git: 71ac81015e41 - main - science/afni: update to 21.2.06

Fernando Apesteguía fernape at FreeBSD.org
Sun Sep 12 14:03:08 UTC 2021 

The branch main has been updated by fernape:

URL: https://cgit.FreeBSD.org/ports/commit/?id=71ac81015e41d55819d25c3ccc61b002205bf9be

commit 71ac81015e41d55819d25c3ccc61b002205bf9be
Author:     Fernando Apesteguía <fernape at FreeBSD.org>
AuthorDate: 2021-08-18 05:57:17 +0000
Commit:     Fernando Apesteguía <fernape at FreeBSD.org>
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 at 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

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