gentoo resync : 14.05.2020

19 files changed, 425 insertions, 211 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index ef11ccf14b64..83981adfa0fe 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/pari/Manifest b/sci-mathematics/pari/Manifest
index 744ee099437d..c25fd6b110f7 100644
--- a/sci-mathematics/pari/Manifest
+++ b/sci-mathematics/pari/Manifest
@@ -1,12 +1,11 @@
 AUX pari-2.11.2-Makefile-LDFLAGS.patch 394 BLAKE2B 534fcd325397a388545acbce5d96bd5417c31005512ee8f256283921fb64ec4a9ec27fb7e721648b117d3be1000816d1e9bc5ae5adc5df63afe1b0490db020c6 SHA512 de3283be39cff0bba916b314eb9e112324626513f30b5c0e0340617535d8e66ee93fdd9613839633bf7e85244caff6fa1379cc5d0c0a7f9484d028a650eb8845
 AUX pari-2.11.2-Makefile-docinstall.patch 867 BLAKE2B e8b83357ef42ebcb00abfe7bb5adc30414d1975fbde128ffe84c42898374969c608cd6f3b8b0061023681f6416e86552c80552ac51aa884e260d716f79b750c1 SHA512 089ab09532b2e888a272495606f5c0eeb6e12f764f3605c268a3e4e20e707d87c33feea2a745f7441e2cff6e7402df64f17f7b118350a8d4a0972ad8a5a82c69
 AUX pari-2.11.2-no-automagic.patch 2626 BLAKE2B 3be495852655cf47cab2ebfc544477707ab9274329a4fc7f380bd683236968e0bafd9f91b9c45289912b2a634aa9ba38f3130e0192cacfb6dc383765803eb5ad SHA512 ff8c00f028da9e782256ad9f6af87a194286cf198e8639bd737663db9b4898903993a9ef01f9084bcd658913f3d639509f89cca9b77963790ede9bb998845821
-AUX pari-2.11.3-incorrect_bnfisunit.patch 1482 BLAKE2B 198aa6e5130f5daaa3fb13e678edc82e6efb8c8ea1ae849a62b3afbe49cf3abe1da6465f9ad8e8a5aaa67dab26afb522f7843bf4c8ed3bb904c9c4b6fb65c087 SHA512 2c061adb6e71c31c7880f51175b0ca24b8d218b543d7afe894466b22db850663ef8db5535e3dd236cbb7704638af9f37a99a3d6c6d0913bc47cc0c259c6224b8
 AUX pari-2.9.4-fltk-detection.patch 572 BLAKE2B 1c2e1fa6e52521c7865c3fd011824c83fa92623903dd1e056bda29c6735eb01013e7937f66d6ffff42d0de83f7ed104c7f933d232ee37be7c4351788e76f8daa SHA512 2ec0d8035a87b693ee6a4dfa913f0b24eed20bb4db7f8cd1a47db444310d33d19e6651d475c635be747e79a02df2705e42f6f7032b60dc763583cf9fa8633b29
 AUX pari-2.9.4-ppc.patch 363 BLAKE2B 135e76972e4121362666a25e3da236c4a5b7cffa058bbc25b59ca19ea20ccb0665327f70701adca5239cb936d513976e3ba7b5cda915a3f77c7b2eb28e75eaa0 SHA512 aaf5960010e56722f11234079a20ee7a7f8819dc084e1f6567fd11ad2820e3ae47617608f312941c2f373b5312a8c09c9cd51bfa44e263ffe1e8062c9fd9877d
 AUX pari-2.9.4-strip.patch 323 BLAKE2B 85a2b56f5501b4dafc0bffe48249c1662d6f96e81f8e8260ad52ecf84f053efef2ee6d6be6a6fda47886c372eb338d8bbf4443910df79a0d4e168b2666228c37 SHA512 50624ead82da41819ccfadfbdb746fb6ff414196ae2576c5d6a86e83c67355740b0e6e901a2860cab202db15adb1b00e346aabba338ab303230bc6aee8d33076
 DIST pari-2.11.2.tar.gz 4433038 BLAKE2B 89fd8c14d6ee8c8640432bec75e10b79897f0180212dcb1b04b654478a3258fc13a7f982bcb400e28997934a21667c0c3cb08fdb2e843a80a24c6499feafb639 SHA512 22f5a6ecad6d9b8b337c2655f538a196a0460f6fe98256d0f49557ce7b843f6b27ad364f45a9472aaafee9506386c886f1f0d62697078e501ec465151d4d10a1
-DIST pari-2.11.3.tar.gz 4441199 BLAKE2B 49b001f2dc27d1be7a742c165881f2b21d55cf387a91d880bd3a16cbc5d69172f931caa779c5ccbe79b6855175695b5e88ff99b420b4f2b7404dd5e4a53a135c SHA512 2624cdd0523ec02324f58af65703003c88ab596bcaa30c366a9ea01123b0ae657285b10016abaa06b6783ba34dd4980f560900b836b8df228b9dbe0ca36a5b11
+DIST pari-2.11.4.tar.gz 4445000 BLAKE2B e910783186eeb71e74a369681c113b77271abd7f87d7a9f366aea83f36ab984f02e312cd451fad7ee6efb2fa285780e8fa78540bb1fd4b135a62d265176c80e0 SHA512 1312f452244cd1d814a1e43e108378c956669b614845f21199b7039fe6462881168983d4badb8a80bb1bac202cd82d92788a2b4f3c23d16f993cae6e251c4fe1
 EBUILD pari-2.11.2.ebuild 3033 BLAKE2B 7e4fd3d274c34a89419ee157bfd798db51b3462444ec886ee9ac71164c30d8d1cbf59d91f78077e792fdc0e55c3ce7ff23c201df43c6ea14bb52dca97d321745 SHA512 72dc95fcf64d2ac470ec9bcb6f30c45b18394662f0f2ab481a43310c410bbedc32c71b0e7a773d859680135c4f9fee9221e5e73bfe58dc1f0094c2f22d03c349
-EBUILD pari-2.11.3.ebuild 3092 BLAKE2B 6f7c636273ec8ddaa545aed868aa9c81628e589fa78ce3042cb2d29272327be4ac5ece9adda69fec3a86b205f2d83ab13543ba255aed1bee0e38378fd10c41c4 SHA512 f8512b9d2f8d6b5f8e2aadcd5c6880540b979300f328f557f2218a6a335c3616bdda38ba3465433fef97ff7d63b4080bf062debdc3e8a5041441c903b0fff9cb
+EBUILD pari-2.11.4.ebuild 3038 BLAKE2B c8933d1bff3611c0f4da34f31a43db38a2f0f32c6f6403e82b297c21018089496632c49080bbf7d3c46ce382c9ef4ed163ac82738ab1bce8714b070c70fa1957 SHA512 6e989812389955f0385c1635ae9e91c3879a973307a407ab2270962e0cb2db943551c2bedc2f15fbcb7bbb95005084a532a5d3d7fbdb36fc28cd78721f3232b3
 MISC metadata.xml 1734 BLAKE2B ffb61a9e3818ed778cd30e0b41279413fec1e624aef0c490e71f501b9797703bbd24413b180b588896d6d74af988e6102f58a04fc1c645f2b876ac2731a399c1 SHA512 b5caa3c3b98405d89681fb25c97dabb3302e971c68fda94e337b10dfc14761963ea548b4689ccb4ac59661425a85a53ea0d424b6acb35a475f42ef145ce9060e
diff --git a/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch b/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch
deleted file mode 100644
index 877cc6ace756..000000000000
--- a/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-From: Karim Belabas <Karim.Belabas@math.u-bordeaux1.fr>
-Date: Mon, 9 Sep 2019 15:20:21 +0000 (+0200)
-Subject: fix #2164
-X-Git-Url: https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=commitdiff_plain;h=c7a1d35f382e96ddf14694be27a0ca5746880700
-
-fix #2164
----
-
-diff --git a/src/basemath/buch2.c b/src/basemath/buch2.c
-index a853d3c48..e31b2278b 100644
---- a/src/basemath/buch2.c
-+++ b/src/basemath/buch2.c
-@@ -2136,7 +2136,8 @@ bnfisunit(GEN bnf,GEN x)
-   for (i = 1; i < RU; i++)
-     if (gexpo(gel(emb,i)) > -1) break;
-   p1 = imag_i( row_i(logunit,i, 1,RU-1) );
--  p1 = RgV_dotproduct(p1, ex); if (!R1) p1 = gmul2n(p1, -1);
-+  p1 = RgV_dotproduct(p1, ex);
-+  if (i > R1) p1 = gmul2n(p1, -1);
-   p1 = gsub(garg(gel(emb,i),prec), p1);
-   /* p1 = arg(the missing root of 1) */
- 
-diff --git a/src/test/32/nf b/src/test/32/nf
-index 16bf83ce3..e6c41f8b5 100644
---- a/src/test/32/nf
-+++ b/src/test/32/nf
-@@ -502,6 +502,7 @@ Mod(1/2*x - 1/2, x^2 + 23)
- [1, 1/2*x - 1/2]
- Mod(0, x)
- Mod(-6/5, x)
-+[0, 2, Mod(0, 2)]~
-   ***   at top-level: nfinit([y^3+2,[1,x]])
-   ***                 ^---------------------
-   *** nfinit: incorrect type in nfinit_basic (t_VEC).
-diff --git a/src/test/in/nf b/src/test/in/nf
-index 49148123b..94d5165bc 100644
---- a/src/test/in/nf
-+++ b/src/test/in/nf
-@@ -156,6 +156,10 @@ K.zk
- nfinit(x, 3)[2]
- nfinit(1/2*x + 3/5, 3)[2]
- 
-+\\ #2164
-+bnf = bnfinit(y^4-y-1);
-+bnfisunit(bnf,-y^3+2*y^2-1)
-+
- \\ ERRORS: keep at end of file
- 
- nfinit([y^3+2,[1,x]])
diff --git a/sci-mathematics/pari/pari-2.11.3.ebuild b/sci-mathematics/pari/pari-2.11.4.ebuild
index 7f3a302bbe4f..564ed9639a71 100644
--- a/sci-mathematics/pari/pari-2.11.3.ebuild
+++ b/sci-mathematics/pari/pari-2.11.4.ebuild
@@ -32,7 +32,6 @@ PATCHES=(
 	"${FILESDIR}/${PN}"-2.9.4-fltk-detection.patch
 	"${FILESDIR}/${PN}"-2.11.2-Makefile-LDFLAGS.patch
 	"${FILESDIR}/${PN}"-2.11.2-Makefile-docinstall.patch
-	"${FILESDIR}/${PN}"-2.11.3-incorrect_bnfisunit.patch
 )
 
 src_prepare() {
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 126511a8fbea..63bf7503661c 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,9 +1,9 @@
-AUX petsc-3.12.1-do_not_run_mpiexec.patch 2648 BLAKE2B 521db3b12644ec692134f11e96d2ec633f3600199e2ac4da5cf2ee6be566fc6e65d0b6a67437752b0c1cf656561ba6c991d2ad603d3975f334b66362d275483c SHA512 b5eb5406203ae4df21d94755f8ccb996c7d6822ef93a60ebe3a82f404436f1aa314809f63bbcbdc15a5613ff143df80e3e69b3e3f48dc9521a2e2855dad73e25
-AUX petsc-3.12.1-make_hypre_configure.patch 3970 BLAKE2B 562cab7e3176acf2bce1b40d4a8563718d419be95881b7fb68fee563591db8bc9fac7444885139c9887e3ab8fe790c4568dbc58cff43f718dbace335564ec1fb SHA512 7f954e6a9a2e3eabe15c9eca6dd385a6a50a5cb7dcda8fd0de8fa2ff49667850fcad62a3b3caade0bc024a1eef1bf4f1f429385e9208b95badb77d814480357c
+AUX petsc-3.13.0-do_not_run_mpiexec.patch 2822 BLAKE2B 6c8e8185c693fdc720c0d8ea803cecff2d4b29ae71e3251e06e3460e05b301b709f30032f9a473f065c3e2a9a7b488241cb0d63ddaebdcdf275513af50257ddc SHA512 c2ea68fd59feed34ea6b7afdcbfe24e27e44d844ed6f077c52b81a20676dabb4613c9add6b33edea7d46f0c1a55993bd020d342092aa15e0f46020cc6bc51609
+AUX petsc-3.13.0-fix_sandbox_violation.patch 1022 BLAKE2B 4883be2a38becba88dd1ceafffae46b775f75a59ce990c2d92808a52fb27e5ab89a14e355599009466be0af58680076e15ae74d82cd243b3bfe867fa90f4f05a SHA512 afd6e4ade2a53941d0211baa78e179de9c8bfead15c4c245d25623cee99fb1c0821d154e58428b3c431654d770689afdec1c2bd631f2fa8eedd99d3c7186656c
+AUX petsc-3.13.0-make_hypre_configure.patch 4055 BLAKE2B e3bc831665fbe2c9a724a13420d1ce7557b7a1a6fcd7537271a6e48622f29f71f72257d649bcbef4aa4f287a804407cdb80579797eb54cfa994ef85d5bcb617f SHA512 47e4971596342c160fc54e1bc6d9fa739ae4bf6a9e3f89659992a3548de0beacdc7ac34a900117c1ee43b6bfaa81e8a58f1c45acea072be612ece3b5d18d7f86
 AUX petsc-3.7.0-disable-rpath.patch 909 BLAKE2B b9b6064886d6c10b382982778398cb7fa254242e5ed0dfb86dd4cd6c094dc51eecfd625f6de5c2779bfc5b3beda351ac44145c69ac246d814a728d7565da8086 SHA512 8241c593d903615feb175bfe8213792ace739a18ac5f4c1d1890155ccea7de30b5ef5d97e2fa3b043e9a1e520e022abedeb038d0b4db671f89045e04edc65a68
-AUX petsc-3.9.0-fix_sandbox_violation.patch 916 BLAKE2B f58ba79c3082d253c9a95b0c9ce0bcc6373fa91b4155fac5a6d4688c21805d938f5c04a939ab9d8b810732e79699e7156bd4916717b9ab0217ab257ca64bb92e SHA512 cde22a54f0f6c73cfa326ea0c0026878b3099381ec703154bb8d2746a502ffc9ae82e65082f63579abce5b3d3f89bccf0cbc7db7d031e642c5c02ca8281e616c
-DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
-DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8 SHA512 df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb
-EBUILD petsc-3.11.3.ebuild 5337 BLAKE2B bdd7062ad5b5b55de97c676a30437901838749d9ee910d274711668de7b43d1f0c630b53e1f4f0b50442ea05b3a9900f5b3f2d5a7d10de3e124f7012ecd0b8b5 SHA512 2e67e5399c57a587e2afac1a412919faf383e4bfa00011ebf54bc3d4af6a353890500463b5f8a138fac7079eccec6b590c161be1419c5193d924fd1be1377f49
-EBUILD petsc-3.12.1.ebuild 5431 BLAKE2B 06e00d3f76c1eb2548fb2973014a7f674ecd2bb3b8928b12fa531acf3704fc8a85d22c194ad3d07c2ba470e228ccb4c5393b9f819e1a914d82dec6da2dd29e5b SHA512 2bfe62beb35946bf365925bc4b7b5c790f45fe6a3a37e45de420b69b983eba7d0d723a0eee3fa5e712a8abf87974baaf6120e8414f99a80dc5b353f5f90654e1
+DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B 0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727 SHA512 0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953
+DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0 SHA512 41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
+EBUILD petsc-3.13.0.ebuild 5335 BLAKE2B 82629d09778a4fb2c2c2c975ac9a864d2cc1b3f134f072257861ea9e4309730df7ea9930fa418b156f13384627ac5cd61ac91a6fccbe97595a23ac76bff2301a SHA512 351b627578c0be08fef91ee42a15f83c6e160bd4ccc7ff19570cf0f367332c815469ecac501a3ad90d2eb663d707674ce56424ea9a296c6c88f016eb31c3111e
+EBUILD petsc-3.13.1.ebuild 5335 BLAKE2B 82629d09778a4fb2c2c2c975ac9a864d2cc1b3f134f072257861ea9e4309730df7ea9930fa418b156f13384627ac5cd61ac91a6fccbe97595a23ac76bff2301a SHA512 351b627578c0be08fef91ee42a15f83c6e160bd4ccc7ff19570cf0f367332c815469ecac501a3ad90d2eb663d707674ce56424ea9a296c6c88f016eb31c3111e
 MISC metadata.xml 1131 BLAKE2B db15101bb24374026158a0b45bab1b4b38ab6869bb13fc1df48eef96ca003cea0a8b9118033a3d53c735cefd5ca7563e074d458aee32e038a39e68a6a91b7364 SHA512 19cf1bcddd8bc1378bf85c47b090dd684474f29896c1877bfbeb53a24b1112ed4bb6e823cbc830ee40c886727c6c90d0852081488b1df63f8b4f071d3d453630
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
index 9c3d5047b0a6..4c46658dec71 100644
--- a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
@@ -1,14 +1,14 @@
 diff --git a/config/BuildSystem/config/packages/MPI.py b/config/BuildSystem/config/packages/MPI.py
-index c85bb504..7720eba9 100644
+index 7e424e71..ee502bd2 100644
 --- a/config/BuildSystem/config/packages/MPI.py
 +++ b/config/BuildSystem/config/packages/MPI.py
-@@ -209,26 +209,11 @@ shared libraries and run with --known-mpi-shared-libraries=1')
+@@ -210,28 +210,11 @@ shared libraries and run with --known-mpi-shared-libraries=1')
            raise RuntimeError('Could not locate MPIEXEC - please specify --with-mpiexec option')
        # Support for spaces and () in executable names; also needs to handle optional arguments at the end
        # TODO: This support for spaces and () should be moved to core BuildSystem
 -      self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(', '\\(').replace(')', '\\)').replace('\ -',' -')
 -      if (hasattr(self, 'ompi_major_version') and int(self.ompi_major_version) >= 3):
--        (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 10, log = self.log)
+-        (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 60, log = self.log, threads = 1)
 -        if out.find('--oversubscribe') >=0:
 -          self.mpiexec = self.mpiexec + ' --oversubscribe'
 +      self.mpiexec = self.mpiexec + ' --oversubscribe'
@@ -16,17 +16,19 @@ index c85bb504..7720eba9 100644
      # using mpiexec environmental variables make sure mpiexec matches the MPI libraries and save the variables for testing in PetscInitialize()
      # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used. PetscInitialize() can check the existence of the environmental variable to
      # determine if the program has been started with the correct mpiexec (will only be set for parallel runs so not clear how to check appropriately)
--    (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 10, log = self.log)
--    if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err)
--    if out.find('MPIR_CVAR_CH3') > -1:
--      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
--    elif  out.find('MPIR_CVAR_CH3') > -1:
--      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
--    elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
--      if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
+-    (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 60, threads = 1, log = self.log)
+-    if ret:
+-      self.logWrite('Unable to run '+self.mpiexec+' with option "-n 1 printenv"\nThis could be ok, some MPI implementations such as SGI produce a non-zero status with non-MPI programs\n'+out+err)
+-    else:
+-      if out.find('MPIR_CVAR_CH3') > -1:
+-        if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
+-      elif  out.find('MPIR_CVAR_CH3') > -1:
+-        if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
+-      elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
+-        if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
+ 
      self.addMakeMacro('MPIEXEC', self.mpiexec)
      self.mpiexec = self.mpiexec + ' -n 1'
- 
diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch
index 97f8dfed4d71..c0dfd53a0112 100644
--- a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch
@@ -1,15 +1,16 @@
 diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
-index 92f190d..047c85b 100644
+index 860faf0f..87898811 100755
 --- a/config/PETSc/options/installDir.py
 +++ b/config/PETSc/options/installDir.py
-@@ -41,12 +41,6 @@ class Configure(config.base.Configure):
+@@ -40,13 +40,6 @@ class Configure(config.base.Configure):
        self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
        self.petscDir = self.dir
        self.petscArch = ''
 -      try:
 -        os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
 -        os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
--      except:
+-      except Exception as e:
+-        self.logPrint('Error trying to to test write permissions on directory '+str(e))
 -        self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
 -        self.installSudo = 'sudo '
      else:
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch
index 9460d57e4617..1453fd519e81 100644
--- a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch
@@ -1,18 +1,18 @@
 diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/config/packages/hypre.py
-index 869a1661..76067c8d 100644
+index 4d915c31..1b05a1ee 100644
 --- a/config/BuildSystem/config/packages/hypre.py
 +++ b/config/BuildSystem/config/packages/hypre.py
 @@ -5,10 +5,6 @@ class Configure(config.package.GNUPackage):
    def __init__(self, framework):
      config.package.GNUPackage.__init__(self, framework)
-     self.version         = '2.18.1'
+     #self.version         = '2.18.2'
 -    self.minversion      = '2.14'
 -    self.versionname     = 'HYPRE_RELEASE_VERSION'
 -    self.versioninclude  = 'HYPRE_config.h'
 -    self.requiresversion = 1
-     self.gitcommit       = 'v'+self.version
+     #self.gitcommit       = 'v'+self.version
+     self.gitcommit       = '93baaa8c9' # v2.18.2+valgrind-fix
      self.download        = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']
-     self.functions       = ['HYPRE_IJMatrixCreate']
 diff --git a/include/petsc/private/petschypre.h b/include/petsc/private/petschypre.h
 index 81ca7136..b403e70e 100644
 --- a/include/petsc/private/petschypre.h
@@ -31,7 +31,7 @@ index 81ca7136..b403e70e 100644
    With scalar type == real, HYPRE_Complex == PetscScalar;
    With scalar type == complex,  HYPRE_Complex is double __complex__ while PetscScalar may be std::complex<double>
 diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c
-index 8e8fe678..3533b99a 100644
+index 0f7470e6..cce3e2b0 100644
 --- a/src/mat/impls/hypre/mhypre.c
 +++ b/src/mat/impls/hypre/mhypre.c
 @@ -15,10 +15,6 @@
@@ -42,10 +42,10 @@ index 8e8fe678..3533b99a 100644
 -#define  hypre_ParCSRMatrixClone(A,B) hypre_ParCSRMatrixCompleteClone(A)
 -#endif
 -
- PETSC_INTERN PetscErrorCode MatPtAP_IS_XAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
- 
  static PetscErrorCode MatHYPRE_CreateFromMat(Mat,Mat_HYPRE*);
-@@ -65,7 +61,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat,Mat,HYPRE_IJMatrix);
+ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat,HYPRE_IJMatrix);
+@@ -63,7 +59,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
          nnz_o[i] = 0;
        }
      }
@@ -53,7 +53,7 @@ index 8e8fe678..3533b99a 100644
      { /* If we don't do this, the columns of the matrix will be all zeros! */
        hypre_AuxParCSRMatrix *aux_matrix;
        aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
-@@ -75,9 +70,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+@@ -73,9 +68,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
        aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
        hypre_AuxParCSRMatrixNeedAux(aux_matrix) = 1;
      }
@@ -63,7 +63,7 @@ index 8e8fe678..3533b99a 100644
      ierr = PetscFree(nnz_d);CHKERRQ(ierr);
      ierr = PetscFree(nnz_o);CHKERRQ(ierr);
    }
-@@ -235,11 +227,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+@@ -233,11 +225,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
    /* need to shift the diag column indices (hdiag->j) back to global numbering since hypre is expecting this */
    hjj = hdiag->j;
    pjj = pdiag->j;
@@ -75,7 +75,7 @@ index 8e8fe678..3533b99a 100644
    ierr = PetscArraycpy(hdiag->data,pdiag->a,pdiag->nz);CHKERRQ(ierr);
    if (sameint) {
      ierr = PetscArraycpy(hoffd->i,poffd->i,pA->A->rmap->n + 1);CHKERRQ(ierr);
-@@ -249,12 +237,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+@@ -247,12 +235,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
  
    /* need to move the offd column indices (hoffd->j) back to global numbering since hypre is expecting this
       If we hacked a hypre a bit more we might be able to avoid this step */
diff --git a/sci-mathematics/petsc/petsc-3.12.1.ebuild b/sci-mathematics/petsc/petsc-3.13.0.ebuild
index 845d7ff75d69..961ff927f725 100644
--- a/sci-mathematics/petsc/petsc-3.12.1.ebuild
+++ b/sci-mathematics/petsc/petsc-3.13.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
 
@@ -54,17 +54,11 @@ DEPEND="${RDEPEND}
 
 PATCHES=(
 	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-	"${FILESDIR}"/${PN}-3.12.1-make_hypre_configure.patch
-	"${FILESDIR}"/${PN}-3.12.1-do_not_run_mpiexec.patch
+	"${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch
 )
 
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
 # petsc uses --with-blah=1 and --with-blah=0 to en/disable options
 petsc_enable() {
 	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.13.1.ebuild
index 50ce3b7f6631..961ff927f725 100644
--- a/sci-mathematics/petsc/petsc-3.11.3.ebuild
+++ b/sci-mathematics/petsc/petsc-3.13.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
 
@@ -36,7 +36,7 @@ RDEPEND="
 	boost? ( dev-libs/boost )
 	fftw? ( sci-libs/fftw:3.0[mpi?] )
 	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+	hypre? ( >=sci-libs/hypre-2.18.0[mpi?] )
 	metis? ( >=sci-libs/parmetis-4 )
 	mpi? ( virtual/mpi[cxx?,fortran?] )
 	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
@@ -53,16 +53,12 @@ DEPEND="${RDEPEND}
 "
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
+	"${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch
 )
 
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
 # petsc uses --with-blah=1 and --with-blah=0 to en/disable options
 petsc_enable() {
 	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
@@ -157,23 +153,23 @@ src_configure() {
 		$(use_with hdf5) \
 		$(petsc_with hypre hypre \
 			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
+		$(use_with sparse suitesparse) \
 		$(petsc_with superlu superlu \
 			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
+		$(use_with X x) \
+		$(use_with X x11) \
 		$(petsc_with scotch ptscotch \
 			/usr/include/scotch \
 		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
 		$(petsc_with mumps scalapack \
 			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
+		$(use_with mumps mumps \
 			/usr/include \
 			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
 		--with-imagemagick=0 \
 		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
+		$(use_with boost) \
+		$(use_with fftw)
 }
 
 src_install() {
diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index f97728d499b7..e74624932965 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -25,6 +25,7 @@ AUX rstudio-1.2.1335-qtsingleapplication.patch 2080 BLAKE2B 3e2c1b5df1c030a0d3f9
 AUX rstudio-1.2.5033-pandoc.patch 1442 BLAKE2B 28a1070057624fb70a2df6de0312dfa827a075ae481f6433733cdc6136a429fe67c72262d3106c6b00f7411f93d3e33ca69f232cc87aa9d8e50e11cad89d2dd6 SHA512 cdbb97f0705f6b56ce8e285d066c57a9f73ce87ef58d8101362a508cb1cc52a32418a742e84a9a9d6476b253984abe0759b45e824d360d8b550e53a98d2d05ca
 AUX rstudio-1.2.5033-paths.patch 6055 BLAKE2B 1c389cbd2980031080955c104e614d2bbcd0d747fd7d925a9650685bf30ddb84c34b66a4a6bcb58a1b18167e51804df9c22734460255eda866365231cda3e9f9 SHA512 ba213cf13ae15df043215e6b87bf554c9daba4124a1a83ecb2e5ccc8f26fd6f1467798901cc24451f04f4d25482da401cc9cdd5071a4c6ac28d9af37c45f51e5
 AUX rstudio-1.2.5033-prefs.patch 3684 BLAKE2B dfa5f7289a7e752704b6481dd6e02f8e88a91aaa36b25c91e8154f17bf3fbfcb2b674fcc790a82ae14deb0718b1d001f4931de6d6ccb99d1ed4dc9c8e71d6149 SHA512 86436aec19da35d99ec64ad1d4c243efad85a277ee72c2eaf94627c49389ba8d4bc626177a9d599bb95d00bc3e66210472e11a5ff38ed74a7a353a719f64fe4d
+AUX rstudio-1.2.5042-boost-1.73.0.patch 728 BLAKE2B 675e5ff75ce5c3242bff5d92b32ca6391e8ceb68c504c2f161f2f30c083ae842e5e9a9c519e848595704bb6d639c5a8dc13a296dcfa445db19295f8ee78168e0 SHA512 214751fff5b027f407b093f397e70e701ed9016451a3972b240dcd4999d9b27a1309b47fb22a9f4f3944c47dc6de6bd8f1165a70a7046b5133bd88923d1b46a6
 AUX rstudio-server.conf 1337 BLAKE2B a9a85c76a1c7c5f32f55606c6e3c9b72662dbd25e4b005f9702ed301afc21425906faf06fca91c18328524c53437aee7c9c4aee26cf293cdc72375e91ec7f701 SHA512 f166f1aa4bd370fcfcb44c5694d4e6af8bc64c5f43671e0c1def10c555d248bebf54199097f37d628a083c65913f522b7b44c3bd6a1227c011cf25eed1dba4a6
 AUX rstudio-server.initd 377 BLAKE2B 4f49b9ae2a81cd60565f79f121d60f5531746febd1f6f68cc93863985bd9af28d4ef04f647bd1b492ca69273724c282bcaedcfb5d08b8f2ac237ddb6f5baa438 SHA512 828a485338088d129c57debec6557ad35db5b042c61489ae4341717ce2218bec59a873541c270f964bb9c708b75896f1a3e2e64a4245a1713979d3bd42c9d5c8
 AUX rstudio-server.service.in 161 BLAKE2B 0be9cb83304063c9123c6fa13b7751b2f848adde282fc586acccfa4110f902e4de9962211ca0c871f66f3563319fe195c9f230daa4d4e429357ff74701e4d2d7 SHA512 bcf1f30e460dd5f0562b20489ca5544c6bcfbfb0ee1c636c4365df433e97e02e9e3b233e4159a0c71ad6d319f34f93c22b8fbf6b36463e29f22df2acd71da173
@@ -40,10 +41,12 @@ DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BL
 DIST rstudio-1.1.463.tar.gz 20203779 BLAKE2B 97f879539cbb7051af362a8469795a47feb42d18ff46dbbdffe36e0685d1cd5704848b3bf5a5611d482a09567722e35288527302cd521b18e2a48b347c919e17 SHA512 987347563a9726363c28d866e1372eae8eb19a5cbd0e33c7ee0e0c8f90471c4b69de0f559c00410523841b6c090b584652e01496f5db33c015a4554d2f4e179b
 DIST rstudio-1.2.1335.tar.gz 20440199 BLAKE2B cdd54a7df5a234bcc6d440f4ba5b45e58ea469f8dac5a17d9088f9d65035495c86b5a308cde28a224648f96a74038299863291f3c516a1d567762ecc5bfb079c SHA512 90657effc55264bf3efa1a8a5d2bbe94a37727f0450202ade99b9fbb71ea75b6dd9fa798d17cd4d1a1a97a16f186de8004d1888b6ea43f36d5252508520d3cde
 DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
+DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
 DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
 DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
 DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c
 EBUILD rstudio-1.1.463-r1.ebuild 8689 BLAKE2B ab91995b112b4d3e888c688b72109ed47468c8b72e13aa3066ecb51c213a46471f42f5bb517e8e2a82a623771eeebf917c02d85cd4322dbb1992687fd93d6c86 SHA512 0bffca8ab03f91e4aa2ee24df21b9a102260eb587d1127f885d591221171dd691c347fb87a5e11a5e191c9a363daf13210310acafbb47405951c2bc2c38c18d0
 EBUILD rstudio-1.2.1335.ebuild 8688 BLAKE2B b02dac6ce848799534e95fa016d481526bf09525c84834f604dc6cbfe625e2b4d278fc4554119be6edfd27ad987c4cb9cfa48f56f0c5d165450ea8bfa2a7f276 SHA512 fd846f875b2a9c3e9e992371b8cd11ebe95f27e7b3252181fad50ce3a7ae3bd77b652742e0f4fb6f163cfd903d90dd4e701a29427509ca07615717c5e3d69912
 EBUILD rstudio-1.2.5033.ebuild 7183 BLAKE2B 38c0baa94c4c002dff6b5faf9ce7737832b74fc9de68d9077cc4e1f1a281a456023810a439d8a0b527d3e0ec6cd5860bac544bb30ab57d7077d22ffdb79fb875 SHA512 eb8460899577ddb1ac3925d42737fb8737798cd1b15f7c731283a4fc5b7e413101233325d15b56355d37aab1a27ef87266582c35771f04ab71e4f6714611cdd2
+EBUILD rstudio-1.2.5042.ebuild 7232 BLAKE2B 6bbc99764eb8e521bcf41cdc45a9d9e777a78d400c7feeb97d6c477c2b002678bca746680fbffedc8e894cbc2d6141dd032e68280f7766d7051a95add514bb1c SHA512 f5faf42857ec815aef7dc4ddc8e7672e0502e6d68fcc368fb334a58dc96c2a5372e73a6ce191920537b21126ad718b359469e7f7529c819e340cb6fa4f2a5168
 MISC metadata.xml 590 BLAKE2B 53dc62775e118c9c26ee05e20ee1da1ac31b6a6b74cf7dac410856fe4e0cce40fbb800c7a03e60f59e14442baf3aad866ad42616ad5fbb5724f7f6d8c1636eea SHA512 7111442aaa52da1e554c34f824113ec0e227798dd11b0ea9148b81e7a31c08b2a527b9995e3adb9363c7a4f2a8594f30cbd4a179545bf31d69f07d5558c20f52
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.5042-boost-1.73.0.patch b/sci-mathematics/rstudio/files/rstudio-1.2.5042-boost-1.73.0.patch
new file mode 100644
index 000000000000..cd024e9ed912
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.5042-boost-1.73.0.patch
@@ -0,0 +1,22 @@
+--- rstudio-1.2.5042-orig/src/cpp/core/system/PosixChildProcessTracker.cpp	2020-04-02 03:16:24.000000000 +1100
++++ rstudio-1.2.5042/src/cpp/core/system/PosixChildProcessTracker.cpp	2020-04-28 15:36:44.839368084 +1000
+@@ -19,6 +19,8 @@
+ 
+ #include <boost/format.hpp>
+ 
++using namespace boost::placeholders;
++
+ namespace rstudio {
+ namespace core {
+ namespace system {
+--- rstudio-1.2.5042-orig/src/cpp/core/system/PosixOutputCapture.cpp	2020-04-02 03:16:24.000000000 +1100
++++ rstudio-1.2.5042/src/cpp/core/system/PosixOutputCapture.cpp	2020-04-28 15:35:50.869185435 +1000
+@@ -28,6 +28,8 @@
+ 
+ #include <core/system/System.hpp>
+ 
++using namespace boost::placeholders;
++
+ namespace rstudio {
+ namespace core {
+ namespace system {
diff --git a/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild b/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild
new file mode 100644
index 000000000000..2de83f6f633f
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild
@@ -0,0 +1,236 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils cmake-utils pam xdg-utils java-pkg-2 java-ant-2 pax-utils prefix qmake-utils vcs-clean
+
+# TODO
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=)' dependencies/common/install-gwt
+GWT_VER=2.8.1
+GIN_VER=2.1.2
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+# It should be PANDOC_VER=2.3.1 however >=app-text/pandoc-2.3.1 is not yet in portage
+PANDOC_VER=1.19.2.1
+# grep -5 QT_CANDIDATES src/cpp/desktop/CMakeLists.txt
+QT_VER=5.10
+QT_SLOT=5
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-java/aopalliance:1
+	dev-java/gin:2.1
+	dev-java/gwt:2.8
+	dev-java/javax-inject
+	=dev-java/validation-api-1.0*:1.0[source]
+	dev-haskell/pandoc-citeproc
+	dev-lang/R
+	dev-libs/boost:=
+	>=dev-libs/mathjax-2.7.4
+	sys-apps/util-linux
+	sys-devel/clang:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebengine-${QT_VER}:${QT_SLOT}[widgets]
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( sys-libs/pam )
+	)
+	dedicated? ( sys-libs/pam )
+	dedicated? (
+		sys-libs/pam
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	server? (
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	!libressl? ( dev-libs/openssl:0= )
+	libressl? ( dev-libs/libressl:0= )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.2.5033-prefs.patch
+	"${FILESDIR}"/${PN}-1.2.5033-paths.patch
+	"${FILESDIR}"/${PN}-1.2.5033-pandoc.patch
+	"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
+	"${FILESDIR}"/${PN}-1.2.1335-qtsingleapplication.patch
+	"${FILESDIR}"/${PN}-1.0.44-systemd.patch
+	"${FILESDIR}"/${PN}-1.2.1335-core.patch
+	"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p1.patch
+	"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p2.patch
+	"${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	cd "${S}" || die
+	mkdir -p dependencies/common/dictionaries
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes
+	sed -i \
+		-e "s@\(DESTINATION \"\)\(extras/themes\"\)@\1${EROOT}/etc/rstudio/\2@" \
+		src/cpp/server/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}/etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS e4a1c219cbf6c10d9aec41461d80171ab3009bef@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+
+	eprefixify src/gwt/build.xml
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	if use !dedicated; then
+		mycmakeargs+=(
+			-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+			-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		)
+	fi
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	local JAVA_ANT_REWRITE_CLASSPATH="yes"
+	local EANT_BUILD_XML="src/gwt/build.xml"
+	local EANT_BUILD_TARGET="clean"
+	java-pkg-2_src_compile
+
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}
diff --git a/sci-mathematics/slepc/Manifest b/sci-mathematics/slepc/Manifest
index c8fc5c686237..03dc04d5a6e5 100644
--- a/sci-mathematics/slepc/Manifest
+++ b/sci-mathematics/slepc/Manifest
@@ -1,5 +1,3 @@
-DIST slepc-3.11.1.tar.gz 4700643 BLAKE2B a624050aad0128d7ef53f27f72484e078e62d8edf9298995dda71a9e8d804dddc7e433542eccf95b2d896be80e8795b1664375e68a4c02c18c56d78d490bffb7 SHA512 a941c2a955953ed2344de7f7d9eaaed79504c3559e27920c633bc09cfb192f883b26fd4aa5dc3bd9909a2fc045f3a34e514feca0e074ca36bc3166aa9c059235
-DIST slepc-3.12.1.tar.gz 4757436 BLAKE2B 607e7b28730ff16fa995768e23fd9861e180c078d2f06e8f65324b1e1761f0688fe5a4c4420983b521583cb2b3fe28b606baea604daf5253c30131f9f54c5572 SHA512 0254ea1a521cf150f9f0402bb936c9d1aa32765264e055ecdd058e44aaa7e87c3df1b63b1889c1989c4a691c652eb0f248a1bbbe6d555ce16f9f8f28d6765b50
-EBUILD slepc-3.11.1.ebuild 1661 BLAKE2B 6844c1e110d47bf7620e5a1712bbd265d6d0a40f65e8961ec3818c0eeb5b56c95b35bf4b76fdeab1a144a4561f549e4be1ad8a4cb27fcd623add77fd3e33af97 SHA512 e827d09af4082f3b6e6a96ae1880042a292f7cc1d44729c2efc77cfac91a554dde8f19ea8210dbc5d532e9f09786ec87d6a92ad379e18326181eee35e6f33d2d
-EBUILD slepc-3.12.1.ebuild 1661 BLAKE2B 6844c1e110d47bf7620e5a1712bbd265d6d0a40f65e8961ec3818c0eeb5b56c95b35bf4b76fdeab1a144a4561f549e4be1ad8a4cb27fcd623add77fd3e33af97 SHA512 e827d09af4082f3b6e6a96ae1880042a292f7cc1d44729c2efc77cfac91a554dde8f19ea8210dbc5d532e9f09786ec87d6a92ad379e18326181eee35e6f33d2d
+DIST slepc-3.13.1.tar.gz 4797627 BLAKE2B 29372b8a2d4c5f3b26e840df743f7aec098bfeeb29e9c108e509baa21d9697da19c737470ba4c132391d5193ebf749ef3f3c6ece600ec7527502d40a239aa0ee SHA512 620c344274808329c0a1009e7844532e03e88d38135bfd5b73bc0bc6815b17b6dfb49341d05399230ba6e06997db688aec17615429eaca3dc94fd886119bf321
+EBUILD slepc-3.13.1.ebuild 1588 BLAKE2B 471e024fa09e1b2bcbdaaccfaa6681449d7180ae0874b9f698cb180f60bc37b467e1cc5ed451ec25acb1dc02d219a2c8734a8113a277e3e95e409aefa81cc510 SHA512 87cfaaf90488b5951aa3ec865ebe288b8dc724323032d540b109511f3b268b107ed00e23f3439046191fb73c19f8b68f96a1f3450706c960b4c19c27ccbafdc5
 MISC metadata.xml 451 BLAKE2B 5268292011dffcbc322504b29332ae20a4e775238e201ffe793e1ebfb8d8c13a836ca1f8eba44b38bc63ba7b21a3634a03df9990e8b801def0152316d1539960 SHA512 7bf6d4cdedaa48f96e9b1d3e237b795f7cbfd840cece0c0181c9efa05ec833477191e8d12cf2b7737a921b85fb5af055d5868e1173415fc70802eb515959c9d5
diff --git a/sci-mathematics/slepc/slepc-3.11.1.ebuild b/sci-mathematics/slepc/slepc-3.11.1.ebuild
deleted file mode 100644
index 52212cabfd52..000000000000
--- a/sci-mathematics/slepc/slepc-3.11.1.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-any-r1 toolchain-funcs
-
-DESCRIPTION="Scalable Library for Eigenvalue Problem Computations"
-HOMEPAGE="http://slepc.upv.es/"
-SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="complex-scalars doc mpi"
-
-RDEPEND="
-	=sci-mathematics/petsc-$(ver_cut 1-2)*:=[mpi=,complex-scalars=]
-	sci-libs/arpack[mpi=]
-	mpi? ( virtual/mpi )
-"
-
-DEPEND="${RDEPEND}
-	${PYTHON_DEPS}
-	virtual/pkgconfig
-	dev-util/cmake
-"
-
-MAKEOPTS="${MAKEOPTS} V=1"
-
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-src_configure() {
-	# *sigh*
-	addpredict "${PETSC_DIR}"/.nagged
-
-	# Make sure that the environment is set up correctly:
-	unset PETSC_DIR
-	unset PETSC_ARCH
-	unset SLEPC_DIR
-	source "${EPREFIX}"/etc/env.d/99petsc
-	export PETSC_DIR
-
-	# configure is a custom python script and doesn't want to have default
-	# configure arguments that we set with econf
-	./configure \
-		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
-		--with-arpack=1 \
-		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
-}
-
-src_install() {
-	emake DESTDIR="${ED}" install
-
-	# add PETSC_DIR to environmental variables
-	cat >> 99slepc <<- EOF
-		SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc
-		LDPATH=${EPREFIX}/usr/$(get_libdir)/slepc/lib
-	EOF
-	doenvd 99slepc
-
-	if use doc ; then
-		dodoc docs/slepc.pdf
-		docinto html
-		dodoc -r docs/*.html docs/manualpages
-	fi
-}
diff --git a/sci-mathematics/slepc/slepc-3.12.1.ebuild b/sci-mathematics/slepc/slepc-3.13.1.ebuild
index 52212cabfd52..be2d085dd6cb 100644
--- a/sci-mathematics/slepc/slepc-3.12.1.ebuild
+++ b/sci-mathematics/slepc/slepc-3.13.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit eutils flag-o-matic python-any-r1 toolchain-funcs
 
@@ -30,12 +30,6 @@ DEPEND="${RDEPEND}
 
 MAKEOPTS="${MAKEOPTS} V=1"
 
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
 src_configure() {
 	# *sigh*
 	addpredict "${PETSC_DIR}"/.nagged
@@ -43,9 +37,10 @@ src_configure() {
 	# Make sure that the environment is set up correctly:
 	unset PETSC_DIR
 	unset PETSC_ARCH
-	unset SLEPC_DIR
 	source "${EPREFIX}"/etc/env.d/99petsc
 	export PETSC_DIR
+	export PETSC_ARCH
+	export SLEPC_DIR="${S}"
 
 	# configure is a custom python script and doesn't want to have default
 	# configure arguments that we set with econf
@@ -53,8 +48,7 @@ src_configure() {
 		--prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \
 		--with-arpack=1 \
 		--with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")"
-
+		--with-arpack-lib="$(usex mpi "-lparpack,-larpack" "-larpack")"
 }
 
 src_install() {
diff --git a/sci-mathematics/z3/Manifest b/sci-mathematics/z3/Manifest
index e0199dadd995..9e05c62bbb36 100644
--- a/sci-mathematics/z3/Manifest
+++ b/sci-mathematics/z3/Manifest
@@ -1,3 +1,5 @@
 DIST z3-4.8.6.tar.gz 4328752 BLAKE2B 4932670f3c1ab9bdba18a6ad80f4fd8812eb70d71705ebdf1f93c3b052ffb632dc10e4f7f4043f098af214288d6d4a4a26ef7f8cc0d1183c9f27b14ef1787c46 SHA512 d338413274a3d11a9e9287202989df9da4c31e095c14428a418d4019e9f86c0e2b681c519d2d0bcbb4cd99a722a2539006f5c86ade568b1ee208545b142369f1
+DIST z3-4.8.8.tar.gz 4520119 BLAKE2B 8d3d9fac61ac7d5a9d8c44323db9f67a7b24ee510b12e67867b249062cbcfe9a3bd0fa3b24c03c9eccd2aaf90451083ff5e9a9253a87c3e8e943fc5cf08a1893 SHA512 a6823cadb7cdad11b8f0db1530676c0ec4853886dfb3c4dbc5b798c5dbd445afb0c61675f81cb7f99c1b1734d9cd0ec96a07c68a948da3c25801fc6767fea47f
 EBUILD z3-4.8.6.ebuild 2335 BLAKE2B e980e31d4d6ab4443b7b385c66aa1a71ab062d4783e1947d1a2d9688986729a19769813e22cb7395d9a8a1a45e1fb898da1a8e6c923c8486aa8dccd601f9874b SHA512 214122932dcbb1cef0e3d3617e37e3057936b28afc7d70fff2fe08bfcaad963516d48f20fe65efaf80729f5ab070b562aa574c163f908c82b620846e5cda7982
-MISC metadata.xml 862 BLAKE2B 1d219fcfb0772a48ec398a51b8916748db336730b91b66e336e8df0b8522b9a47df718d6303aff5f305b699e9297aaad9b352c69d529a93f66cf2a1b76c8f094 SHA512 2a5cc11ae87199a23c72ffb7366c65cbb33683bb6ad142d1df84a65b56bd69f50907bca69f066a1c860947254c241089521c026bac9ff92bd405038c266907ef
+EBUILD z3-4.8.8.ebuild 2415 BLAKE2B fa4d5fe952685eb5d8d2aa1f679b008e6887c0eaa25ec7101635db290b33ae5c5936216b5cd1ba11cf49006ac1de242a566e7b47923e608dbace24c6c5b85d08 SHA512 b4e757bfdf1a252f0b33f28fb1dd470025966dd16cf77e5925d0e52a30011672475097789d46557fcddce00cf5d308c9f417f6da858c2a66965933547c2d4d75
+MISC metadata.xml 732 BLAKE2B dec39a80325f9dba9e79d65f448d828c3ee19327a1a12505e487a39fd58fb49f47446e439d713a9fa2603bc971f22f4eb8c1a12e93e18281aeba5e183642add8 SHA512 7d081840634a8dc578acc60c4b85ef1a35f025c2ac251d2f7633a807af7395061ef4fb96716e96a96a876ae318b52333dfc0200fa1e72e35889433676a56e58b
diff --git a/sci-mathematics/z3/metadata.xml b/sci-mathematics/z3/metadata.xml
index 15735c68e920..65ab90b88bdf 100644
--- a/sci-mathematics/z3/metadata.xml
+++ b/sci-mathematics/z3/metadata.xml
@@ -15,9 +15,6 @@
     <email>sci@gentoo.org</email>
     <name>Gentoo Science Project</name>
   </maintainer>
-  <longdescription lang="en">
-Z3 is a high-performance theorem prover being developed at Microsoft Research.
-  </longdescription>
   <use>
     <flag name="isabelle">Add integration support for the Isabelle/HOL
   theorem prover.</flag>
diff --git a/sci-mathematics/z3/z3-4.8.8.ebuild b/sci-mathematics/z3/z3-4.8.8.ebuild
new file mode 100644
index 000000000000..949c33e2e2b1
--- /dev/null
+++ b/sci-mathematics/z3/z3-4.8.8.ebuild
@@ -0,0 +1,95 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7,8} )
+
+inherit cmake-multilib python-single-r1 toolchain-funcs
+
+DESCRIPTION="An efficient theorem prover"
+HOMEPAGE="https://github.com/Z3Prover/z3/"
+SRC_URI="https://github.com/Z3Prover/z3/archive/${P}.tar.gz"
+S=${WORKDIR}/z3-${P}
+
+SLOT="0/4.8"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~arm ~arm64 ~ppc64 ~x86"
+IUSE="doc examples gmp isabelle java python"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	gmp? ( dev-libs/gmp:0=[cxx,${MULTILIB_USEDEP}] )"
+DEPEND="${RDEPEND}
+	java? ( >=virtual/jdk-1.8 )"
+BDEPEND="
+	doc? ( app-doc/doxygen )"
+
+CMAKE_BUILD_TYPE=RelWithDebInfo
+
+multilib_src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_DOCDIR="${EPREFIX}/usr/share/doc/${P}"
+		-DZ3_USE_LIB_GMP=$(usex gmp)
+		-DZ3_ENABLE_EXAMPLE_TARGETS=OFF
+		-DZ3_BUILD_DOCUMENTATION=$(multilib_native_usex doc)
+		-DZ3_BUILD_PYTHON_BINDINGS=$(multilib_native_usex python)
+		-DZ3_BUILD_JAVA_BINDINGS=$(multilib_native_usex java)
+		-DZ3_INCLUDE_GIT_DESCRIBE=OFF
+		-DZ3_INCLUDE_GIT_HASH=OFF
+	)
+
+	cmake-utils_src_configure
+}
+
+multilib_src_test() {
+	cmake-utils_src_make test-z3
+	set -- "${BUILD_DIR}"/test-z3 /a
+	echo "${@}" >&2
+	"${@}" || die
+}
+
+multilib_src_install_all() {
+	dodoc README.md RELEASE_NOTES
+	use examples && dodoc -r examples
+	use python && python_optimize
+
+	if use isabelle; then
+		insinto /usr/share/Isabelle/contrib/${P}/etc
+		newins - settings <<-EOF
+			Z3_COMPONENT="\$COMPONENT"
+			Z3_HOME="${EPREFIX}/usr/bin"
+			Z3_SOLVER="${EPREFIX}/usr/bin/z3"
+			Z3_REMOTE_SOLVER="z3"
+			Z3_VERSION="${PV}"
+			Z3_INSTALLED="yes"
+			Z3_NON_COMMERCIAL="yes"
+		EOF
+	fi
+}
+
+pkg_postinst() {
+	if use isabelle; then
+		if [[ -f ${ROOT}/etc/isabelle/components ]]; then
+			sed -e "/contrib\/${PN}-[0-9.]*/d" \
+				-i "${ROOT}/etc/isabelle/components" || die
+			cat <<-EOF >> "${ROOT}/etc/isabelle/components" || die
+				contrib/${P}
+			EOF
+		fi
+	fi
+}
+
+pkg_postrm() {
+	if use isabelle; then
+		if [[ ! ${REPLACING_VERSIONS} ]]; then
+			if [[ -f "${ROOT}/etc/isabelle/components" ]]; then
+				# Note: this sed should only match the version of this ebuild
+				# Which is what we want as we do not want to remove the line
+				# of a new Isabelle component being installed during an upgrade.
+				sed -e "/contrib\/${P}/d" \
+					-i "${ROOT}/etc/isabelle/components" || die
+			fi
+		fi
+	fi
+}