ANTsRCore installation issue: "ITK_DIR variable is defined but corresponds to non-existing directory ([1])"

What might be the solution to this?
R CMD INSTALL ANTsRCore
* installing to library ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘ANTsRCore’ ...
linux-gnu 0
Cloning into 'ants'...
remote: Counting objects: 20425, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 20425 (delta 3), reused 8 (delta 3), pack-reused 20417
Receiving objects: 100% (20425/20425), 18.81 MiB | 3.53 MiB/s, done.
Resolving deltas: 100% (14030/14030), done.
Checking connectivity... done.
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Already up-to-date.
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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 6bc3e65... Merge pull request #459 from muschellij2/master
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /usr/bin/git (found version "2.7.4")
-- SuperBuild - ANTS => Requires ITKv4,
CMake Error at SuperBuild/External_ITKv4.cmake:31 (message):
  ITK_DIR variable is defined but corresponds to non-existing directory ([1])
Call Stack (most recent call first):
  CMake/SlicerMacroCheckExternalProjectDependency.cmake:69 (include)
  SuperBuild.cmake:205 (SlicerMacroCheckExternalProjectDependency)
  CMakeLists.txt:60 (include)

-- Configuring incomplete, errors occurred!
See also "/mnt/c/Users/dp/ANTsRCore/src/antb/CMakeFiles/CMakeOutput.log".
See also "/mnt/c/Users/dp/ANTsRCore/src/antb/CMakeFiles/CMakeError.log".
** libs
Makevars:3: *** missing separator.  Stop.
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsRCore’

Install ITKR?
John
On Wed, Jul 19, 2017 at 7:36 PM, dorianps<EMAIL_ADDRESS>wrote:

What might be the solution to this?
R CMD INSTALL ANTsRCore

installing to library ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3’
installing source package ‘ANTsRCore’ ...
linux-gnu 0
Cloning into 'ants'...
remote: Counting objects: 20425, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 20425 (delta 3), reused 8 (delta 3), pack-reused 20417
Receiving objects: 100% (20425/20425), 18.81 MiB | 3.53 MiB/s, done.
Resolving deltas: 100% (14030/14030), done.
Checking connectivity... done.
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Already up-to-date.
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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
HEAD is now at 6bc3e65... Merge pull request #459 from muschellij2/master
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /usr/bin/git (found version "2.7.4")
-- SuperBuild - ANTS => Requires ITKv4,
CMake Error at SuperBuild/External_ITKv4.cmake:31 (message):
ITK_DIR variable is defined but corresponds to non-existing directory ([1])
Call Stack (most recent call first):
CMake/SlicerMacroCheckExternalProjectDependency.cmake:69 (include)
SuperBuild.cmake:205 (SlicerMacroCheckExternalProjectDependency)
CMakeLists.txt:60 (include)
-- Configuring incomplete, errors occurred!
See also "/mnt/c/Users/dp/ANTsRCore/src/antb/CMakeFiles/CMakeOutput.log".
See also "/mnt/c/Users/dp/ANTsRCore/src/antb/CMakeFiles/CMakeError.log".
** libs
Makevars:3: *** missing separator.  Stop.
ERROR: compilation failed for package ‘ANTsRCore’

removing ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsRCore’

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/stnava/ANTsR/issues/176, or mute the thread
https://github.com/notifications/unsubscribe-auth/ABBnrti3jDG89fd_ik6Sb_u78_jI_kagks5sPpMHgaJpZM4Odbee
.

I had done it, but maybe something didn't go well. I installed everything with devtools, and now I can also install ANTsRCore with the same R CMD INSTALL ANTsRCore command.
Closing, will open if the problem re-presents.

I replicated the problem in another machine (also virtual Ubuntu in Windows 10). ITKR installed properly with R CMD INSTALL and I could load it in R. ANTsRCore could not be installed because of the ITK_DIR variable defined but corresponding to a non-existing directory (same logs as above, with R v3.4).
On our computing cluster, instead, the error is different, and persists both with R CMD and with devtools install. Here are the two tries:
ANTsRCore failure logs.txt

Here is the logs from a third Ubuntu machine (clipped to the end of ITKR installation):
installing to /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ITKR)
dp@DP-PC:/mnt/c/Users/DP$
dp@DP-PC:/mnt/c/Users/DP$ R CMD INSTALL ANTsRCore
* installing to library ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘ANTsRCore’ ...
linux-gnu 0
M       Examples/include/ants.h
Switched to branch 'master'
Your branch is up-to-date with 'origin/master'.
remote: Counting objects: 247, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 247 (delta 175), reused 180 (delta 175), pack-reused 67
Receiving objects: 100% (247/247), 88.04 KiB | 0 bytes/s, done.
Resolving deltas: 100% (176/176), completed with 40 local objects.
From https://github.com/stnava/ANTs
   961ac54..f02e878  master     -> origin/master
 * [new branch]      rigidTemplate -> origin/rigidTemplate
 * [new tag]         v2.2.0     -> v2.2.0
Updating 961ac54..f02e878
Fast-forward
 ANTS.cmake                                                       |   14 +-
 CMakeLists.txt                                                   |    6 +-
 Examples/CMakeLists.txt                                          |    2 +-
 Examples/ImageMath.cxx                                           |    3 -
 Examples/ImageMath_Templates.hxx                                 |  151 ++-
 Examples/LabelGeometryMeasures.cxx                               |    2 +-
 Examples/MeasureImageSimilarity.cxx                              |  850 +++++++++++------
 Examples/NonLocalSuperResolution.cxx                             |   80 +-
 Examples/SmoothDisplacementField.cxx                             |   14 +-
 Examples/TestSuite/ANTS_CC_1_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_CC_2_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_CC_3_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_ELASTIC_test.cmake                       |   34 +-
 Examples/TestSuite/ANTS_EXP_test.cmake                           |   62 +-
 Examples/TestSuite/ANTS_GSYN_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_MI_1_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_MI_2_test.cmake                          |   62 +-
 Examples/TestSuite/ANTS_MSQ_test.cmake                           |   62 +-
 Examples/TestSuite/ANTS_PSE_MSQ_IMG_test.cmake                   |   62 +-
 Examples/TestSuite/ANTS_ROT_EXP_test.cmake                       |   36 +-
 Examples/TestSuite/ANTS_ROT_GSYN_test.cmake                      |   20 +-
 Examples/TestSuite/ANTS_SYN_WITH_TIME_test.cmake                 |   10 +-
 Examples/TestSuite/ANTS_SYN_test.cmake                           |   62 +-
 Examples/TestSuite/CMakeLists.txt                                |  202 ++--
 Examples/antsApplyTransforms.cxx                                 |   54 +-
 ...placementAndVelocityFieldRegistrationCommandIterationUpdate.h |    6 +-
 Examples/antsRegistration.cxx                                    |    6 +-
 ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx         |    9 +-
 README.md                                                        |    8 +
 Scripts/antsASLProcessing.R                                      |   16 +-
 Scripts/antsBrainExtraction.sh                                   |  138 +--
 Scripts/antsCookTemplatePriors.sh                                |  631 ++++++++++++
 Scripts/antsJointLabelFusion.sh                                  |  119 ++-
 Scripts/antsLongitudinalCorticalThickness.sh                     |   65 +-
 Scripts/antsLongitudinalJointLabelFusion.sh                      | 1380 +++++++++++++++++++++++++++
 Scripts/antsMultivariateTemplateConstruction2.sh                 |   33 +-
 Scripts/antsNeuroimagingBattery                                  |  142 ++-
 Scripts/antsRegistrationSpaceTime.sh                             |    2 +-
 Scripts/antsRegistrationSyN.sh                                   |  154 +--
 Scripts/antsRegistrationSyNQuick.sh                              |  154 +--
 Scripts/cbf_pcasl_robust_batch.R                                 |    2 +-
 SuperBuild/External_ITKv4.cmake                                  |    7 +-
 Utilities/antsSCCANObject.h                                      |  102 +-
 Utilities/antsSCCANObject.hxx                                    |    1 +
 Utilities/itkAdaptiveNonLocalMeansDenoisingImageFilter.h         |    1 +
 Utilities/itkAdaptiveNonLocalMeansDenoisingImageFilter.hxx       |   30 +-
 Utilities/itkNonLocalSuperresolutionImageFilter.h                |   27 +-
 Utilities/itkNonLocalSuperresolutionImageFilter.hxx              |   91 +-
 Version.cmake                                                    |    2 +-
 49 files changed, 3947 insertions(+), 1277 deletions(-)
 create mode 100644 Scripts/antsCookTemplatePriors.sh
 create mode 100755 Scripts/antsLongitudinalJointLabelFusion.sh
M       Examples/include/ants.h
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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 6bc3e65... Merge pull request #459 from muschellij2/master
mkdir: cannot create directory ‘antb’: File exists
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- SuperBuild - ANTS => Requires ITKv4,
CMake Error at SuperBuild/External_ITKv4.cmake:31 (message):
  ITK_DIR variable is defined but corresponds to non-existing directory ([1])
Call Stack (most recent call first):
  CMake/SlicerMacroCheckExternalProjectDependency.cmake:69 (include)
  SuperBuild.cmake:205 (SlicerMacroCheckExternalProjectDependency)
  CMakeLists.txt:60 (include)

-- Configuring incomplete, errors occurred!
See also "/mnt/c/Users/DP/ANTsRCore/src/antb/CMakeFiles/CMakeOutput.log".
See also "/mnt/c/Users/DP/ANTsRCore/src/antb/CMakeFiles/CMakeError.log".
** libs
Makevars:3: *** missing separator.  Stop.
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsRCore’

Have you tried installing from GitHub versions?
John
On Thu, Jul 20, 2017 at 10:13 AM, dorianps<EMAIL_ADDRESS>wrote:

Here is the logs from a third Ubuntu machine (clipped to the end of ITKR
installation):
installing to /home/dp/R/x86_64-pc-linux-gnu-library/3.3/ITKR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

DONE (ITKR)
dp@DP-PC:/mnt/c/Users/DP$
dp@DP-PC:/mnt/c/Users/DP$ R CMD INSTALL ANTsRCore
installing to library ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3’
installing source package ‘ANTsRCore’ ...
linux-gnu 0
M       Examples/include/ants.h
Switched to branch 'master'
Your branch is up-to-date with 'origin/master'.
remote: Counting objects: 247, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 247 (delta 175), reused 180 (delta 175), pack-reused 67
Receiving objects: 100% (247/247), 88.04 KiB | 0 bytes/s, done.
Resolving deltas: 100% (176/176), completed with 40 local objects.
From https://github.com/stnava/ANTs
961ac54..f02e878  master     -> origin/master
[new branch]      rigidTemplate -> origin/rigidTemplate
[new tag]         v2.2.0     -> v2.2.0
Updating 961ac54..f02e878
Fast-forward
ANTS.cmake                                                       |   14 +-
CMakeLists.txt                                                   |    6 +-
Examples/CMakeLists.txt                                          |    2 +-
Examples/ImageMath.cxx                                           |    3 -
Examples/ImageMath_Templates.hxx                                 |  151 ++-
Examples/LabelGeometryMeasures.cxx                               |    2 +-
Examples/MeasureImageSimilarity.cxx                              |  850 +++++++++++------
Examples/NonLocalSuperResolution.cxx                             |   80 +-
Examples/SmoothDisplacementField.cxx                             |   14 +-
Examples/TestSuite/ANTS_CC_1_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_CC_2_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_CC_3_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_ELASTIC_test.cmake                       |   34 +-
Examples/TestSuite/ANTS_EXP_test.cmake                           |   62 +-
Examples/TestSuite/ANTS_GSYN_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_MI_1_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_MI_2_test.cmake                          |   62 +-
Examples/TestSuite/ANTS_MSQ_test.cmake                           |   62 +-
Examples/TestSuite/ANTS_PSE_MSQ_IMG_test.cmake                   |   62 +-
Examples/TestSuite/ANTS_ROT_EXP_test.cmake                       |   36 +-
Examples/TestSuite/ANTS_ROT_GSYN_test.cmake                      |   20 +-
Examples/TestSuite/ANTS_SYN_WITH_TIME_test.cmake                 |   10 +-
Examples/TestSuite/ANTS_SYN_test.cmake                           |   62 +-
Examples/TestSuite/CMakeLists.txt                                |  202 ++--
Examples/antsApplyTransforms.cxx                                 |   54 +-
...placementAndVelocityFieldRegistrationCommandIterationUpdate.h |    6 +-
Examples/antsRegistration.cxx                                    |    6 +-
ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx         |    9 +-
README.md                                                        |    8 +
Scripts/antsASLProcessing.R                                      |   16 +-
Scripts/antsBrainExtraction.sh                                   |  138 +--
Scripts/antsCookTemplatePriors.sh                                |  631 ++++++++++++
Scripts/antsJointLabelFusion.sh                                  |  119 ++-
Scripts/antsLongitudinalCorticalThickness.sh                     |   65 +-
Scripts/antsLongitudinalJointLabelFusion.sh                      | 1380 +++++++++++++++++++++++++++
Scripts/antsMultivariateTemplateConstruction2.sh                 |   33 +-
Scripts/antsNeuroimagingBattery                                  |  142 ++-
Scripts/antsRegistrationSpaceTime.sh                             |    2 +-
Scripts/antsRegistrationSyN.sh                                   |  154 +--
Scripts/antsRegistrationSyNQuick.sh                              |  154 +--
Scripts/cbf_pcasl_robust_batch.R                                 |    2 +-
SuperBuild/External_ITKv4.cmake                                  |    7 +-
Utilities/antsSCCANObject.h                                      |  102 +-
Utilities/antsSCCANObject.hxx                                    |    1 +
Utilities/itkAdaptiveNonLocalMeansDenoisingImageFilter.h         |    1 +
Utilities/itkAdaptiveNonLocalMeansDenoisingImageFilter.hxx       |   30 +-
Utilities/itkNonLocalSuperresolutionImageFilter.h                |   27 +-
Utilities/itkNonLocalSuperresolutionImageFilter.hxx              |   91 +-
Version.cmake                                                    |    2 +-
49 files changed, 3947 insertions(+), 1277 deletions(-)
create mode 100644 Scripts/antsCookTemplatePriors.sh
create mode 100755 Scripts/antsLongitudinalJointLabelFusion.sh
M       Examples/include/ants.h
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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
HEAD is now at 6bc3e65... Merge pull request #459 from muschellij2/master
mkdir: cannot create directory ‘antb’: File exists
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- SuperBuild - ANTS => Requires ITKv4,
CMake Error at SuperBuild/External_ITKv4.cmake:31 (message):
ITK_DIR variable is defined but corresponds to non-existing directory ([1])
Call Stack (most recent call first):
CMake/SlicerMacroCheckExternalProjectDependency.cmake:69 (include)
SuperBuild.cmake:205 (SlicerMacroCheckExternalProjectDependency)
CMakeLists.txt:60 (include)
-- Configuring incomplete, errors occurred!
See also "/mnt/c/Users/DP/ANTsRCore/src/antb/CMakeFiles/CMakeOutput.log".
See also "/mnt/c/Users/DP/ANTsRCore/src/antb/CMakeFiles/CMakeError.log".
** libs
Makevars:3: *** missing separator.  Stop.
ERROR: compilation failed for package ‘ANTsRCore’

removing ‘/home/dp/R/x86_64-pc-linux-gnu-library/3.3/ANTsRCore’

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
https://github.com/stnava/ANTsR/issues/176#issuecomment-316716368, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ABBnrpmLJndS5lgZlkwVkbev9e18lCcMks5sP2CkgaJpZM4Odbee
.

devtools::install_github('stnava/ANTsR') worked on two other Ubuntu machines. Not sure why devtools installation works, but R CMD doesn't work.
On the cluster (CENTOS) nothing works. The error is the always the same, both with R CMD and with devtools:
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore
* installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
* installing *source* package 'ANTsRCore' ...
linux-gnu 0
-- Found Git: /usr/bin/git
-- SuperBuild - ANTS => Requires ITKv4,
-- SuperBuild -   ITKv4[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /data/jag/dpustina/engine/ANTsRCore/src/antb
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/data/jag/dpustina/engine/ANTsRCore/src -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Examples/include/   -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Utilities -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Examples/ -I../inst/include/  -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
In file included from ../inst/include/RcppANTsR.h:72,
                 from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'
* removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'

Can you show the devtools output? Also the ITKR versions.
John
On Thu, Jul 20, 2017 at 12:28 PM, dorianps<EMAIL_ADDRESS>wrote:

devtools::install_github('stnava/ANTsR') worked on two other Ubuntu
machines. Not sure why devtools installation works, but R CMD doesn't work.
On the cluster (CENTOS) nothing works. The error is the always the same,
both with R CMD and with devtools:
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore

installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
installing source package 'ANTsRCore' ...
linux-gnu 0
-- Found Git: /usr/bin/git
-- SuperBuild - ANTS => Requires ITKv4,
-- SuperBuild -   ITKv4[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /data/jag/dpustina/engine/ANTsRCore/src/antb
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/data/jag/dpustina/engine/ANTsRCore/src -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Examples/include/   -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Utilities -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Examples/ -I../inst/include/  -I/data/jag/dpustina/engine/ANTsRCore/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
In file included from ../inst/include/RcppANTsR.h:72,
from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'
removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
https://github.com/stnava/ANTsR/issues/176#issuecomment-316757998, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ABBnrgRe_Efa8IBwbtU6kbbplsY1eQicks5sP4BLgaJpZM4Odbee
.

Here it is:
> packageVersion('ITKR')
[1] '<IP_ADDRESS>'

dpustina@compute-0-0:engine$ R
>
> devtools::install_github('stnava/ANTsR')
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Downloading GitHub repo stnava/ANTsR@master
from URL https://api.github.com/repos/stnava/ANTsR/zipball/master
Installing ANTsR
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  unsupported URL scheme
Downloading GitHub repo stnava/ANTsRCore@master
from URL https://api.github.com/repos/stnava/ANTsRCore/zipball/master
Installing ANTsRCore
Running command /share/apps/R/R-3.2.5/bin/R
Arguments:
CMD
INSTALL
/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1
--library=/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1
--install-tests

* installing *source* package 'ANTsRCore' ...
linux-gnu 0
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Cloning into 'ants'...
Already on 'master'
Already up-to-date.
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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 6bc3e65... Merge pull request #459 from muschellij2/master
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /opt/rocks/bin/git (found version "<IP_ADDRESS>")
-- SuperBuild - ANTS => Requires ITKv4,
-- SuperBuild -   ITKv4[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/antb
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ResampleImage.cpp -o ResampleImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
In file included from ../inst/include/RcppANTsR.h:72,
                 from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
-./inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'
* removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'
* restoring previous '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error
Running command /share/apps/R/R-3.2.5/bin/R
Arguments:
CMD
INSTALL
/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a4f65536d/stnava-ANTsR-f512a94
--library=/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1
--install-tests

* installing *source* package 'ANTsR' ...
linux-gnu 0
Error in library.dynam(lib, package, package.lib) :
  shared object 'ANTsRCore.so' not found
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Warning message:
S3 methods 'apply.antsImage', 'apply.default', 'as.array.antsImage', 'as.data.frame.antsMatrix', 'as.matrix.antsImage', 'boxplot.antsImage', 'cut.antsImage', 'density.antsImage', 'hist.antsImage', 'mean.antsImage', 'median.antsImage', 'plot.antsImage', 'quantile.antsImage', 'subset.antsImage', 'unique.antsImage', 'var.antsImage', 'var.default' were declared in NAMESPACE but not found
Execution halted
Error in library.dynam(lib, package, package.lib) :
  shared object 'ANTsRCore.so' not found
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Warning message:
S3 methods 'apply.antsImage', 'apply.default', 'as.array.antsImage', 'as.data.frame.antsMatrix', 'as.matrix.antsImage', 'boxplot.antsImage', 'cut.antsImage', 'density.antsImage', 'hist.antsImage', 'mean.antsImage', 'median.antsImage', 'plot.antsImage', 'quantile.antsImage', 'subset.antsImage', 'unique.antsImage', 'var.antsImage', 'var.default' were declared in NAMESPACE but not found
Execution halted
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a4f65536d/stnava-ANTsR-f512a94/src    -I   -I../inst/include/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/include"   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
|nts.h: No such file or directoryp:5:18:
CreateJacobianDeterminantImage.cpp: In function 'SEXPREC* CreateJacobianDeterminantImage(SEXPREC*)':
-reateJacobianDeterminantImage.cpp:17: error: 'ants' has not been declared
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package 'ANTsR'
* removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR'
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error
Warning message:
GitHub repo contains submodules, may not function as expected!

That is a VERY old version of git (may not do checkouts well)
All builds are tested with clang - change compiler if necessary
R Version is 3.2.4 - consider upgrading - not tested against this.
Please devtools::install_github("stnava/ITKR"), then
devtools::install_github("stnava/ANTsRCore", upgrade_dependencies = FALSE)
, then
devtools::install_github("stnava/ANTsR", upgrade_dependencies = FALSE)
to see how each progresses.
Please run devtools::session_info() before running.

John
On Thu, Jul 20, 2017 at 2:36 PM, dorianps<EMAIL_ADDRESS>wrote:

Here it is:

packageVersion('ITKR')
[1] '<IP_ADDRESS>'

dpustina@compute-0-0:engine$ R

devtools::install_github('stnava/ANTsR')
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'ANTsR' is not available and has been replaced
by .GlobalEnv when processing object ''
Downloading GitHub repo stnava/ANTsR@master
from URL https://api.github.com/repos/stnava/ANTsR/zipball/master
Installing ANTsR
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
unsupported URL scheme
Downloading GitHub repo stnava/ANTsRCore@master
from URL https://api.github.com/repos/stnava/ANTsRCore/zipball/master
Installing ANTsRCore
Running command /share/apps/R/R-3.2.5/bin/R
Arguments:
CMD
INSTALL
/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1
--library=/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1
--install-tests

installing source package 'ANTsRCore' ...
linux-gnu 0
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Cloning into 'ants'...
Already on 'master'
Already up-to-date.
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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 6bc3e65... Merge pull request #459 from muschellij2/master
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /opt/rocks/bin/git (found version "<IP_ADDRESS>")
-- SuperBuild - ANTS => Requires ITKv4,
-- SuperBuild -   ITKv4[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/antb
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ResampleImage.cpp -o ResampleImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a1b41fe54/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
In file included from ../inst/include/RcppANTsR.h:72,
from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
-./inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'

removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'

restoring previous '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error
Running command /share/apps/R/R-3.2.5/bin/R
Arguments:
CMD
INSTALL
/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a4f65536d/stnava-ANTsR-f512a94
--library=/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1
--install-tests

installing source package 'ANTsR' ...
linux-gnu 0
Error in library.dynam(lib, package, package.lib) :
shared object 'ANTsRCore.so' not found
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne ->
Warning message:
S3 methods 'apply.antsImage', 'apply.default', 'as.array.antsImage', 'as.data.frame.antsMatrix', 'as.matrix.antsImage', 'boxplot.antsImage', 'cut.antsImage', 'density.antsImage', 'hist.antsImage', 'mean.antsImage', 'median.antsImage', 'plot.antsImage', 'quantile.antsImage', 'subset.antsImage', 'unique.antsImage', 'var.antsImage', 'var.default' were declared in NAMESPACE but not found
Execution halted
Error in library.dynam(lib, package, package.lib) :
shared object 'ANTsRCore.so' not found
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne ->
Warning message:
S3 methods 'apply.antsImage', 'apply.default', 'as.array.antsImage', 'as.data.frame.antsMatrix', 'as.matrix.antsImage', 'boxplot.antsImage', 'cut.antsImage', 'density.antsImage', 'hist.antsImage', 'mean.antsImage', 'median.antsImage', 'plot.antsImage', 'quantile.antsImage', 'subset.antsImage', 'unique.antsImage', 'var.antsImage', 'var.default' were declared in NAMESPACE but not found
Execution halted
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a4f65536d/stnava-ANTsR-f512a94/src    -I   -I../inst/include/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/include"   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
|nts.h: No such file or directoryp:5:18:
CreateJacobianDeterminantImage.cpp: In function 'SEXPREC* CreateJacobianDeterminantImage(SEXPREC*)':
-reateJacobianDeterminantImage.cpp:17: error: 'ants' has not been declared
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package 'ANTsR'

removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsR'
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error
Warning message:
GitHub repo contains submodules, may not function as expected!

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
https://github.com/stnava/ANTsR/issues/176#issuecomment-316792453, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ABBnrmWBOokud7p5mT8Gq2e5m8UhVelRks5sP54UgaJpZM4Odbee
.

Thanks for these suggestions, John. We are on CENTOS 6 here, so we're stuck with R 3.2.3. We have a system to run different environments as needed but it's not trivial. I will try these steps and get back to you.

The suggested solution at point 4 did not work. The error is the same:
> devtools::install_github("stnava/ITKR")
Skipping install of 'ITKR' from a github remote, the SHA1 (3c4a1729) has not changed since last install.
  Use `force = TRUE` to force installation
> devtools::install_github("stnava/ANTsRCore", upgrade_dependencies = FALSE)
Downloading GitHub repo stnava/ANTsRCore@master
from URL https://api.github.com/repos/stnava/ANTsRCore/zipball/master
Installing ANTsRCore
Running command /share/apps/R/R-3.2.5/bin/R
Arguments:
CMD
INSTALL
/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1
--library=/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1
--install-tests

* installing *source* package 'ANTsRCore' ...
linux-gnu 0
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Cloning into 'ants'...
Already on 'master'
Already up-to-date.
Note: checking out '6bc3e652d7628b428896ddaec837248a61d2af3b'.

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 6bc3e65... Merge pull request #459 from muschellij2/master
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /opt/rocks/bin/git (found version "<IP_ADDRESS>")
-- SuperBuild - ANTS => Requires ITKv4,
-- SuperBuild -   ITKv4[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/antb
** libs
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ResampleImage.cpp -o ResampleImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=c++0x -I/share/apps/R/R-3.2.5/include -DNDEBUG -I/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/libs/include/ITK-4.12/ -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/include/   -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Utilities -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Examples/ -I../inst/include/  -I/tmp/3490087.1.qlogin.q/RtmpY7Gb63/devtools593a18a99a9e/stnava-ANTsRCore-7427de1/src/ants//Tensor/  -I/usr/local/include -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include" -I"/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ITKR/include"   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
In file included from ../inst/include/RcppANTsR.h:72,
                 from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
|./inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'
* removing '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'
* restoring previous '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore'
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error

> devtools::session_info()
Session info ------------------------------------------------------------------
 setting  value
 version  R version 3.2.5 (2016-04-14)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.iso885915
 tz       <NA>
 date     2017-07-20

Packages ----------------------------------------------------------------------
 package    * version     date       source
 assertthat   0.2.0       2017-04-11 cran (@0.2.0)
 base       * 3.2.5       2016-09-26 local
 callr        <IP_ADDRESS>00  2017-06-07 Github (r-pkgs/callr@7c65427)
 crayon       1.3.2       2016-06-28 cran (@1.3.2)
 curl         0.9.6       2016-02-17 CRAN (R 3.1.1)
 datasets   * 3.2.5       2016-09-26 local
 debugme      1.0.2       2017-03-01 cran (@1.0.2)
 devtools     <IP_ADDRESS>00 2017-06-07 Github (hadley/devtools@c4099b3)
 digest       0.6.12      2017-01-27 cran (@0.6.12)
 git2r        0.16.0      2016-11-20 CRAN (R 3.1.1)
 graphics   * 3.2.5       2016-09-26 local
 grDevices  * 3.2.5       2016-09-26 local
 httr         1.2.1       2016-07-03 CRAN (R 3.1.1)
 knitr        1.12.3      2016-01-22 CRAN (R 3.1.1)
 memoise      1.1.0       2017-04-21 cran (@1.1.0)
 methods    * 3.2.5       2016-09-26 local
 pkgbuild     <IP_ADDRESS>00  2017-06-07 Github (r-pkgs/pkgbuild@8aab60b)
 pkgload      <IP_ADDRESS>00  2017-06-07 Github (r-pkgs/pkgload@119cf9a)
 processx     2.0.1       2017-06-07 Github (r-pkgs/processx@88e7761)
 R6           2.2.1       2017-05-10 cran (@2.2.1)
 Rcpp         0.12.12     2017-07-15 cran (@0.12.12)
 rlang        <IP_ADDRESS>00  2017-06-07 Github (hadley/rlang@7f53e56)
 stats      * 3.2.5       2016-09-26 local
 tools        3.2.5       2016-09-26 local
 utils      * 3.2.5       2016-09-26 local
 withr        1.0.2       2016-06-20 cran (@1.0.2)

Same error for me on CentOS 6 with R 3.2.3, but it builds on my Mac with R 3.2.4.
Session info -------------------------------------------------------------------
 setting  value
 version  R version 3.2.4 (2016-03-10)
 system   x86_64, darwin13.4.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 tz       America/New_York
 date     2017-07-20

Packages -----------------------------------------------------------------------
 package    * version date       source
 curl         0.9.6   2016-02-17 CRAN (R 3.2.3)
 devtools   * 1.10.0  2016-01-23 CRAN (R 3.2.3)
 digest       0.6.9   2016-01-08 CRAN (R 3.2.3)
 git2r        0.14.0  2016-03-13 CRAN (R 3.2.4)
 httr         1.1.0   2016-01-28 CRAN (R 3.2.3)
 knitr        1.12.3  2016-01-22 CRAN (R 3.2.3)
 memoise      1.0.0   2016-01-29 CRAN (R 3.2.3)
 R6           2.1.2   2016-01-26 CRAN (R 3.2.3)
 rstudioapi   0.5     2016-01-24 CRAN (R 3.2.3)
 withr        1.0.1   2016-02-04 CRAN (R 3.2.3)

I think there were some updates to Rcpp, so you may want to try:
devtools::install_github("stnava/ITKR", force = TRUE)
and then try again to make sure Rcpp build is the same for ITKR/ANTsRCore.
Otherwise looks to maybe a compiler issue:
https://stackoverflow.com/questions/19225458/error-c2899-typename-cannot-be-used-outside-a-template-declaration
What gcc/clang does your Mac have?
I see GNU 4.4.7 for the box
It seems like it may be due to an old compiler issue (which is a
pain/nightmare because you may have to upgrade R or roll your own R):
https://github.com/Oslandia/SFCGAL/issues/44
John
On Thu, Jul 20, 2017 at 5:25 PM, Philip Cook<EMAIL_ADDRESS>wrote:

Same error for me on CentOS 6 with R 3.2.3, but it builds on my Mac with R
3.2.4.
Session info -------------------------------------------------------------------
setting  value
version  R version 3.2.4 (2016-03-10)
system   x86_64, darwin13.4.0
ui       X11
language (EN)
collate  en_US.UTF-8
tz       America/New_York
date     2017-07-20
Packages -----------------------------------------------------------------------
package    * version date       source
curl         0.9.6   2016-02-17 CRAN (R 3.2.3)
devtools   * 1.10.0  2016-01-23 CRAN (R 3.2.3)
digest       0.6.9   2016-01-08 CRAN (R 3.2.3)
git2r        0.14.0  2016-03-13 CRAN (R 3.2.4)
httr         1.1.0   2016-01-28 CRAN (R 3.2.3)
knitr        1.12.3  2016-01-22 CRAN (R 3.2.3)
memoise      1.0.0   2016-01-29 CRAN (R 3.2.3)
R6           2.1.2   2016-01-26 CRAN (R 3.2.3)
rstudioapi   0.5     2016-01-24 CRAN (R 3.2.3)
withr        1.0.1   2016-02-04 CRAN (R 3.2.3)
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
https://github.com/stnava/ANTsR/issues/176#issuecomment-316834800, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ABBnrhE9-8oSNr5nw0KG2isLbNAdac-oks5sP8XjgaJpZM4Odbee
.

Yes GNU 4.4.7 on Linux. I have "AppleClang <IP_ADDRESS>00042" on my Mac.
Force didn't help. Might be time for us to update. I'll try in a Centos 7 VM, but our sysadmin is away right now so might take me a while.

I went back to try installing the binaries in the releases. Looks like all new ANtsRCore versions 0.3.* can be installed, but cannot be loaded because of /usr/lib64/libstdc++.so.6: versionGLIBCXX_3.4.15' not found`. Going back to earlier versions, I could install and load ANTsRCore 0.1, but ANTsR requires >0.2. The 0.2 release has been deleted from Github for some reason.
These tests suggest that at some point last month the compilers that build the binaries switched to more recent version. There is several pages on google that explain theGLIBCXX_3.4.15 problem:
https://www.google.com/search?q=version+`GLIBCXX_3.4.15'+not+found
https://stackoverflow.com/questions/31525271/usr-lib64-libstdc-so-6-version-glibcxx-3-4-15-not-found
My naive questions are:

Was the compiler upgrade necessary? Can we push binaries that are compatible with older compilers/systems?
Is the ../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]': error coming from an upgrade of ITK or from changes in ANTsRCore that we can fix?

Here are the logs of trying to install from binaries:
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore.tar.gz
* installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
* installing *binary* package 'ANTsRCore' ...
* DONE (ANTsRCore)
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsR.tar.gz
* installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
* installing *binary* package 'ANTsR' ...
* DONE (ANTsR)
dpustina@compute-0-0:engine$ R
> library(ANTsR)
Loading required package: ANTsRCore
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so)
In addition: Warning messages:
1: package 'ANTsR' was built under R version 3.4.0
2: package 'ANTsRCore' was built under R version 3.4.0
Error: package 'ANTsRCore' could not be loaded
> library(ANTsRCore)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so)
In addition: Warning message:
package 'ANTsRCore' was built under R version 3.4.0
Error: package or namespace load failed for 'ANTsRCore'
>
> q()
Save workspace image? [y/n/c]: n
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore
ANTsRCore/                                      ANTsRCore.tar.gz
ANTsRCore_<IP_ADDRESS>_R_x86_64-pc-linux-gnu.tar.gz
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore_<IP_ADDRESS>_R_x86_64-pc-linux-gnu.tar.gz
* installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
* installing *binary* package 'ANTsRCore' ...
* DONE (ANTsRCore)
dpustina@compute-0-0:engine$ R
> library(ANTsRCore)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1/ANTsRCore/libs/ANTsRCore.so)
In addition: Warning message:
package 'ANTsRCore' was built under R version 3.4.0
Error: package or namespace load failed for 'ANTsRCore'
> packageVersion('ANTsRCore')
[1] '<IP_ADDRESS>'
> q()
Save workspace image? [y/n/c]: n
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore_0.
ANTsRCore_0.1_R_x86_64-pc-linux-gnu.tar.gz      ANTsRCore_<IP_ADDRESS>_R_x86_64-pc-linux-gnu.tar.gz
dpustina@compute-0-0:engine$ R CMD INSTALL ANTsRCore_0.1_R_x86_64-pc-linux-gnu.tar.gz
* installing to library '/home/dpustina/R/x86_64-unknown-linux-gnu-library/3.1'
* installing *binary* package 'ANTsRCore' ...
* DONE (ANTsRCore)
dpustina@compute-0-0:engine$ R
> library(ANTsRCore)
Warning message:
package 'ANTsRCore' was built under R version 3.4.0
> library(ANTsR)
Error: package 'ANTsRCore' 0.1 is loaded, but >= 0.2 is required by 'ANTsR'
In addition: Warning message:
package 'ANTsR' was built under R version 3.4.0

Going back a few commits in ANTsRCore fixes the problem, these two commands finally install ANTsRCore and ANTsR in our cluster:
devtools::install_github('stnava/ANTsRCore', ref='c382d45', upgrade_dependencies = FALSE)
devtools::install_github('stnava/ANTsR', upgrade_dependencies = FALSE)

Haven't tried the R CMD version yet, but it should work the same.
The problem, therefore, is some change made to ANTsRCore after https://github.com/stnava/ANTsRCore/commit/c382d45a47ed68d42c7d3543bc8170743105e4cc
These are the full logs of the installation if curious:
ANTsR sucess installation.txt

thanks for tracking this down @dorianps
there was one code error for which i just pushed a fix.  the error read as:
In file included from ../inst/include/RcppANTsR.h:72,
                 from antsImage.cpp:5:
../inst/include/RcppANTsR/RcppANTsR_ImageImp.h: In function 'SEXPREC* Rcpp::wrap(const T&) [with T = itk::SmartPointer<itk::Image<double, 2u> >]':
|./inst/include/RcppANTsR/RcppANTsR_ImageImp.h:53: error: using 'typename' outside of template
make: *** [antsImage.o] Error 1
ERROR: compilation failed for package 'ANTsRCore'

and this commit (probably) fixes it https://github.com/stnava/ANTsRCore/commit/e8518e0c637bf0b3808192fb8959aac76e93157d
meaning that you can probably use:
devtools::install_github('stnava/ANTsRCore', upgrade_dependencies = FALSE)

note that i have not verified this yet.

ok - verified that standard devtools install (with latest github version) works on
CentOS release 6.8 (Final)

Thanks everyone, this will help us keep up to date on our cluster

Yes, it worked on the cluster.
I also checked the original problem of ITK_DIR on a Ubuntu machine (uninstalled ITKR/ANTsRCore/ANTsR, and reinstalled with R CMD). This time I did not see the ITK_DIR problem. Not sure if this was fixed by the commit or something else happened to my system, but it's good news.


Print git version in status page

Use the -X flag to the linker to embed git version information in the server binary, and print this information in the status page:
{
 "CurrSize": 0,
 "MaxSize":<PHONE_NUMBER>0,
 "NumFiles": 0,
 "ServerTime":<PHONE_NUMBER>,
 "ServerVersion": "a701b69-dirty"
}

Good idea! Is there a way to also add this to the Bazel build rules? I typically publish the docker image using those.

I believe that the only clean solution is for C++ with the linkstamp feature: https://groups.google.com/forum/m/#!topic/bazel-discuss/9kqLmOq_m_U
Otherwise, we'd have a genrule depending on .git, which is pretty horrible IMHO.

After rebasing on master, I tried a couple different ways of getting this working with bazel.
diff --git a/server/BUILD.bazel b/server/BUILD.bazel
index 7edc2d6..d4ef0bc 100644
--- a/server/BUILD.bazel
+++ b/server/BUILD.bazel
@@ -2,7 +2,7 @@ load("@io_bazel_rules_go//go:def.bzl", "go_library", "go_test")

 go_library(
     name = "go_default_library",
-    srcs = ["http.go"],
+    srcs = ["http.go", ":gitrev"],
     importpath = "github.com/buchgr/bazel-remote/server",
     visibility = ["//visibility:public"],
     deps = ["//cache:go_default_library"],
@@ -17,3 +17,11 @@ go_test(
         "//utils:go_default_library",
     ],
 )
+
+genrule(
+    name = "gitrev",
+    srcs = [],
+    outs = ["rev.go"],
+    cmd = 'echo -e "//GENERATED BY BAZEL\npackage server\nfunc init(){ServerVersion=\\"$$REVISION\\"}" > $@',
+    stamp = True,
+)

Now, bazel build --stamp --action_env=REVISION=$(git describe --always --dirty) //:bazel-remote embeds the revision string. However, bazel now refuses to build if --action_env=REVISION=... is left off. I'm not sure how to fix this - any thoughts?
Also, is --action_env a safe way to do this or must we use --workspace_status_command=...?

Second attempt, with workspace_status_command:
diff --git a/server/BUILD.bazel b/server/BUILD.bazel
index 7edc2d6..8bc7457 100644
--- a/server/BUILD.bazel
+++ b/server/BUILD.bazel
@@ -2,7 +2,7 @@ load("@io_bazel_rules_go//go:def.bzl", "go_library", "go_test")

 go_library(
     name = "go_default_library",
-    srcs = ["http.go"],
+    srcs = ["http.go", ":gitrev"],
     importpath = "github.com/buchgr/bazel-remote/server",
     visibility = ["//visibility:public"],
     deps = ["//cache:go_default_library"],
@@ -17,3 +17,20 @@ go_test(
         "//utils:go_default_library",
     ],
 )
+genrule(
+    name = "gitrev",
+    srcs = [],
+    outs = ["rev.go"],
+    cmd = '''
+rev=$$(sed -n 's/^REVISION=\\(.*\\)/\\1/p;' bazel-out/volatile-status.txt)
+echo $$rev
+cat >$@ <<EOI
+//GENERATED FILE - DO NOT EDIT. 'bazel build //server:gitrev'
+package server
+func init(){
+    ServerVersion="$$rev"
+}
+EOI
+''',
+    stamp = True,
+)

cat version.sh
#!/bin/sh
echo REVISION=$(git describe --always --dirty)

Run with bazel build --stamp --workspace_status_command=$PWD/version.sh //:bazel-remote. This does not reliably rebuild when the status command's output changes (?!)