gentoo resync : 09.07.2022

3 files changed, 175 insertions, 37 deletions

diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
index 6b189cb879cb..7121f15e1aec 100644
--- a/sci-biology/blat/Manifest
+++ b/sci-biology/blat/Manifest
@@ -1,5 +1,5 @@
-AUX blat-34-fix-build-system.patch 5249 BLAKE2B d32fcb326cd204c847a678cabd3fc666ed9285876ec4a3f3dc1873b9b8c83042eb705cf62e63d00b6f388540571d4ebadc497eef51827a30443d3a2aebed9420 SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246
+AUX blat-34-fix-build-system.patch 10498 BLAKE2B e2aaf5173b8b6d33733c8c16b3cc5a45d9dd431e77cdd272336baef9265b6da93e0c36b24e64127887224102309e82eda7538fa64747445b3ebdbca2cbc73a44 SHA512 60a07f9c71cfee31f2107b0b87e63f8b845f00f9f39d93f0c9b71f3e228c40c068507b352b1804d95cd049e71252e36a972bf1ebc639a040b22ad26e14ebb42e
 AUX blat-34-fno-common.patch 466 BLAKE2B 51dd1778f09e51ce1e345ae9474d3aaeb8535b739bc6d46e5d9271204b7043e1c5da0865ed3392b62d85b75c4d6c6611015042d359a113a9b0540c9ae1f6e448 SHA512 fa0b327f212137afa41d8d21717b02c77cf7e8228fe6b104af4a9a430fb0ed11a49be1ae38e8b51016ed5b6c43073c6cbbf27cd8b6f8396d39e623039d700abf
 DIST blatSrc34.zip 2142975 BLAKE2B 88a2da3b1551d5d50aaa507978c17cbe34de5a27efee9405829aea51b0950b748775f21e8d806470ba5ee7831fe71d6d87cd126c38727f25306a0f793543912e SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8
-EBUILD blat-34-r2.ebuild 845 BLAKE2B feb7d63cdcf1e1a7b3bb9829fa1d918d26ece463fd4bf58e338b4a31f8ad6e3424c7995c3d6a7f6367ef2744d0c136b5a8513acb61f021c97ddedf3ab2337d19 SHA512 b19c81da2e15b7b39d22a612df4fd23754f3a63ca2290d9d2c8701f77acb15748bcd72187f70157d3538a622e29c50fa30a2ab1814d2d5bc3df477f7c0bb14c4
+EBUILD blat-34-r3.ebuild 835 BLAKE2B 4ee22000d73ec11b3f3f48db343e0d6088958c82baa193a7a45747c1ff2d72bb9a0ebfa5dd3a2f17a4508ea84a9f298d51b022d87d50d6df19780653d61d1bf3 SHA512 5c4effb62bc3c94c8fc34a2a08ace02f47d67d3facfe962e4fe36619c801748a71cdc7e3f78dc1a784dcc6e5b539b6b54a7c87559c39e68646cd62407b3d2a2b
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r3.ebuild
index 7c7004cf950e..18c4128ec578 100644
--- a/sci-biology/blat/blat-34-r2.ebuild
+++ b/sci-biology/blat/blat-34-r3.ebuild
@@ -1,25 +1,22 @@
-# Copyright 2022 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit toolchain-funcs
 
-MY_PN=${PN}Src
+MY_PN="${PN}Src"
 
 DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
 HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
 SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
+S="${WORKDIR}/${MY_PN}"
 
 LICENSE="blat"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
-RDEPEND=""
-DEPEND="app-arch/unzip"
-
-S=${WORKDIR}/${MY_PN}
+BDEPEND="app-arch/unzip"
 
 PATCHES=(
 	"${FILESDIR}"/${PN}-34-fix-build-system.patch
diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch
index 361149cc1211..9aca3f841315 100644
--- a/sci-biology/blat/files/blat-34-fix-build-system.patch
+++ b/sci-biology/blat/files/blat-34-fix-build-system.patch
@@ -1,34 +1,36 @@
 --- a/blat/makefile
 +++ b/blat/makefile
-@@ -7,7 +7,7 @@
+@@ -7,8 +7,7 @@
  O = blat.o
  
  blat: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
- 	${STRIP} ${BINDIR}/blat${EXE}
+-	${STRIP} ${BINDIR}/blat${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
  
  all:
+ 	cd ../lib && ${MAKE}
 --- a/gfClient/makefile
 +++ b/gfClient/makefile
-@@ -8,5 +8,5 @@
+@@ -8,5 +8,4 @@
  X = gfClient
  
  gfClient: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
- 	${STRIP} ${BINDIR}/$X${EXE}
+-	${STRIP} ${BINDIR}/$X${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
 --- a/gfServer/makefile
 +++ b/gfServer/makefile
-@@ -8,7 +8,7 @@
+@@ -8,8 +8,7 @@
  X = gfServer
  
  gfServer: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
- 	${STRIP} ${BINDIR}/$X${EXE}
+-	${STRIP} ${BINDIR}/$X${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
  
  test:
+ 	${MKDIR} tests/output
 --- a/hg/pslPretty/makefile
 +++ b/hg/pslPretty/makefile
 @@ -8,7 +8,7 @@
@@ -36,7 +38,7 @@
  
  pslPretty: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
  
  test:: testRna testDnax
  
@@ -47,7 +49,7 @@
  
  pslReps: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
  
  lib:
  	cd ../../lib && ${MAKE}
@@ -58,10 +60,20 @@
  
  pslSort: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
++	${CC} ${LDFLAGS} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
  
  
  lib:
+--- a/inc/cgi_build_rules.mk
++++ b/inc/cgi_build_rules.mk
+@@ -12,7 +12,6 @@
+ 	mv $A${EXE} ${CGI_BIN}-beta/$A
+ 
+ strip::  compile
+-	${STRIP} $A${EXE}
+ 	chmod g+w $A${EXE}
+ 	chmod a+rx $A${EXE}
+ 
 --- a/inc/common.mk
 +++ b/inc/common.mk
 @@ -1,20 +1,15 @@
@@ -87,15 +99,24 @@
    endif
  endif
  # Apply the stronger checks to all code on our development machine:
-@@ -37,7 +32,7 @@
+@@ -36,9 +31,6 @@
+     BINDIR = ${HOME}/bin/${MACHTYPE}
  endif
  MKDIR=mkdir -p
- ifeq (${STRIP},)
+-ifeq (${STRIP},)
 -   STRIP=strip
-+   STRIP=true
- endif
+-endif
  CVS=cvs
  
+ # portable naming of compiled executables: add ".exe" if compiled on 
+@@ -55,6 +47,6 @@
+ STRINGIFY = ${BINDIR}/stringify
+ 
+ %.o: %.c
+-	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
++	${CC} ${CPPFLAGS} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
+ 
+ 
 --- a/jkOwnLib/makefile
 +++ b/jkOwnLib/makefile
 @@ -9,7 +9,7 @@
@@ -107,6 +128,15 @@
  
  ../lib/$(MACHTYPE):
  	mkdir ../lib/$(MACHTYPE)
+--- a/jkOwnLib/tests/freen/makefile
++++ b/jkOwnLib/tests/freen/makefile
+@@ -7,5 +7,5 @@
+ O = freen.o
+ 
+ hello: freen.o
+-	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
+ 
 --- a/lib/makefile
 +++ b/lib/makefile
 @@ -32,7 +32,7 @@
@@ -118,6 +148,102 @@
  
  $(MACHTYPE):
  	mkdir $(MACHTYPE)
+--- a/lib/tests/makefile
++++ b/lib/tests/makefile
+@@ -14,22 +14,19 @@
+ 	${MKDIR} output ${BIN_DIR}
+ 
+ errCatchTest: errCatchTest.o ${MYLIBS} mkdirs
+-	${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
+-	${STRIP} ${BIN_DIR}/errCatchTest${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
+ 	${BIN_DIR}/errCatchTest secret > output/errCatch.good
+ 	diff expected/errCatch.good output/errCatch.good
+ 	${BIN_DIR}/errCatchTest bad > output/errCatch.bad
+ 	diff expected/errCatch.bad output/errCatch.bad
+ 
+ htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs
+-	${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
+-	${STRIP} ${BIN_DIR}/htmlExpandUrlTest${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
+ 	${BIN_DIR}/htmlExpandUrlTest > output/htmlExpandUrlTest 2>&1
+ 	diff expected/htmlExpandUrlTest output/htmlExpandUrlTest
+ 
+ htmlPageTest: htmlPageTest.o ${MYLIBS} mkdirs
+-	${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
+-	${STRIP} ${BIN_DIR}/htmlPageTest${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
+ 	${BIN_DIR}/htmlPageTest input/google.html > output/google.out
+ 	diff expected/google.out output/google.out
+ 
+@@ -86,20 +83,20 @@
+ 	diff -b expected/$@.err output/$@.err
+ 
+ ${BIN_DIR}/pipelineTester:  mkdirs pipelineTester.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
+ 
+ 
+ dyStringTest: ${BIN_DIR}/dyStringTester mkdirs
+ 	${BIN_DIR}/dyStringTester
+ 
+ ${BIN_DIR}/dyStringTester:  mkdirs dyStringTester.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
+ 
+ 
+ mimeTests: mime1 mime2 mime3 mime4 mimeBin mime5 mimeAltHead mimeAutoBoundary mimeBlat
+ 
+ ${BIN_DIR}/mimeTester:  mkdirs mimeTester.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
+ 
+ 
+ mime1: ${BIN_DIR}/mimeTester mkdirs
+@@ -142,7 +139,7 @@
+ 	${BIN_DIR}/mimeTester -sizeSeries=3000
+ 
+ ${BIN_DIR}/htmlMimeTest:  mkdirs htmlMimeTest.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
+ 
+ htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs
+ 	${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out
+@@ -152,7 +149,7 @@
+ base64Tests: base64Encode base64Decode
+ 
+ ${BIN_DIR}/testBase64:  mkdirs testBase64.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
+ 
+ base64Encode: ${BIN_DIR}/testBase64 mkdirs
+ 	${BIN_DIR}/testBase64 'My Test String' > output/$@.out
+@@ -167,7 +164,7 @@
+ quotedPTests: quotedPEncode quotedPDecode
+ 
+ ${BIN_DIR}/testQuotedP:  mkdirs testQuotedP.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
+ 
+ quotedPEncode: ${BIN_DIR}/testQuotedP mkdirs
+ 	${BIN_DIR}/testQuotedP 'taxes are quite high ' > output/$@.out
+@@ -178,14 +175,14 @@
+ 	diff expected/$@.out output/$@.out
+ 
+ ${BIN_DIR}/mimeDecodeTest:  mkdirs mimeDecodeTest.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
+ 
+ mimeDecodeTest: ${BIN_DIR}/mimeDecodeTest mkdirs
+ 	${BIN_DIR}/mimeDecodeTest -cid -autoBoundary output < input/$@.txt
+ 	diff expected/noName1.html output/noName1.html
+ 
+ ${BIN_DIR}/safeTester:  mkdirs safeTester.o ${MYLIBS}
+-	${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
+ 
+ safeTest: ${BIN_DIR}/safeTester mkdirs
+ 	${BIN_DIR}/safeTester
 --- a/makefile
 +++ b/makefile
 @@ -1,18 +1,18 @@
@@ -160,18 +286,19 @@
  
  faToNib: $O $(MYLIBS)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
 --- a/utils/faToTwoBit/makefile
 +++ b/utils/faToTwoBit/makefile
-@@ -7,7 +7,7 @@
+@@ -7,8 +7,7 @@
  O = faToTwoBit.o
  
  faToTwoBit: $O ${MYLIBS}
 -	${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
-+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
- 	${STRIP} ${BINDIR}/faToTwoBit${EXE}
+-	${STRIP} ${BINDIR}/faToTwoBit${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
  
  clean:
+ 	rm -f $O
 --- a/utils/nibFrag/makefile
 +++ b/utils/nibFrag/makefile
 @@ -4,7 +4,7 @@
@@ -179,29 +306,43 @@
  
  nibFrag: $(O)
 -	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
-+	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
  
  
  
 --- a/utils/twoBitInfo/makefile
 +++ b/utils/twoBitInfo/makefile
-@@ -7,7 +7,7 @@
+@@ -7,8 +7,7 @@
  O = twoBitInfo.o
  
  twoBitInfo: $O ${MYLIBS}
 -	${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
-+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
- 	${STRIP} ${BINDIR}/twoBitInfo${EXE}
+-	${STRIP} ${BINDIR}/twoBitInfo${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
  
  clean:
+ 	rm -f $O
 --- a/utils/twoBitToFa/makefile
 +++ b/utils/twoBitToFa/makefile
-@@ -8,7 +8,7 @@
+@@ -8,8 +8,7 @@
  O = twoBitToFa.o
  
  twoBitToFa: $O ${MYLIBS}
 -	${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
-+	${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
- 	#${STRIP} ${BINDIR}/twoBitToFa${EXE}
+-	#${STRIP} ${BINDIR}/twoBitToFa${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
  
  clean:
+ 	rm -f $O
+--- a/webBlat/makefile
++++ b/webBlat/makefile
+@@ -7,8 +7,7 @@
+ O = webBlat.o
+ 
+ webBlat: $O ${MYLIBS}
+-	${CC} ${COPT} -o webBlat $O ${MYLIBS} $L
+-	${STRIP} webBlat${EXE}
++	${CC} ${LDFLAGS} ${CFLAGS} -o webBlat $O ${MYLIBS} $L
+ 
+ installOsX: webBlat
+ 	cp webBlat /Library/WebServer/CGI-Executables