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Sun, 3 Mar 2024 17:09:45 GMT (envelope-from git) Date: Sun, 3 Mar 2024 17:09:45 GMT Message-Id: <202403031709.423H9jeG000385@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Fernando =?utf-8?Q?Apestegu=C3=ADa?= Subject: git: 04a6a89cf6ea - main - science/afni: update to 24.0.09 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org 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: 04a6a89cf6ea0a1c3a54996a049ef6a489b866a5 Auto-Submitted: auto-generated The branch main has been updated by fernape: URL: https://cgit.FreeBSD.org/ports/commit/?id=04a6a89cf6ea0a1c3a54996a049ef6a489b866a5 commit 04a6a89cf6ea0a1c3a54996a049ef6a489b866a5 Author: Fernando Apesteguía AuthorDate: 2024-02-29 08:14:46 +0000 Commit: Fernando Apesteguía CommitDate: 2024-03-03 17:08:15 +0000 science/afni: update to 24.0.09 --- science/afni/Makefile | 2 +- science/afni/distinfo | 6 +++--- science/afni/files/patch-Makefile.INCLUDE | 14 +++++++------- .../afni/files/patch-crorden_dcm2niix__console_makefile | 12 ++++++------ science/afni/pkg-plist | 1 + 5 files changed, 18 insertions(+), 17 deletions(-) diff --git a/science/afni/Makefile b/science/afni/Makefile index 3cf61a264707..1ec4d0fe1f08 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 24.0.08 +DISTVERSION= 24.0.09 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 507cf615a19f..bcabddda8027 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1708694522 -SHA256 (afni-afni-AFNI_24.0.08_GH0.tar.gz) = e71066f7a1539e01e17004b2bbd09e82b241e7044b3aa82ab1f77cfb8c591f26 -SIZE (afni-afni-AFNI_24.0.08_GH0.tar.gz) = 52917832 +TIMESTAMP = 1709194473 +SHA256 (afni-afni-AFNI_24.0.09_GH0.tar.gz) = 0ea8350ef4ef49563c29f761e3d7594d7685a9851267d7f6a0d76d9d591a1acc +SIZE (afni-afni-AFNI_24.0.09_GH0.tar.gz) = 52934713 diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE index de01b18022f6..a892005530a3 100644 --- a/science/afni/files/patch-Makefile.INCLUDE +++ b/science/afni/files/patch-Makefile.INCLUDE @@ -1,6 +1,6 @@ ---- Makefile.INCLUDE.orig 2021-09-01 13:56:01 UTC +--- Makefile.INCLUDE.orig 2024-02-29 01:05:45 UTC +++ Makefile.INCLUDE -@@ -99,7 +99,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a +@@ -105,7 +105,7 @@ MISC = $(MISC_TEXT) 3d*.lib ## 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 -@@ -112,7 +112,7 @@ EXTRAS = cjpeg djpeg whirlgif myget rmz aiv mycat qu +@@ -118,7 +118,7 @@ PROGS_1 = afni to3d from3d 3dclust nsize 3dinfo 3dmer 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 \ -@@ -125,7 +125,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn +@@ -131,7 +131,7 @@ 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 \ -@@ -148,7 +148,7 @@ PROGS_3 = 3dAnhist 3dAFNIto3D 3dWarp nicat +@@ -154,7 +154,7 @@ PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPer 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 \ -@@ -175,7 +175,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4) +@@ -182,7 +182,7 @@ PROGRAMS_NOPLUG = PROGRAMS_NOPLUG = \ afni to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ imreg imstat count fim2 imand immask imdump imaver 3dhistog imupsam \ @@ -45,7 +45,7 @@ 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval 3dMannWhitney \ 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna imstack byteorder \ 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot 24swap 3dTsmooth RSFgen \ -@@ -213,7 +213,7 @@ PROGRAMS_NOPLUG = +@@ -221,7 +221,7 @@ PROGRAMS_EXE = PROGRAMS_EXE = \ afni.exe to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate \ imreg imstat 3dnvals count fim2 imand immask imdump imaver 3dhistog \ diff --git a/science/afni/files/patch-crorden_dcm2niix__console_makefile b/science/afni/files/patch-crorden_dcm2niix__console_makefile index 284366c03452..ad2ce657740c 100644 --- a/science/afni/files/patch-crorden_dcm2niix__console_makefile +++ b/science/afni/files/patch-crorden_dcm2niix__console_makefile @@ -1,4 +1,4 @@ ---- crorden/dcm2niix_console/makefile.orig 2023-08-17 23:49:49 UTC +--- crorden/dcm2niix_console/makefile.orig 2024-02-29 01:05:45 UTC +++ crorden/dcm2niix_console/makefile @@ -1,5 +1,5 @@ # Regular use @@ -7,16 +7,16 @@ # Debugging #CFLAGS=-g -@@ -35,7 +35,7 @@ ifneq ($(OS),Windows_NT) - #CFLAGS= -O3 +@@ -34,7 +34,7 @@ ifneq ($(OS),Windows_NT) + #CFLAGS=-dead_strip -O3 # ponder -sectcreate later [rickr] # CFLAGS=-O3 -sectcreate __TEXT __info_plist Info.plist -- CFLAGS=-O3 -+ CXXFLAGS=-O3 +- CFLAGS= -O3 ++ CXXFLAGS= -O3 #Apple notarization requires a Info.plist # For .app bundles, the Info.plist is a separate file, for executables it is appended as a section #you can check that the Info.plist section has been inserted with either of these commands -@@ -46,4 +46,4 @@ ifneq ($(OS),Windows_NT) +@@ -45,4 +45,4 @@ all: endif endif all: diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index 9638c0d23c3f..38a698402448 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -837,6 +837,7 @@ lib/afni/plug_zeropad.so %%PYTHON_SITELIBDIR%%/afnipy/lib_apqc_stats_dset.py %%PYTHON_SITELIBDIR%%/afnipy/lib_apqc_tcsh.py %%PYTHON_SITELIBDIR%%/afnipy/lib_b0_corr.py +%%PYTHON_SITELIBDIR%%/afnipy/lib_cbar_pbar.py %%PYTHON_SITELIBDIR%%/afnipy/lib_cdiflist.py %%PYTHON_SITELIBDIR%%/afnipy/lib_csv.py %%PYTHON_SITELIBDIR%%/afnipy/lib_decay_timing.py