From owner-dev-commits-ports-main@freebsd.org Sun Sep 12 14:03:08 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 30DBE666AB0; Sun, 12 Sep 2021 14:03:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4H6rt40fn1z4q57; Sun, 12 Sep 2021 14:03:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id EC3EC15382; Sun, 12 Sep 2021 14:03:07 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 18CE37UN074182; Sun, 12 Sep 2021 14:03:07 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 18CE379n074181; Sun, 12 Sep 2021 14:03:07 GMT (envelope-from git) Date: Sun, 12 Sep 2021 14:03:07 GMT Message-Id: <202109121403.18CE379n074181@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: =?utf-8?Q?Fernando Apestegu=C3=ADa?= Subject: git: 71ac81015e41 - main - science/afni: update to 21.2.06 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: fernape X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 71ac81015e41d55819d25c3ccc61b002205bf9be Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 12 Sep 2021 14:03:08 -0000 The branch main has been updated by fernape: URL: https://cgit.FreeBSD.org/ports/commit/?id=71ac81015e41d55819d25c3ccc61b002205bf9be commit 71ac81015e41d55819d25c3ccc61b002205bf9be Author: Fernando Apesteguía AuthorDate: 2021-08-18 05:57:17 +0000 Commit: Fernando Apesteguía CommitDate: 2021-09-12 13:58:20 +0000 science/afni: update to 21.2.06 * Remove openmp support. We don't seem to need it. * Adjust patch * Add -fcommon to make it build in 13 and 14-current * Add patch to include -DPIC -fPIC in i386. Otherwise we get: ld: error: can't create dynamic relocation R_386_32 against symbol: .L.str.13 in readonly segment --- science/afni/Makefile | 5 +++-- science/afni/distinfo | 6 +++--- science/afni/files/patch-Makefile | 12 ++++++++++++ science/afni/files/patch-Makefile.INCLUDE | 14 +++++++------- science/afni/pkg-plist | 1 + 5 files changed, 26 insertions(+), 12 deletions(-) diff --git a/science/afni/Makefile b/science/afni/Makefile index 0566618f8e34..b4725b3cf8f3 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 21.2.01 +DISTVERSION= 21.2.06 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org @@ -30,7 +30,7 @@ RUN_DEPENDS= endian:sysutils/endian \ R:math/R \ ${CRAN_DEPENDS} -USES= compiler:openmp gettext gl gmake gnome iconv jpeg:run motif +USES= gettext gl gmake gnome iconv jpeg:run motif USES+= perl5 python shebangfix tar:xz xorg USE_GITHUB= yes USE_GL= gl glu @@ -50,6 +50,7 @@ SHEBANG_FILES= scripts_install/* \ MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share MAKE_JOBS_UNSAFE=yes +CFLAGS+= -fcommon ALL_TARGET= vastness suma diff --git a/science/afni/distinfo b/science/afni/distinfo index 53dc9c9cb1e0..d55949fa6d16 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1626703703 -SHA256 (afni-afni-AFNI_21.2.01_GH0.tar.gz) = 923895d96494e2ec46f19585910a6bff36dc9b823a80f91e6f0fd903dc9fe3c3 -SIZE (afni-afni-AFNI_21.2.01_GH0.tar.gz) = 43782105 +TIMESTAMP = 1630649707 +SHA256 (afni-afni-AFNI_21.2.06_GH0.tar.gz) = 9b684d2c45ed085db62fe88f504565057e3d4ac0f6476d28141e5747d627f530 +SIZE (afni-afni-AFNI_21.2.06_GH0.tar.gz) = 43809366 diff --git a/science/afni/files/patch-Makefile b/science/afni/files/patch-Makefile new file mode 100644 index 000000000000..3712c13ebd00 --- /dev/null +++ b/science/afni/files/patch-Makefile @@ -0,0 +1,12 @@ +--- Makefile.orig 2021-09-09 09:32:21 UTC ++++ Makefile +@@ -48,9 +48,7 @@ LD? = ${CC} + + CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG + CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA +-ifeq (${ARCH}, amd64) + CEXTRA += -DPIC -fPIC +-endif + ifeq (${ARCH}, ia64) + CEXTRA += -DPIC -fPIC + endif diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE index dbe6cf979eac..de01b18022f6 100644 --- a/science/afni/files/patch-Makefile.INCLUDE +++ b/science/afni/files/patch-Makefile.INCLUDE @@ -1,6 +1,6 @@ ---- Makefile.INCLUDE.orig 2020-09-02 01:23:07 UTC +--- Makefile.INCLUDE.orig 2021-09-01 13:56:01 UTC +++ Makefile.INCLUDE -@@ -94,7 +94,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a +@@ -99,7 +99,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a ## AFNI package, but included because they are useful. Some of ## them are Open Source programs, not from the AFNI group at all. @@ -9,7 +9,7 @@ # mpegtoppm in above list -@@ -107,7 +107,7 @@ EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat qu +@@ -112,7 +112,7 @@ EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat qu PROGS_1 = afni to3d from3d 3dclust nsize 3dinfo 3dmerge count \ sfim tfim imrotate imreg imstat 3dnvals \ fim2 imand immask imdump imaver 3dhistog 3daxialize \ @@ -18,7 +18,7 @@ waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ 3dNLfim 3dTSgen plugout_tt plugout_ijk \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ -@@ -120,7 +120,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn +@@ -125,7 +125,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \ 3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \ 3dEntropy 3ddelay 3dRowFillin 1dgrayplot 3dToutcount 1dsum \ @@ -27,7 +27,7 @@ 3dGetrow 3dTcorrelate 3dcopy Vecwarp 3dCM fdrval \ 3dAFNItoANALYZE 3dAFNItoNIFTI \ 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dBrickStat \ -@@ -143,7 +143,7 @@ PROGS_3 = 3dAnhist 3dAFNIto3D 3dWarp nicat +@@ -148,7 +148,7 @@ PROGS_3 = 3dAnhist 3dAFNIto3D 3dWarp nicat PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \ 3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \ 3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \ @@ -36,7 +36,7 @@ 1dCorrelate 3dNwarpCalc dicom_hinfo apsearch 1dBport \ 3dNormalityTest 3dmask_tool FIRdesign help_format 2perm \ 3dClustCount column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog \ -@@ -170,7 +170,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4) +@@ -175,7 +175,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4) PROGRAMS_NOPLUG = \ afni to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ imreg imstat count fim2 imand immask imdump imaver 3dhistog imupsam \ @@ -45,7 +45,7 @@ 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval 3dMannWhitney \ 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna imstack byteorder \ 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot 24swap 3dTsmooth RSFgen \ -@@ -208,7 +208,7 @@ PROGRAMS_NOPLUG = +@@ -213,7 +213,7 @@ PROGRAMS_NOPLUG = PROGRAMS_EXE = \ afni.exe to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ imreg imstat 3dnvals count fim2 imand immask imdump imaver 3dhistog \ diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index 08e9691967be..38b17fd89d60 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -1939,6 +1939,7 @@ lib/afni/plug_zeropad.so %%PORTDOCS%%%%DOCSDIR%%/README.render_scripts %%PORTDOCS%%%%DOCSDIR%%/README.roi %%PORTDOCS%%%%DOCSDIR%%/README.setup +%%PORTDOCS%%%%DOCSDIR%%/README.texlike %%PORTDOCS%%%%DOCSDIR%%/README.volreg %%PORTDOCS%%%%DOCSDIR%%/README.web %%PORTDOCS%%%%DOCSDIR%%/README.ziad