afni (18.0.05+git24-gb25b21054~dfsg.1-1~nd+1) sid; urgency=medium * Backported for sid. * Used following sed expression to modify debian/control: -e 's/\(^Depends:\) */\1 neurodebian-popularity-contest, /g' -e 's/^Maintainer:.*$/Maintainer: NeuroDebian Maintainers \nX-Original-&/'. -- NeuroDebian Maintainers Tue, 23 Jan 2018 13:20:20 -0500 afni (18.0.05+git24-gb25b21054~dfsg.1-1) neurodebian; urgency=medium * Update Debian packaging for the package after a long time - reenabled running tests at package build time - new commands etc were added to the build - dcm2niix is recommended and symlinked as dcm2niix_afni to avoid the need of fragile patching - xfonts-base into Build-Depends and Suggests (needs to avoid Fonts related warnings while running the tests) - libgiftiio-dev removed from Build-Depends since we are building/using bundled copy -- Yaroslav Halchenko Tue, 23 Jan 2018 09:46:33 -0500 afni (16.2.07~dfsg.1-5) neurodebian; urgency=medium * Remove bdepends on hardening-includes which were removed in >=stretch, and just rely on dpkg-buildflags output -- Yaroslav Halchenko Fri, 09 Jun 2017 18:28:40 -0400 afni (16.2.07~dfsg.1-4) neurodebian; urgency=medium * Placed in build-time conflict with libglw1-mesa-dev == 8.0.0-1.1 which is a known version to not carry the patch (see #863826) http://marc.info/?l=cygwin-xfree&m=141268983004514&w=2 -- Yaroslav Halchenko Fri, 02 Jun 2017 13:53:17 -0400 afni (16.2.07~dfsg.1-3) neurodebian; urgency=medium * BF for amd64 precise -- explicitly specify -fPIC for CFLAGS -- Yaroslav Halchenko Wed, 31 Aug 2016 08:21:05 -0400 afni (16.2.07~dfsg.1-2) neurodebian; urgency=medium * install lib_fat_plot_sel.py lib_vars_object.py lib_fat_Rfactor.py libraries and unWarpEPI.py script (thanks Jeffrey Mark Siskind for the report) -- Yaroslav Halchenko Sat, 27 Aug 2016 22:38:54 -0400 afni (16.2.07~dfsg.1-1) neurodebian; urgency=medium * Major update after a long time - New programs: 3dToyProg, nifti_tool, nifti1_tool, nifti1_test, nifti_stats, gifti_tool, cifti_tool, images_equal, uniq_images, GLTsymtest, 3dPval, 3dETC, stimband, 1dNLfit, csfft_cache, 3dLocalACF, 3dNormalizer, 3dVecRGB_to_HSL, 3ddot_beta, 3dLombScargle, 3dAmpToRSFC, tokens, csfft_cache - New scripts: @Install_DBSproc, @Install_D99_macaque, @Install_3dPFM_Demo, 3dPFM, @diff.files, @diff.tree, @get.afni.version, @GradFlipTest, @fat_tract_colorize - New Python scripts: fat_lat_csv.py fat_mat_sel.py fat_mvm_review.py, read_matlab_files.py, afni_skeleton.py, @DoPerRoi.py, lpc_align.py, parse_fs_lt_log.py - New Matlab scripts: afni_isdigit.m, afni_swapbytes.m - 19 new faces, 10 new splashes, and 172 new quotes - run afni_history for a more detailed account of upstream changes * Now built as a fork from upstream's github repo * Updated CMake build system * Build and bundle AFNI's copy of both gifti and nifti - due to the latest versions being here in AFNI rather than upstream :-/ * debian/patches - up_include_right: some include fixes * Bump debian/compat to 9 -- Michael Hanke Fri, 05 Aug 2016 12:49:14 +0200 afni (0.20141224~dfsg.1-1) neurodebian; urgency=medium * Fresh upstream code * debian/patches -- 1 updated -- Yaroslav Halchenko Thu, 25 Dec 2014 11:33:53 -0500 afni (0.20141212~dfsg.1-1) neurodebian; urgency=medium * New upstream code * debian/patches - refreshed all - cmake_tests: allow for "Out of Cheese Error" -- Yaroslav Halchenko Mon, 15 Dec 2014 20:14:24 -0500 afni (0.20141118~dfsg.1-1) neurodebian; urgency=medium * New upstream code * debian/patches - cmake_sharedlibs was split into two (-noncmake and -cmake) with cmake files being only in -cmake one while -noncmake containing sattelite patches - cmake_sharedlibs-cmake updated for introduced few new files -- Yaroslav Halchenko Fri, 21 Nov 2014 16:26:20 -0500 afni (0.20141107~dfsg.1-1) neurodebian; urgency=medium * New upstream code * debian/patches - updated for changes in upstream code (new sources, one patch was adopted) -- Yaroslav Halchenko Thu, 13 Nov 2014 11:02:42 -0500 afni (0.20140910~dfsg.1-1) neurodebian; urgency=medium * debian/patches - accounted for added roiing.* files - accounted for renames/new python mvm scripts - accounted in AFNIio.R for the rename R_io.so -> librio.so in our build -- Yaroslav Halchenko Sun, 12 Oct 2014 17:00:23 -0400 afni (0.20140908~dfsg.1-1) neurodebian; urgency=medium * New upstream code * debian/patches - removed up_meica_fixes from the series (conflicts, and anyways previous version was not working) - debian_paths -- updated for now a function get_env_atlas_path allowing for paths to AFNI atlases being overriden via AFNI_ATLAS_PATH, and otherwise using default path on Debian systems (/usr/share/afni/atlases) - cmake_sharedlibs, ffmpeg_support, up_3dNetCorrFix, up_condition_dset_unload -- refreshed, with some conflicts resolved - cmake_sharedlibs - updated for changes in upstream build infrastructure - removed meicaX.py -- Yaroslav Halchenko Mon, 08 Sep 2014 11:59:31 -0400 afni (0.20140612~dfsg.1-1) neurodebian; urgency=low * New upstream code. - New programs: afni_open, 3dConformist, 3dTORTOISEtoHere, 3dEigsToDT, 3dDTtoNoisyDWI - 3dProbTrackID is officially deprecated (but still shipped) - New scripts: @afni.run.me, 3dRprogDemo - New Python scripts gen_ss_review_table.py - 9 new faces and 52 new quotes - run afni_history for a more detailed account of upstream changes * Updated CMake build system. * debian/patches - up_char_cast was successfully upstreamed - up_meica_fixes was a problematic patch to update. Might not be 100%. -- Alex Waite Thu, 05 Jun 2014 13:48:03 +0200 afni (0.20140227~dfsg.1-1) neurodebian; urgency=low * New upstream code. Updated CMake build system. -- Alex Waite Fri, 28 Feb 2014 13:20:33 +0200 afni (0.20131204~dfsg.1-2) neurodebian; urgency=low * Prune any @update.afni.* script (e.g. @update.afni.binaries) from installation so it doesn't interfer with packaged installation -- Yaroslav Halchenko Thu, 05 Dec 2013 16:48:02 -0500 afni (0.20131204~dfsg.1-1) neurodebian; urgency=low [ Andreas Tille ] * Perspective team upload (for now no upload to Debian proper) * debian/upstream: Add citation information from Debian Science task neuroscience-cognitive [ Yaroslav Halchenko ] * Fresh upstream snapshot * debian/patches - updated for new locations - up_char_cast (forwared upstream) to avoid FTBFS with -Werror=format-security - cmake_tests - ignore freshly introduced errors/failures to determine window position (irrelevant for this stage of testing) -- Yaroslav Halchenko Thu, 05 Dec 2013 16:48:01 -0500 afni (0.20130912~dfsg.1-3) neurodebian; urgency=low * debian/patches - cmake_sharedlibs - enable gifti support (-DGIFTI) and link libmri against it (Closes Nick#D902704B-139A-450D-91DC-A7AFBF78FC5A@gmail.com) -- Yaroslav Halchenko Tue, 19 Nov 2013 20:58:28 -0500 afni (0.20130912~dfsg.1-2) neurodebian; urgency=low * debian/rules - disable -D_FORTIFY_SOURCE=2 until upstream resolves code with undefined sprintf behavior (http://afni.nimh.nih.gov/afni/community/board/read.php?1,142574,142574#msg-142574) -- Yaroslav Halchenko Thu, 19 Sep 2013 22:42:55 -0400 afni (0.20130912~dfsg.1-1) neurodebian; urgency=low * Fresh upstream snapshot * debian/patches - deb_path_to_doexamples - removed (upstream now) - cmake_sharedlibs - add model_conv_cosine4 - debian_paths - refreshed - cmake_tests - SUMA should not spit our errors now, thus make do.examples test more stringent -- Yaroslav Halchenko Fri, 13 Sep 2013 10:04:55 -0400 afni (0.20130903~dfsg.1-1) neurodebian; urgency=low * Fresh upstream snapshot * debian/patches - cmake_tests - switch to have 'up to' specified # of "Error" and "Failed to " messages. Should "fix" build on i686 13.04 build where no SUMA error gets reported upon exit -- Yaroslav Halchenko Fri, 06 Sep 2013 08:29:02 -0400 afni (0.20130830~dfsg.1-3) neurodebian; urgency=low * debian/control - afni-atlases should be in Recommends not Depends * debian/patches - cmake_sharedlibs - MOTIF library (libXm) must be linked before other X libraries (Xt in particular). Therefore placing it first among TARGET_LINK_LIBRARIES and disabling --as-needed for this linkage while (re)enabling it right after -- Yaroslav Halchenko Wed, 04 Sep 2013 09:16:08 -0400 afni (0.20130830~dfsg.1-2) UNRELEASED; urgency=low * debian/patches: - cmake_sharedlibs - add SUMA_gts_insert.c to libSUMAGTS and link SurfMesh against it - absorb librickr into libmri -- upstream dropped separate librickr as of 0.20080129~dfsg.1. - absorb libafni_warp into libmri -- upstream does "the same" and if split -- there is a circular dependency between afni_warp and mri forbidding robust building/linking - link lib3DEdge against m, and segtools and tracktools against mri - make SEGTOOLS_LIBS list only segtools - enforce --no-as-needed ld flag while building segtools due to libgsl not linking against libgslcblas thus failing to build with --as-needed which is defauilt on Ubuntus - cmake_tests - disable 3dedge test requiring data (waiting on upstream) - xvfb-driver -- allow to specify # of errors expected, so we could already test @DO.examples which should have 1 error on exit * debian/rules: - remove explicit -Wl,--allow-shlib-undefined which was introduced awaiting for a fix to #624156 long RIP. - add -Wl,--no-undefined for exe and shared linker flags - do not ignore tests failures -- Yaroslav Halchenko Tue, 03 Sep 2013 13:12:23 -0400 afni (0.20130830~dfsg.1-1) neurodebian; urgency=low * Fresh upstream snapshot: some enhancements and even more holidays to celebrate * debian/patches: - cmake_sharedlibs: - include retroicor.c functionality into libmri.so to be shared by tools and plugins -- resolves "Failed to open plugin /usr/lib/afni/plugins/plug_retroicor.so" upon AFNI startup. - cmake_tests: - basic test to verify that AFNI starts without reporting any failure -- Yaroslav Halchenko Fri, 30 Aug 2013 18:04:14 -0400 afni (0.20130827~dfsg.1-1) UNRELEASED; urgency=low * New upstream snapshot: bulk of fixes and enhancements * debian/control - add tcsh, libjpeg-progs to build-depends -- needed for testing @DO.examples * debian/patches/cmake_tests - tests/xvfb-driver -- link faces as pics under a temporary test directory so that @DO.examples has it available when afni is not yet installed -- Yaroslav Halchenko Wed, 28 Aug 2013 11:24:14 -0400 afni (0.20130821~dfsg.1-1) neurodebian; urgency=low * Fresh upstream snapshot - bulk of changes for graph datasets support - @DO.example could now be used in automated mode without interaction with users (-auto_test) * debian/control - recommend afni-atlases * debian/rules - explicitly include hardening.make and adjust LDFLAGS and CFLAGS instead of relying on "magic" of DEB_BUILD_HARDENING which seems to not play with ccache nicely all the times. Also exclude -fPIE since conflicts with -fPIC when gcc < 4.8 * debian/patches - cmake_sharedlibs: - do not bother with -D*_STAND_ALONE -- not used by upstream since a while - fix building of inspec, quickspec, CreateIcosahedron, MapIcosahedron - drop binaries not provided by upstream: SUMA_FreeSurfer, SUMA_SureFit, SUMA_Ply_Read, SUMA_Map_SurfacetoSurface, ShowCmap -- their functionality is within the library and exposed by other binaries - add zcross.c functionality to lib3dedge - minor typos - cmake_tests: - initiated collecting rudimentary tests - deb_path_to_doexamples: - find .do examples on Debian installations among docs - exit with code 1 if those could not be found - debian_paths: - search for images in SUMA_LoadImageNIDOnel under reasonable for images locations instead of PATH. Fixed 'funstuff' paths in demo*.niml.do files. - specify path to READMEs to be under /usr/share/doc/afni-common -- Yaroslav Halchenko Thu, 22 Aug 2013 22:05:21 -0400 afni (0.20130815~dfsg.1-1) neurodebian; urgency=low * Fresh upstream snapshot * debian/rules -- AFNI_BUILD_WITH_LESSTIF2:BOOL=OFF to actually build against Open Motif as we thought we were doing since 2010 ;) -- Yaroslav Halchenko Sat, 17 Aug 2013 09:39:38 -0400 afni (0.20130813~dfsg.1-1) UNRELEASED; urgency=low * New upstream code, mostly compilation fixes -- Alex Waite Wed, 14 Aug 2013 10:46:43 +0200 afni (0.20130809~dfsg.1-1) UNRELEASED; urgency=low * New upstream code; updated CMake. Adds 3dUnifize, 3dNwarpCat, 3dLocalHistog, 3dNwarpAdjust, 3dNwarpFuncs, 3dTproject, @compute_gcor, 3dLME, @move.to.series.dirs, @toMNI_Awarp, @toMNI_Qwarpar, @simulate_motion HalloSuma, afni_system_check.py, auto_warp.py, 3dROIMaker, 3dMatch, 3dNetCorr, meicaX.py, optcom.py, optcom_surf.py, t2smap.py, tedanaX.py * Patches accepted upstream: up_secure_snprintf -- Alex Waite Mon, 12 Aug 2013 18:23:22 +0200 afni (0.20121123~dfsg.1-2) neurodebian; urgency=low * Add afni-dbg package to provide debug symbols * debian/patches: - up_3rd_no_RefreshHTML_AtEvent -- to not even mention RefreshHTML from the patched XmHTML - up_condition_dset_unload -- avoid dereferencing NULL - cmake_sharedlibs: - link against lib3DEdge after libSUMA, since otherwise binaries do not get linked against it on Ubuntu systems - no need to manually extend list of libraries for SUMA_Map_SurfacetoSurface since it is added to the PROGRAMS and they are all linked against SUMA_LIBS * debian/rules: - since we --allow-shlib-undefined (because of the plugins) added a primitive check for few SUMA commands that they link against SUMA and 3DEdge libraries -- Yaroslav Halchenko Tue, 04 Jun 2013 11:08:09 -0400 afni (0.20121123~dfsg.1-1) neurodebian; urgency=low [ Michael Hanke, Yaroslav Halchenko ] * New upstream code. Updated CMake build system: - 3dedge library is now GPL-ed, thus not stripped - New scripts: meica.py (requires nibabel and MDP, now Recommended) * Built with OpenMP support (libgomp1 dependency added) * New patches: up_pragma_var_definition, up_glut_init, up_meica_tedana_upstream_mdp_api, up_meica_fixes, up_secure_sprintf * Enabled hardening (where applicable) -- Yaroslav Halchenko Wed, 28 Nov 2012 14:59:31 -0500 afni (0.20120420~dfsg.1-1) UNRELEASED; urgency=low [ Alex Waite] * New upstream code; updated CMake. Adds 3dCountSpikes, 3dNwarpCalc, @Quiet_Talkers and @radial_correlate * Upstream: New R scripts: 1dRplot.R and 3dICC_REML.R * Upstream: New Python scripts: gen_group_command.py, gen_ss_review_scripts.py, make_pq_script.py, slow_surf_clustsim.py, uber_align_test.py, uber_proc.py, uber_skel.py, uber_subject.py and uber_ttest.py * Upstream: Major improvements to 3dSurfMask for mask creation and voxel distance computations. See examples under 3dSurfMask -help. * Upstream: You can have multiple instances of programs talk to eachother. * Upstream: Generic Atlas Support and new atlases. Cytoarchitectonic atlases from Zilles, Eickhoff updated to 1.8. Three new probabilistic atlases from the Desai group. * Upstream: New AFNI tips system has better formatting and includes images. * Upstream: afni_proc.py now processes surface data. * Fixed missing qhull dependency for 3dSkullStrip [ Michael Hanke ] * Added build-dependency on xmhtml1-dev for "new" tooltip system. [ Alex Waite ] * New upstream code. Updated CMake build system. * Upstream: New I/O library for R uses AFNI's c library. * Upstream: Web-based access atlases available. Able to query web atlases from whereami and open webpages. * Upstream new programs: dicom_hinfo, apsearch, quick.alpha.vals.py, 3dLSS, @AfniEnv, @Atlasize, 1dBport, SurfExtrema, 3dinfill, 3dNormalityTest, 3dTnorm * Upstream: Many bug fixes and overall code cleanup. * Now build and ship libSUMAGTS.so -- Alex Waite Wed, 25 Apr 2012 18:58:59 +0200 afni (0.20110610~dfsg.1-1) UNRELEASED; urgency=low [ Alex Waite ] * New upstream code. Updated CMake build system. [ Michael Hanke ] * Upstream introduced circular dependencies between the internal libraries, hence linking is now done with --allow-shlib-undefined. * Added get-orig-source target to debian/rules. -- Michael Hanke Wed, 22 Jun 2011 15:21:32 -0400 afni (0.20101222~dfsg.1-3) UNRELEASED; urgency=low * Added patch to let @FindAfniDsetPath also search AFNI_TTATLAS_DATASET -- a configuration setting that is supported by thd_ttatlas_query.c and used by the Debian setup. Thanks to Alex Waite for the bug report. -- Michael Hanke Mon, 17 Jan 2011 12:46:45 -0500 afni (0.20101222~dfsg.1-2) UNRELEASED; urgency=low * Install @RetinoProc which has been left-out accidentally. * Bugfix of @RetinoProc to work with Debian's 3dSkullStrip. * Install AFNI's Matlab library. * Added 'r-base' as a suggested dependency. * Added 'python' as a recommended dependency. -- Michael Hanke Wed, 05 Jan 2011 13:55:16 -0500 afni (0.20101222~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. Adds tools: niccc, 3dkmeans, 3dRankizer, 3dXYZcat. Adds scripts: @ElectroGrid, ExamineXmat, 1dRplot, @2dwarper.Allin, @help.AFNI. Adds plugin: plug_aslA3D3. * Updated CMake patch. * Merged some small portion of the shared libarary related patches with upstream. * Make afni_wrapper more robust. Thanks to Alex Waite for the patch. -- Michael Hanke Thu, 23 Dec 2010 11:34:20 -0500 afni (0.20101018~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. Added 3dDTtoDWI tool. * Switch build-dependency from lesstif2 to openmotif. Because openmotif is non-free AFNI is now a 'contrib' package. This move was necessary, because AFNI doesn't play nicely with lesstif (segfaults). Upstream doesn't want to support lesstif, because it is currently unmaintained. * Added build-dependency x11proto-print-dev to ease backporting to Debian lenny. -- Michael Hanke Tue, 19 Oct 2010 15:25:53 -0400 afni (0.20101001~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. * Update CMake patch to install new 1dSVAR.R. * Load AFNI atlases in addition to the AFNI_GLOBAL_SESSION. -- Michael Hanke Sun, 03 Oct 2010 10:51:03 -0400 afni (0.20100928~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. * Update CMake patch to install lib_textdata.py that was missing before. * Added netpbm as a recommended package. * Added patch to set Debian-specific locations for faces, poems and atlases. -- Michael Hanke Wed, 29 Sep 2010 15:26:27 -0400 afni (0.20100917~dfsg.1-1) UNRELEASED; urgency=low * New upstream code, and updated CMAKE setup. * Switched to source package format 3.0 (quilt) and from CDBS to debhelper's "dh". -- Michael Hanke Tue, 21 Sep 2010 11:51:13 -0400 afni (0.20100114~dfsg.1-1) UNRELEASED; urgency=low * New upstream code, and updated CMAKE setup. * Updated copyright file -- still incomplete. -- Michael Hanke Sun, 17 Jan 2010 13:27:49 -0500 afni (0.20091204~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. * Major bugfix caused by multiple, but different, versions of f2c.h -- causing int to be int32 or int64 for different parts of AFNI, at the same time. -- Michael Hanke Mon, 07 Dec 2009 20:47:56 -0500 afni (0.20091028~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. * Add patch to allow AFNI to use ffmpeg instead of the stripped mpeg_encode. -- Michael Hanke Thu, 29 Oct 2009 14:29:18 -0400 afni (0.20091023~dfsg.1-1) UNRELEASED; urgency=low * New upstream code. * New CMake buildsystem based on an initial patch by Bernd Feige. * New afni-dev package with static libraries and header files for AFNI plugin development. * Add wrapper to start AFNI's without GUI without having to manually source the config file. * Add afni.desktop and afni.menu for desktop integration. -- Michael Hanke Tue, 27 Oct 2009 09:42:40 -0400 afni (0.20091009~dfsg.1-1) UNRELEASED; urgency=low * Initial packaging working toward closing ITP #409849. -- Michael Hanke Sun, 18 Oct 2009 20:43:08 -0400