biology/trnascan-se')
| -rw-r--r-- | sci-biology/trnascan-se/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch | 62 | ||||
| -rw-r--r-- | sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild (renamed from sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild) | 4 |
3 files changed, 67 insertions, 2 deletions
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest index 3fb1acc44f13..fe9a68dc5419 100644 --- a/sci-biology/trnascan-se/Manifest +++ b/sci-biology/trnascan-se/Manifest @@ -1,5 +1,6 @@ +AUX trnascan-se-1.31-clang16.patch 1548 BLAKE2B 75c8132478bf4e202fa0b6ff4f98c30313e6396b0821b4bc0b4203f0ec0802ac8af33fac6e585ce0d33a25b73ea3346f350ea0a41eea7c5347d44d900185b7fa SHA512 ebd0bc29a44706c536ab4f032cbd0b4c747f6a689d8d1d696ee8a48c05fed88c3fce4b7362ddf639c77aab6c78ca8a9cd8130de3665f8b99c10b1eb58bca7458 AUX trnascan-se-1.31-makefile.patch 5126 BLAKE2B 792cbd1226966c9f518672a730e8476f65cb0b4056b52e5416d43a6a1b5264666ae22fce88e4d7bfcf48d537ac4ec4d26ba8e737e60d31fbbc867de98d4315f2 SHA512 543ea32ed47279f5930485f5406d3b2912cba1df99681b2eb7e5d6df28579f48a07c9aba9ffe46819990543f5dbe69de6b086b8f86ed67de76e174dcc80563c4 AUX trnascan-se-1.31-portable-perl-shebangs.patch 634 BLAKE2B 8089d6320bce63e560791c62a9baecea1dd1f8e54c618360072463507c73087a6412742669624db0539ec4b1cf2a4db0b6edb9b064eaf67e8ad1c3b77643004e SHA512 a910b02e35cb9dcc94f6f9ec3c44936e0f7faa1ec81d9bf6f397cb516b3bd20ba7cd8e334e452e94302b4254876187c36ec8f94ebb2bd8039c8fc3e1a2b5720f DIST trnascan-se-1.31.tar.gz 740960 BLAKE2B 995bfb7ad9f9d46543f15a36134aaec6c27921144c8900a323dbd6152f25e1faa587b5c817dcb8cb838dc1fde8ec7537e5fd6ca8930a4dd1aaadce41c575d651 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d -EBUILD trnascan-se-1.31-r2.ebuild 925 BLAKE2B c3903dc93120d03a61d02efaae2ba9fff10cc0e804ea70f03b9ac86b9935b58721a319c0e51a452190444b91942192415d8c2406883aaca6fa07881d628b1f55 SHA512 fe165c6732fe579e739fdff25738ea8996974ef41cf927452aa51a91cfba1dc7485b6172adc81bb583fef442d44f5414c4ac2608b214dfc1c315c97799eb140f +EBUILD trnascan-se-1.31-r3.ebuild 1048 BLAKE2B 1158a914c9637a8b9b195eaf55a5880bd7f29627870628825c329c0e567b1734ec94d91a8c2f506eccf099d52f0475f6f7770654187f26e1a9cd180c8264ffa3 SHA512 e53f0275053af255847feffc82020f659c20bf39c9c7421f57e6b527cc822252bdde0836b89287ecb7111b5274b4b119245e7dc50d4ef35a3f8f4acc636b62c9 MISC metadata.xml 602 BLAKE2B 8f0a2a924d5e25b00f3850b903de327eff6811931047cd282386837db9d7905fa0a384b36821aea7c869d5da38969a6efbb43c3f1fd1d82dba50919bdda64172 SHA512 ace918d99f937c74013b854b34eaaeb0404dab2e5e9c21bcf876b471a617db7008cd1a7062a83dd00ba3e69027391a0b81915be8560a10d3ff9062c21862c0c2 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 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() { |