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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

Greedy registration in ANTsR ? #125

Closed dorianps closed 7 years ago

dorianps commented 7 years ago

Hi all, Now that Paul's greedy registration is available, is there any plan to wrap it in ANTsR? It's supposed to be much faster than SyNCC with minimal loss in accuracy. I am looking forward to use it in a lesion segmentaiton tool I have created in ANTsR.

Maybe @jeffduda knows if this is feasible? The greedy tool is located in the cluster in /data/picsl/pauly/bin.

Dorian

stnava commented 7 years ago

interesting - but unlikely that we will introduce another separate but parallel registration framework to antsr.

ultimately, itk multithreading will improve anyway.

if you want a fast and non-symmetric method then there are plenty of options in ants/antsr already.

brian

On Thu, Dec 22, 2016 at 10:41 AM, dorianps notifications@github.com wrote:

Hi all, Now that Paul's greedy registration https://sites.google.com/view/greedyreg is available, is there any plan to wrap it in ANTsR? It's supposed to be much faster than SyNCC with minimal loss in accuracy. I am looking forward to use it in a lesion segmentaiton tool https://github.com/dorianps/LINDA I have created in ANTsR.

Maybe @jeffduda https://github.com/jeffduda knows if this is feasible? The greedy tool is located in the cluster in /data/picsl/pauly/bin.

Dorian

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jeffduda commented 7 years ago

I'll take a look, but I would assume it's feasible. Possibly a better approach would be a separate package that just has ANTsR as a dependency

-jeff

On Thu, Dec 22, 2016 at 10:41 AM dorianps notifications@github.com wrote:

Hi all, Now that Paul's greedy registration https://sites.google.com/view/greedyreg is available, is there any plan to wrap it in ANTsR? It's supposed to be much faster than SyNCC with minimal loss in accuracy. I am looking forward to use it in a lesion segmentaiton tool https://github.com/dorianps/LINDA I have created in ANTsR.

Maybe @jeffduda https://github.com/jeffduda knows if this is feasible? The greedy tool is located in the cluster in /data/picsl/pauly/bin.

Dorian

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stnava/ANTsR/issues/125, or mute the thread https://github.com/notifications/unsubscribe-auth/AAfWiIjxXjKXlLGMoAGRAmZC7eMiIK7Oks5rKpongaJpZM4LUGPD .

stnava commented 7 years ago

i think @jeffduda has the right idea

with the advent of neuroconductor (soon), this will be easier.

here is one example of such a package: https://github.com/stnava/ANTsRNpy

which is much more lightweight ...

brian

On Thu, Dec 22, 2016 at 1:08 PM, Jeffrey Duda notifications@github.com wrote:

I'll take a look, but I would assume it's feasible. Possibly a better approach would be a separate package that just has ANTsR as a dependency

-jeff

On Thu, Dec 22, 2016 at 10:41 AM dorianps notifications@github.com wrote:

Hi all, Now that Paul's greedy registration https://sites.google.com/view/greedyreg is available, is there any plan to wrap it in ANTsR? It's supposed to be much faster than SyNCC with minimal loss in accuracy. I am looking forward to use it in a lesion segmentaiton tool https://github.com/dorianps/LINDA I have created in ANTsR.

Maybe @jeffduda https://github.com/jeffduda knows if this is feasible? The greedy tool is located in the cluster in /data/picsl/pauly/bin.

Dorian

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stnava/ANTsR/issues/125, or mute the thread https://github.com/notifications/unsubscribe-auth/ AAfWiIjxXjKXlLGMoAGRAmZC7eMiIK7Oks5rKpongaJpZM4LUGPD .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stnava/ANTsR/issues/125#issuecomment-268856851, or mute the thread https://github.com/notifications/unsubscribe-auth/AATyfvNpKPEM3OPB0CuuOFazy-rtFoA8ks5rKryEgaJpZM4LUGPD .

dorianps commented 7 years ago

I think having access to greedy in R is interesting. But an integration in ANTsR can allow options for speeding up existing tools, such asjointLabelFusion3D.R. Anyway, this was just an idea.

ntustison commented 7 years ago

If you’re looking to speed up joint fusion, a major bottleneck is the actual R code which should be replaced by calling the .cxx version.

stnava commented 7 years ago

yes - @ntustison is correct. the R code was an initial version that should be swapped out for the c++ version which is probably 10-100x faster.

stnava commented 7 years ago

this commit https://github.com/stnava/ANTsR/commit/a79151f2b071f6ed2c7f6b4324d8694e58c72535 implements the R wrapping of the C++ joint label fusion program. it does not (yet) support the full functionality but may do so in the future, if there is demand. e.g. it does not support multiple modalities though it could be extended fairly trivially to do so.

ntustison commented 7 years ago

Hey Dorian,

Quick question---have you done any sort of evaluation with Paul's registration algorithm? I've been doing some work in parallel with Mike Yassa and keeping Paul informed and so I know a little about Paul's goals regarding this work. In fact, I'm visiting Penn in March for completely unrelated lung conference and we plan to discuss.

For JLF, specifically, It makes complete sense to dump the whole diffeomorphic constraint for the registration since the voxelwise neighborhood search is potentially going to break that correspondence anyway. I wonder, though, how comparable timing and performance would be using antsRegistration tools with simply a change in options. Have you or anybody else done any of this type of exploration?

stnava commented 7 years ago

i would also like to know the answer to this question.

the gaussiandisplacementfield transform would probably be quite fast and achieve similar results wrt JLF

brian

On Tue, Dec 27, 2016 at 3:25 PM, Nick Tustison notifications@github.com wrote:

Hey Dorian,

Quick question---have you done any sort of evaluation with Paul's registration algorithm? I've been doing some work https://github.com/stnava/ANTsR/blob/master/R/segmentationRefinement.R in parallel with Mike Yassa and keeping Paul informed and so I know a little about Paul's goals regarding this work. In fact, I'm visiting Penn in March for completely unrelated lung conference and we plan to discuss.

For JLF, specifically, It makes complete sense to dump the whole diffeomorphic constraint for the registration since the voxelwise neighborhood search is potentially going to break that correspondence anyway. I wonder, though, how comparable timing and performance would be using antsRegistration tools with simply a change in options. Have you or anybody else done any of this type of exploration?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stnava/ANTsR/issues/125#issuecomment-269378061, or mute the thread https://github.com/notifications/unsubscribe-auth/AATyfg7ZpYC3Yuf36WtJBP5T_uP6Q4NMks5rMXQcgaJpZM4LUGPD .

dorianps commented 7 years ago

Nope, I haven't tried it myself, and I am not knowledgeable on alternative algorithms. Paul mentioned the results are decent from his comparisons. Maybe he can answer better this question (@pyushkevich).

From what I know, Sandy has tried the new ASHS that uses 'greedy' and processing time is down to under an hour from several hours required previously.

jeffduda commented 7 years ago

@dorianps , I messed around with greedy today and managed to get a proof-of-concept R package together. Lots of "hacky" components at the moment, but definitely illustrates that an ANTsR compatible version is possible and is as straight forward as possible to implement since @pyushkevich seems to have coded things with this type of thing in mind. It's not in a useful state, but can be tested via:

install_github("jeffduda/greedyr") library(greedyr) fixed = mergeChannels(list(ANTsR::antsImageRead( ANTsR::getANTsRData( "r16" ) ))) moving = mergeChannels(list(ANTsR::antsImageRead( ANTsR::getANTsRData( "r30" ) ))) flag = greedyregistration(fixed, moving)

mergeChannels() is needed as the GreedyAPI expects itk::VectorImage inputs, luckily we already have those implemented.

A variety of output will scroll past, and the transform will be written to "greedy.mat" (Wasn't joking when I said it's not useful yet). I'm not entirely familiar with the parameters yet, so I just plugged in values similar to what is used in the example on the webpage.

dorianps commented 7 years ago

Thanks Jeff.

I am getting this error in the cluster:

> library(devtools)
> install_github("jeffduda/greedyr")
Downloading GitHub repo jeffduda/greedyr@master
from URL https://api.github.com/repos/jeffduda/greedyr/zipball/master
Installing greedyr
Error in if (capabilities("libcurl")) { : argument is of length zero
> capabilities("libcurl")
named logical(0)
dorianps commented 7 years ago

Tried in my Windows Ubuntu and started working after installing libcurl, but ended up failing for other reasons:


> library(devtools)
> install_github("jeffduda/greedyr")
Downloading GitHub repo jeffduda/greedyr@master
from URL https://api.github.com/repos/jeffduda/greedyr/zipball/master
Installing greedyr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769'  \
  --library='/home/dp/R/x86_64-pc-linux-gnu-library/3.3'  \
  --install-tests 

* installing *source* package ‘greedyr’ ...
linux-gnu 0
Cloning into 'greedy'...
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Already up-to-date.
Note: checking out '2887f29d261396a58913620799b6a0c61e9f1ba9'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 2887f29... Initiated package cmake script and added parameter/API support for moving mask. But moving mask not yet implemented
-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_ALL_ANTS_APPS
    BUILD_TESTING
    COPY_SCRIPT_FILES_TO_BIN_DIR
    USE_SYSTEM_ITK

-- Build files have been written to: /tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild
** libs
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I`/usr/lib/R/bin/Rscript -e 'ITKR:::itkIncludes()'` -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedy/src/ -I/Users/jtduda/pkg/ANTsR/src   -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsR/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppANTsR.cpp -o RcppANTsR.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I`/usr/lib/R/bin/Rscript -e 'ITKR:::itkIncludes()'` -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedy/src/ -I/Users/jtduda/pkg/ANTsR/src   -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsR/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c greedyregistration.cpp -o greedyregistration.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I`/usr/lib/R/bin/Rscript -e 'ITKR:::itkIncludes()'` -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src -I/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedy/src/ -I/Users/jtduda/pkg/ANTsR/src   -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsR/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c makeImage2.cpp -o makeImage2.o
cd /tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild && make -j 2
make[1]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[2]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
Scanning dependencies of target test_accum
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[ 16%] Building CXX object CMakeFiles/test_accum.dir/testing/src/TestOneDimensionalInPlaceAccumulateFilter.cxx.o
Scanning dependencies of target greedyapi
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[ 33%] Building CXX object CMakeFiles/greedyapi.dir/src/lddmm_data.cxx.o
Linking CXX executable test_accum
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[ 33%] Built target test_accum
[ 50%] Building CXX object CMakeFiles/greedyapi.dir/src/GreedyAPI.cxx.o
[ 66%] Building CXX object CMakeFiles/greedyapi.dir/src/GreedyParameters.cxx.o
Linking CXX static library libgreedyapi.a
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[ 66%] Built target greedyapi
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
Scanning dependencies of target lddmm
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
Scanning dependencies of target greedy
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[ 83%] make[3]: Entering directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[100%] Building CXX object CMakeFiles/lddmm.dir/src/lddmm_main.cxx.o
Building CXX object CMakeFiles/greedy.dir/src/greedy_main.cxx.o
Linking CXX executable greedy
Linking CXX executable lddmm
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[100%] Built target greedy
make[3]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
[100%] Built target lddmm
make[2]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
make[1]: Leaving directory `/tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild'
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/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOMeta-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIONIFTI-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIONRRD-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOPNG-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOSiemens-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOSpatialObjects-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOStimulate-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOTIFF-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOTransformBase-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOTransformHDF5-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOTransformInsightLegacy-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKIOTransformMatlab-4.11.a 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/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKReview-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKSpatialObjects-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKStatistics-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKTransform-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKVNLInstantiation-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKVTK-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKWatersheds-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKgiftiio-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKniftiio-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libITKznz-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkMGHIO-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkNetlibSlatec-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkdouble-conversion-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmCommon-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmDICT-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmDSED-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmIOD-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmMEXD-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmMSFF-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmcharls-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmjpeg12-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmjpeg16-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmjpeg8-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmopenjpeg-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmsocketxx-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkgdcmuuid-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkhdf5.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkhdf5_cpp.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkjpeg-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitknetlib-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkopenjpeg-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkpng-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitksys-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitktestlib-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitktiff-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkv3p_netlib-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkvcl-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkvnl-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkvnl_algo-4.11.a /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs/lib/libitkzlib-4.11.a /tmp/RtmpAlkHMG/devtools15303657240b/jeffduda-greedyr-e62f769/src/greedybuild/libgreedyapi.a -L/usr/lib/R/lib -lR
installing to /home/dp/R/x86_64-pc-linux-gnu-library/3.3/greedyr/libs
** R
** preparing package for lazy loading
** help
No man pages found in package  ‘greedyr’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/dp/R/x86_64-pc-linux-gnu-library/3.3/greedyr/libs/greedyr.so':
  /home/dp/R/x86_64-pc-linux-gnu-library/3.3/greedyr/libs/greedyr.so: undefined symbol: _ZTIN3itk20TriangleCellTopologyE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3/greedyr’
Error: Command failed (1)
jeffduda commented 7 years ago

@dorianps I got rid of some stray uses of "typename" that were causing problems and used the ANTsR trick of passing the library many times to the linker. Just compiled and ran the example on the cluster with no problems.