[Neurodebian-devel] ANTS

Tue Mar 11 19:28:52 UTC 2014

Hi Gert,

Any obvious clue why lintian complaints
http://lintian.debian.org/tags/shlib-with-non-pic-code.html#ants
while I see only that we did build with -fPIC and -shared:

~/deb/builds/ants/2.0.0-1$ grep libl_ANTS.so.2.0.0 ants_2.0.0-1_amd64.build | grep --color shared
/usr/bin/c++  -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -fPIC  -Wno-array-bounds  -Wno-deprecated  -Wl,-z,relro -Wl,--as-needed   -shared -Wl,-soname,libl_ANTS.so.2 -o ../lib/libl_ANTS.so.2.0.0 CMakeFiles/l_ANTS.dir/ANTS.cxx.o CMakeFiles/l_ANTS.dir/__/Utilities/antsCommandLineParser.cxx.o CMakeFiles/l_ANTS.dir/__/Utilities/antsCommandLineOption.cxx.o ../lib/libantsUtilities.a /usr/lib/libitkdouble-conversion-4.5.so.1 /usr/lib/libitksys-4.5.so.1 /usr/lib/libitkvnl_algo-4.5.so.1 /usr/lib/libitkvnl-4.5.so.1 /usr/lib/libitkv3p_netlib-4.5.so.1 /usr/lib/libITKCommon-4.5.so.1 /usr/lib/libitkNetlibSlatec-4.5.so.1 /usr/lib/libITKStatistics-4.5.so.1 /usr/lib/libITKIOImageBase-4.5.so.1 /usr/lib/libITKIOBMP-4.5.so.1 /usr/lib/libITKIOBioRad-4.5.so.1 /usr/lib/libITKGDCM-4.5.so.1 /usr/lib/libITKIOGDCM-4.5.so.1 -lz /usr/lib/libITKIOGIPL-4.5.so.1 -ljpeg /usr/lib/libITKIOJPEG-4.5.so.1 -ltiff /usr/lib/libITKIOTIFF-4.5.so.1 /usr/lib/libITKIOLSM-4.5.so.1 /usr/lib/libITKMetaIO-4.5.so.1 /usr/lib/libITKIOMeta-4.5.so.1 /usr/lib/libITKznz-4.5.so.1 /usr/lib/libITKniftiio-4.5.so.1 /usr/lib/libITKIONIFTI-4.5.so.1 /usr/lib/libITKNrrdIO-4.5.so.1 /usr/lib/libITKIONRRD-4.5.so.1 -lpng /usr/lib/libITKIOPNG-4.5.so.1 /usr/lib/libITKIOStimulate-4.5.so.1 /usr/lib/libITKIOVTK-4.5.so.1 /usr/lib/libITKMesh-4.5.so.1 /usr/lib/libITKSpatialObjects-4.5.so.1 /usr/lib/libITKPath-4.5.so.1 /usr/lib/libITKLabelMap-4.5.so.1 /usr/lib/libITKQuadEdgeMesh-4.5.so.1 /usr/lib/libITKOptimizers-4.5.so.1 /usr/lib/libITKPolynomials-4.5.so.1 /usr/lib/libITKBiasCorrection-4.5.so.1 /usr/lib/libITKBioCell-4.5.so.1 -ldcmpstat -ldcmtls -ldcmqrdb -ldcmnet -ldcmjpeg -ldcmimage -ldcmimgle -ldcmdata -loflog -lofstd -lijg12 -lijg16 -lijg8 -lpthread /usr/lib/libITKDICOMParser-4.5.so.1 /usr/lib/libITKEXPAT-4.5.so.1 /usr/lib/libITKIOXML-4.5.so.1 /usr/lib/libITKIOSpatialObjects-4.5.so.1 /usr/lib/libITKFEM-4.5.so.1 /usr/lib/libITKgiftiio-4.5.so.1 /usr/lib/libITKIOMesh-4.5.so.1 /usr/lib/libitkhdf5_cpp-4.5.so.1 /usr/lib/libitkhdf5-4.5.so.1 /usr/lib/libITKIOCSV-4.5.so.1 /usr/lib/libITKIOIPL-4.5.so.1 /usr/lib/libITKIOGE-4.5.so.1 /usr/lib/libITKIOSiemens-4.5.so.1 /usr/lib/libITKIOHDF5-4.5.so.1 /usr/lib/libITKIOMRC-4.5.so.1 /usr/lib/libITKIOTransformBase-4.5.so.1 /usr/lib/libITKIOTransformHDF5-4.5.so.1 /usr/lib/libITKIOTransformInsightLegacy-4.5.so.1 /usr/lib/libITKIOTransformMatlab-4.5.so.1 /usr/lib/libITKKLMRegionGrowing-4.5.so.1 /usr/lib/libITKVTK-4.5.so.1 /usr/lib/libITKWatersheds-4.5.so.1 /usr/lib/libitkopenjpeg-4.5.so.1 /usr/lib/libITKReview-4.5.so.1 /usr/lib/libITKVideoCore-4.5.so.1 /usr/lib/libITKVideoIO-4.5.so.1 /usr/lib/libITKgiftiio-4.5.so.1 /usr/lib/libITKIOBMP-4.5.so.1 /usr/lib/libITKIOBioRad-4.5.so.1 /usr/lib/libITKIOGDCM-4.5.so.1 /usr/lib/libITKGDCM-4.5.so.1 -lgdcmDICT -lgdcmMSFF /usr/lib/libITKIOGIPL-4.5.so.1 /usr/lib/libITKIOJPEG-4.5.so.1 -ljpeg /usr/lib/libITKIOTIFF-4.5.so.1 -ltiff /usr/lib/libITKIOMeta-4.5.so.1 /usr/lib/libITKIONIFTI-4.5.so.1 /usr/lib/libITKniftiio-4.5.so.1 /usr/lib/libITKznz-4.5.so.1 /usr/lib/libITKIONRRD-4.5.so.1 /usr/lib/libITKNrrdIO-4.5.so.1 /usr/lib/libITKIOPNG-4.5.so.1 -lpng /usr/lib/libITKIOStimulate-4.5.so.1 /usr/lib/libITKIOVTK-4.5.so.1 /usr/lib/libITKLabelMap-4.5.so.1 /usr/lib/libITKQuadEdgeMesh-4.5.so.1 /usr/lib/libITKBiasCorrection-4.5.so.1 /usr/lib/libITKPolynomials-4.5.so.1 /usr/lib/libITKBioCell-4.5.so.1 /usr/lib/libITKIOSpatialObjects-4.5.so.1 /usr/lib/libITKIOXML-4.5.so.1 /usr/lib/libITKEXPAT-4.5.so.1 /usr/lib/libITKFEM-4.5.so.1 /usr/lib/libITKMetaIO-4.5.so.1 /usr/lib/libITKOptimizers-4.5.so.1 /usr/lib/libITKIOSiemens-4.5.so.1 /usr/lib/libITKIOGE-4.5.so.1 /usr/lib/libITKIOIPL-4.5.so.1 /usr/lib/libITKIOTransformHDF5-4.5.so.1 /usr/lib/libitkhdf5_cpp-4.5.so.1 /usr/lib/libitkhdf5-4.5.so.1 -lz /usr/lib/libITKIOTransformInsightLegacy-4.5.so.1 /usr/lib/libITKIOTransformMatlab-4.5.so.1 /usr/lib/libITKIOTransformBase-4.5.so.1 /usr/lib/libITKKLMRegionGrowing-4.5.so.1 /usr/lib/libITKVTK-4.5.so.1 /usr/lib/libITKWatersheds-4.5.so.1 /usr/lib/libITKSpatialObjects-4.5.so.1 /usr/lib/libITKMesh-4.5.so.1 /usr/lib/libITKPath-4.5.so.1 /usr/lib/libITKStatistics-4.5.so.1 /usr/lib/libitkNetlibSlatec-4.5.so.1 /usr/lib/libitkopenjpeg-4.5.so.1 /usr/lib/libITKIOImageBase-4.5.so.1 /usr/lib/libITKVideoCore-4.5.so.1 /usr/lib/libITKCommon-4.5.so.1 /usr/lib/libitkdouble-conversion-4.5.so.1 /usr/lib/libitksys-4.5.so.1 -lpthread -ldl /usr/lib/libITKVNLInstantiation-4.5.so.1 /usr/lib/libitkvnl_algo-4.5.so.1 /usr/lib/libitkv3p_lsqr-4.5.so.1 /usr/lib/libitkvnl-4.5.so.1 /usr/lib/libitkvcl-4.5.so.1 /usr/lib/libitkv3p_netlib-4.5.so.1 -lm -lm 

also -- now we got all the libraries under /usr/lib (while before went under
/usr/lib/ants) -- any good reason for polluting public space? ;)

On Wed, 26 Feb 2014, Gert Wollny wrote:

> Hi Yaroslav,

> >> * is the -fpermissive really needed? Or is this a leftover from 1.9?

> >was originally added in

> >commit 1d6102bbb822b917a891faad58353e8c6911cdb1
> >Author: Yaroslav Halchenko <debian at onerussian.com>
> >Date:   Fri May 4 10:31:17 2012 -0400
> >     BF: patch from Matthias Klosse for gcc 4.7 (Closes: #667099)

> >not sure if still needed.  build would show ;)
> Okay, I will test this.

> >if we could address them -- cool.  if not -- I do not care and consider
> >illformatted manpage better than none quite often.
> I guess I will leave it for now.

> >indeed itk4 is currently available only for x86, but it might come to other
> >archs eventually.  better to get ready IMHO ;)
> Okay.  BTW, I've seen that ITK is at version 4.2 in NeuroDebian,
> afaik ANTS will need 4.4 at least. Well, since we need  ANTS and ITK
> 4.5 on wheezy I will run builds over the weekend to see how this
> goes.

> >>* As for the data, can we just add it in the debian/ directory?
> >>Since there are binary files, this may violate Debian policy, but
> >>then again it's data. There seems to be an option to set the test
> >>data root to avoid downloading.

> >could go anywhere but I do not see benefits for under debian/ instead of some
> >directory overlayed over upstream code.  It is upstream data after all, and as
> >a data collection might even be copyrightable.

> Well, I always thought everything that is not in the original
> tarball has to be provided as patches or in some other way through
> debian/. That's the only reason I choose this approach.

> If you can give me a pointer how to add properly overlay over
> upstream code that doesn't require a patch in debian/ I'll happily
> add the data differently. It seems I figured out how I can point the
> test data download url to where ever I want it :)

> I will ask about the copyright of the data.

> Best
> Gert

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-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        