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ANTsX / ANTsR

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

itkVectorCastImageFilter.h: No such file or directory #282

Closed muratmaga closed 4 years ago

muratmaga commented 4 years ago

I just cloned the recent repos to get the newest changes. I am doing the R CMD INSTALL. ITKR seems installed fine, but ANTsR is failing with this error...

sR/src -I/usr/lib64/R/library/ANTsRCore/include/ -I../inst/include/ -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/ITKR/include" -I"/usr/lib64/R/library/ANTsRCore/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o In file included from /usr/lib64/R/library/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0, from CreateJacobianDeterminantImage.cpp:8: /usr/lib64/R/library/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:38: fatal error: itkVectorCastImageFilter.h: No such file or directory

include "itkVectorCastImageFilter.h"

muschellij2 commented 4 years ago

What OS are you using?

Ran into this at https://ci.appveyor.com/project/muschellij2/antsrcore I think the past. I think this should be updated with a newer ITKR.

muschellij2 commented 4 years ago

Please post sessioninfo::session_info() and run:

  fname = system.file( "data", "softwareVersions.csv", package = "ITKR")
  tag = NULL
  if (file.exists(fname)) {
    tag = utils::read.csv(fname, sep = ";", as.is = TRUE)
    tag = tag$GitTag[ tag$Dependency == "ITK"]
  }
muratmaga commented 4 years ago

This is a Centos 7.7 system Output of sessioninfo

> ─ Session info ───────────────────────────────────────────────────────────────
>  setting  value                       
>  version  R version 3.6.0 (2019-04-26)
>  os       CentOS Linux 7 (Core)       
>  system   x86_64, linux-gnu           
>  ui       X11                         
>  language (EN)                        
>  collate  en_US.UTF-8                 
>  ctype    en_US.UTF-8                 
>  tz       US/Pacific                  
>  date     2019-10-10                  
> 
> ─ Packages ───────────────────────────────────────────────────────────────────
>  package     * version date       lib source        
>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.0)
>  cli           1.1.0   2019-03-19 [1] CRAN (R 3.6.0)
>  crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.0)
>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0)
>  withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.0)
> 
> [1] /usr/lib64/R/library
> [2] /usr/share/R/library

And the output spinnet

> > fname = system.file( "data", "softwareVersions.csv", package = "ITKR")
> >   tag = NULL
> >   if (file.exists(fname)) {
> +     tag = utils::read.csv(fname, sep = ";", as.is = TRUE)
> +     tag = tag$GitTag[ tag$Dependency == "ITK"]
> +   }
> > fname
> [1] "/usr/lib64/R/library/ITKR/data/softwareVersions.csv"
> > tag
> [1] "81c14ce858a530699ee2fbf7fa48b884ad26b984"
>
gdevenyi commented 4 years ago

Possibly related https://github.com/InsightSoftwareConsortium/ITK/pull/1311

muratmaga commented 4 years ago

Is there a solution?

dorianps commented 4 years ago

I think I have the same problem on two different systems, a host Centos 7.7 (with gcc 7.3.1) and a docker image using Debian (with gcc 9.2.1). To my untrained eye looks the first problem is always a break in ANTsVersion.cxx.

Currently ANTsR is uninstallable.

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"
-- Build files have been written to: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build
[ 82%] Performing forcebuild step for 'ANTS'
[ 88%] Performing build step for 'ANTS'
make[4]: Entering directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[5]: Entering directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
Scanning dependencies of target antsUtilities
make[6]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
[  1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistrationTemplateHeader.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DDouble.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DFloat.cxx.o
[  5%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DDouble.cxx.o
[  6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o
[  7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o
[  8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o
[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o
[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o
[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o
[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MAJOR;
     ^~~~~~
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MINOR;
     ^~~~~~
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:
/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_PATCH;
     ^~~~~~
make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[5]: *** [Examples/CMakeFiles/antsUtilities.dir/all] Error 2
make[5]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[3]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
make[3]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb'
make[2]: *** [CMakeFiles/ANTS.dir/all] Error 2
make[2]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb'
make: *** [libs] Error 2
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
* restoring previous ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
Installation failed: Command failed (1)
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests 

* installing *source* package ‘ANTsR’ ...
linux-gnu 0
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959/src    -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/   -I../inst/include/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include" -I/usr/local/include   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
In file included from /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0,
                 from CreateJacobianDeterminantImage.cpp:8:
/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:10: fatal error: itkVectorCastImageFilter.h: No such file or directory
 #include "itkVectorCastImageFilter.h"
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package ‘ANTsR’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR’
Installation failed: Command failed (1)
> devtools::session_info()
Session info ------------------------------------------------------------
 setting  value                       
 version  R version 3.5.0 (2018-04-23)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.456)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2019-10-19                  

Packages ----------------------------------------------------------------
 package   * version date       source        
 base      * 3.5.0   2018-05-13 local         
 compiler    3.5.0   2018-05-13 local         
 curl        3.3     2019-01-10 cran (@3.3)   
 datasets  * 3.5.0   2018-05-13 local         
 devtools    1.13.5  2018-02-18 CRAN (R 3.5.0)
 digest      0.6.18  2018-10-10 cran (@0.6.18)
 git2r       0.21.0  2018-01-04 CRAN (R 3.5.0)
 graphics  * 3.5.0   2018-05-13 local         
 grDevices * 3.5.0   2018-05-13 local         
 httr        1.3.1   2017-08-20 CRAN (R 3.5.0)
 knitr       1.20    2018-02-20 cran (@1.20)  
 memoise     1.1.0   2017-04-21 CRAN (R 3.5.0)
 methods   * 3.5.0   2018-05-13 local         
 R6          2.4.0   2019-02-14 cran (@2.4.0) 
 stats     * 3.5.0   2018-05-13 local         
 tools       3.5.0   2018-05-13 local         
 utils     * 3.5.0   2018-05-13 local         
 withr       2.1.2   2018-03-15 CRAN (R 3.5.0)
 yaml        2.1.19  2018-05-01 cran (@2.1.19)

On a docker container using a debian:

PRETTY_NAME="Debian GNU/Linux bullseye/sid"
NAME="Debian GNU/Linux"
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
[  6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o
[  7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o
[  8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o
[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o
[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o
[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o
[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   43 |     return ANTS_VERSION_MAJOR;
      |     ^~~~~~
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   47 |     return ANTS_VERSION_MINOR;
      |     ^~~~~~
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   51 |     return ANTS_VERSION_PATCH;
      |     ^~~~~~
make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[5]: *** [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2
make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[4]: *** [Makefile:163: all] Error 2
make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[3]: *** [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make[2]: *** [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2
make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make[1]: *** [Makefile:117: all] Error 2
make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make: *** [Makevars:12: libs] Error 2
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/usr/local/lib/R/site-library/ANTsRCore’
Error: Failed to install 'ANTsR' from GitHub:
  Failed to install 'ANTsRCore' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status
[  6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o
[  7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o
[  8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o
[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o
[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o
[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o
[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   43 |     return ANTS_VERSION_MAJOR;
      |     ^~~~~~
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   47 |     return ANTS_VERSION_MINOR;
      |     ^~~~~~
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:
/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
   51 |     return ANTS_VERSION_PATCH;
      |     ^~~~~~
make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[5]: *** [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2
make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[4]: *** [Makefile:163: all] Error 2
make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build'
make[3]: *** [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make[2]: *** [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2
make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make[1]: *** [Makefile:117: all] Error 2
make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb'
make: *** [Makevars:12: libs] Error 2
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/usr/local/lib/R/site-library/ANTsRCore’
Error: Failed to install 'ANTsR' from GitHub:
  Failed to install 'ANTsRCore' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status
muschellij2 commented 4 years ago

This has been discussed a bit on the other issues pages. Currently, you cannot install antsrcore with devtools or remotes, you have to install them with the full git history

On Sun, Oct 20, 2019 at 12:11 AM dorianps notifications@github.com wrote:

I think I have the same problem on two different systems, a host Centos 7.7 (with gcc 7.3.1) and a docker image using Debian (with gcc 9.2.1). To my untrained eye looks the first problem is always a breack in ANTsVersion.cxx.

Currently ANTsR is uninstallable.

NAME="CentOS Linux"

VERSION="7 (Core)"

ID="centos"

ID_LIKE="rhel fedora"

VERSION_ID="7"

PRETTY_NAME="CentOS Linux 7 (Core)"

ANSI_COLOR="0;31"

CPE_NAME="cpe:/o:centos:centos:7"

HOME_URL="https://www.centos.org/"

BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"

CENTOS_MANTISBT_PROJECT_VERSION="7"

REDHAT_SUPPORT_PRODUCT="centos"

REDHAT_SUPPORT_PRODUCT_VERSION="7"

-- Build files have been written to: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build

[ 82%] Performing forcebuild step for 'ANTS'

[ 88%] Performing build step for 'ANTS' make[4]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[5]: Entering directory/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[6]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' Scanning dependencies of target antsUtilities make[6]: Leaving directory/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[6]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' [ 1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o [ 2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistrationTemplateHeader.cxx.o [ 3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DDouble.cxx.o [ 4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DFloat.cxx.o [ 5%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DDouble.cxx.o [ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o [ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o [ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o [ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o [ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o [ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o [ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_MAJOR; ^~~~~~ /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_MINOR; ^~~~~~ /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_PATCH; ^~~~~~ make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: *** Waiting for unfinished jobs.... make[6]: Leaving directory/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[5]: [Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[4]: [all] Error 2 make[4]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[3]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make[2]: [CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make[1]: [all] Error 2 make[1]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make: *** [libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’

  • restoring previous ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’ Installation failed: Command failed (1) '/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL '/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959' \ --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

  • installing source package ‘ANTsR’ ... linux-gnu 0 ** libs g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959/src -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/ -I../inst/include/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include" -I/usr/local/include -fpic -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o In file included from /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0, from CreateJacobianDeterminantImage.cpp:8: /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:10: fatal error: itkVectorCastImageFilter.h: No such file or directory

    include "itkVectorCastImageFilter.h"

      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

    compilation terminated. make: *** [CreateJacobianDeterminantImage.o] Error 1 ERROR: compilation failed for package ‘ANTsR’

  • removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR’ Installation failed: Command failed (1)

    devtools::session_info() Session info ------------------------------------------------------------ setting value version R version 3.5.0 (2018-04-23) system x86_64, linux-gnu ui RStudio (1.1.456) language (EN) collate en_US.UTF-8 tz America/New_York date 2019-10-19

Packages ---------------------------------------------------------------- package version date source base 3.5.0 2018-05-13 local compiler 3.5.0 2018-05-13 local curl 3.3 2019-01-10 cran (@3.3) datasets 3.5.0 2018-05-13 local devtools 1.13.5 2018-02-18 CRAN (R 3.5.0) digest 0.6.18 2018-10-10 cran (@0.6.18) git2r 0.21.0 2018-01-04 CRAN (R 3.5.0) graphics 3.5.0 2018-05-13 local grDevices 3.5.0 2018-05-13 local httr 1.3.1 2017-08-20 CRAN (R 3.5.0) knitr 1.20 2018-02-20 cran (@1.20) memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) methods 3.5.0 2018-05-13 local R6 2.4.0 2019-02-14 cran (@2.4.0) stats 3.5.0 2018-05-13 local tools 3.5.0 2018-05-13 local utils 3.5.0 2018-05-13 local withr 2.1.2 2018-03-15 CRAN (R 3.5.0) yaml 2.1.19 2018-05-01 cran (@2.1.19)

On a docker container using a debian:

PRETTY_NAME="Debian GNU/Linux bullseye/sid"

NAME="Debian GNU/Linux"

ID=debian

HOME_URL="https://www.debian.org/"

SUPPORT_URL="https://www.debian.org/support"

BUG_REPORT_URL="https://bugs.debian.org/"

[ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o

[ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o

[ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o

[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o

[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o

[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o

[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

43 | return ANTS_VERSION_MAJOR;

  |     ^~~~~~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

47 | return ANTS_VERSION_MINOR;

  |     ^~~~~~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

51 | return ANTS_VERSION_PATCH;

  |     ^~~~~~

make[6]: [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: Waiting for unfinished jobs.... make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[5]: [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[4]: [Makefile:163: all] Error 2 make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[3]: [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[2]: [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[1]: [Makefile:117: all] Error 2 make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make: [Makevars:12: libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/usr/local/lib/R/site-library/ANTsRCore’ Error: Failed to install 'ANTsR' from GitHub:

    Failed to install 'ANTsRCore' from GitHub:

    (converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status

[ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o

[ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o

[ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o

[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o

[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o

[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o

[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

43 | return ANTS_VERSION_MAJOR;

  |     ^~~~~~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

47 | return ANTS_VERSION_MINOR;

  |     ^~~~~~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’: /tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

51 | return ANTS_VERSION_PATCH;

  |     ^~~~~~

make[6]: [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: Waiting for unfinished jobs.... make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[5]: [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[4]: [Makefile:163: all] Error 2 make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[3]: [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[2]: [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[1]: [Makefile:117: all] Error 2 make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make: [Makevars:12: libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/usr/local/lib/R/site-library/ANTsRCore’ Error: Failed to install 'ANTsR' from GitHub:

    Failed to install 'ANTsRCore' from GitHub:

    (converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/282?email_source=notifications&email_token=AAIGPLWQ2E74U6SDICXCY7TQPPK6JA5CNFSM4I7F6UMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBYB6ZI#issuecomment-544218981, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIGPLUBHS3OWBLJYY4PE7TQPPK6JANCNFSM4I7F6UMA .

-- Best, John

stnava commented 4 years ago

I made a recent commit to ants that may resolve at least part of this issue but we will have to Try it out after Propagating changes through

On Sun, Oct 20, 2019 at 10:33 AM John Muschelli notifications@github.com wrote:

This has been discussed a bit on the other issues pages. Currently, you cannot install antsrcore with devtools or remotes, you have to install them with the full git history

On Sun, Oct 20, 2019 at 12:11 AM dorianps notifications@github.com wrote:

I think I have the same problem on two different systems, a host Centos 7.7 (with gcc 7.3.1) and a docker image using Debian (with gcc 9.2.1). To my untrained eye looks the first problem is always a breack in ANTsVersion.cxx.

Currently ANTsR is uninstallable.

NAME="CentOS Linux"

VERSION="7 (Core)"

ID="centos"

ID_LIKE="rhel fedora"

VERSION_ID="7"

PRETTY_NAME="CentOS Linux 7 (Core)"

ANSI_COLOR="0;31"

CPE_NAME="cpe:/o:centos:centos:7"

HOME_URL="https://www.centos.org/"

BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"

CENTOS_MANTISBT_PROJECT_VERSION="7"

REDHAT_SUPPORT_PRODUCT="centos"

REDHAT_SUPPORT_PRODUCT_VERSION="7"

-- Build files have been written to: /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build

[ 82%] Performing forcebuild step for 'ANTS'

[ 88%] Performing build step for 'ANTS' make[4]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[5]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[6]: Entering directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' Scanning dependencies of target antsUtilities make[6]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[6]: Entering directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' [ 1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o [ 2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistrationTemplateHeader.cxx.o [ 3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DDouble.cxx.o [ 4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DFloat.cxx.o [ 5%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DDouble.cxx.o [ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o [ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o [ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o [ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir//Utilities/ReadWriteData.cxx.o [ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir//Utilities/antsCommandLineOption.cxx.o [ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o [ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_MAJOR; ^~

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_MINOR; ^~

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:

/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive] return ANTS_VERSION_PATCH; ^~ make[6]: [Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: Waiting for unfinished jobs.... make[6]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[5]: *** [Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[4]: [all] Error 2 make[4]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build' make[3]: [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make[2]: *** [CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory /tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make[1]: [all] Error 2 make[1]: Leaving directory `/tmp/RtmpbO9ECw/devtools78fb3596c6ea/ANTsX-ANTsRCore-ac85804/src/antb' make: [libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’

  • restoring previous ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’ Installation failed: Command failed (1) '/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL '/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959' \ --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

  • installing source package ‘ANTsR’ ... linux-gnu 0 ** libs g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpbO9ECw/devtools78fb8eac4b/ANTsX-ANTsR-c9fe959/src -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/ -I../inst/include/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include" -I/usr/local/include -fpic -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o In file included from /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0, from CreateJacobianDeterminantImage.cpp:8:

/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:10: fatal error: itkVectorCastImageFilter.h: No such file or directory

include "itkVectorCastImageFilter.h"

^~~~~~~~ compilation terminated. make: *** [CreateJacobianDeterminantImage.o] Error 1 ERROR: compilation failed for package ‘ANTsR’

  • removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR’ Installation failed: Command failed (1)

    devtools::session_info() Session info ------------------------------------------------------------ setting value version R version 3.5.0 (2018-04-23) system x86_64, linux-gnu ui RStudio (1.1.456) language (EN) collate en_US.UTF-8 tz America/New_York date 2019-10-19

Packages ---------------------------------------------------------------- package version date source base 3.5.0 2018-05-13 local compiler 3.5.0 2018-05-13 local curl 3.3 2019-01-10 cran (@3.3) datasets 3.5.0 2018-05-13 local devtools 1.13.5 2018-02-18 CRAN (R 3.5.0) digest 0.6.18 2018-10-10 cran (@0.6.18) git2r 0.21.0 2018-01-04 CRAN (R 3.5.0) graphics 3.5.0 2018-05-13 local grDevices 3.5.0 2018-05-13 local httr 1.3.1 2017-08-20 CRAN (R 3.5.0) knitr 1.20 2018-02-20 cran (@1.20) memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) methods 3.5.0 2018-05-13 local R6 2.4.0 2019-02-14 cran (@2.4.0) stats 3.5.0 2018-05-13 local tools 3.5.0 2018-05-13 local utils 3.5.0 2018-05-13 local withr 2.1.2 2018-03-15 CRAN (R 3.5.0) yaml 2.1.19 2018-05-01 cran (@2.1.19)

On a docker container using a debian:

PRETTY_NAME="Debian GNU/Linux bullseye/sid"

NAME="Debian GNU/Linux"

ID=debian

HOME_URL="https://www.debian.org/"

SUPPORT_URL="https://www.debian.org/support"

BUG_REPORT_URL="https://bugs.debian.org/"

[ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o

[ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o

[ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o

[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o

[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o

[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o

[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

43 | return ANTS_VERSION_MAJOR;

| ^~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

47 | return ANTS_VERSION_MINOR;

| ^~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

51 | return ANTS_VERSION_PATCH;

| ^~ make[6]: [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: Waiting for unfinished jobs.... make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[5]: [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[4]: [Makefile:163: all] Error 2 make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[3]: [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[2]: [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[1]: [Makefile:117: all] Error 2 make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make: [Makevars:12: libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/usr/local/lib/R/site-library/ANTsRCore’ Error: Failed to install 'ANTsR' from GitHub:

Failed to install 'ANTsRCore' from GitHub:

(converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status

[ 6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o

[ 7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o

[ 8%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o

[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o

[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o

[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o

[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

43 | return ANTS_VERSION_MAJOR;

| ^~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

47 | return ANTS_VERSION_MINOR;

| ^~

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:

/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]

51 | return ANTS_VERSION_PATCH;

| ^~ make[6]: [Examples/CMakeFiles/antsUtilities.dir/build.make:206: Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1 make[6]: Waiting for unfinished jobs.... make[6]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[5]: [CMakeFiles/Makefile2:876: Examples/CMakeFiles/antsUtilities.dir/all] Error 2 make[5]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[4]: [Makefile:163: all] Error 2 make[4]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb/ANTS-build' make[3]: [CMakeFiles/ANTS.dir/build.make:114: ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2 make[3]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[2]: [CMakeFiles/Makefile2:73: CMakeFiles/ANTS.dir/all] Error 2 make[2]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make[1]: [Makefile:117: all] Error 2 make[1]: Leaving directory '/tmp/RtmpqSGzYA/R.INSTALLc10a6fb5ab39/ANTsRCore/src/antb' make: [Makevars:12: libs] Error 2 ERROR: compilation failed for package ‘ANTsRCore’

  • removing ‘/usr/local/lib/R/site-library/ANTsRCore’ Error: Failed to install 'ANTsR' from GitHub:

Failed to install 'ANTsRCore' from GitHub:

(converted from warning) installation of package ‘/tmp/RtmpJA9HIB/file21e2fa12309/ANTsRCore_0.7.1.tar.gz’ had non-zero exit status

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brian

SlicerMorph commented 4 years ago

So just for clarification gcc>=5 is a requirement for all ANTsX ecosystem, not just for ANTs?

dorianps commented 4 years ago

Not sure if the merge has propagated properly (or where to look for the tag), but the error for me is still the same. Here is the full log.

> devtools::install_github('ANTsX/ANTsR')
Downloading GitHub repo ANTsX/ANTsR@master
from URL https://api.github.com/repos/ANTsX/ANTsR/zipball/master
Installing ANTsR
Downloading GitHub repo ANTsX/ANTsRCore@master
from URL https://api.github.com/repos/ANTsX/ANTsRCore/zipball/master
Installing ANTsRCore
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

* installing *source* package ‘ANTsRCore’ ...
linux-gnu 0
fatal: not a git repository (or any of the parent directories): .git
Cloning into 'ants'...
remote: Enumerating objects: 148, done.
remote: Counting objects: 100% (148/148), done.
remote: Compressing objects: 100% (116/116), done.
remote: Total 23666 (delta 53), reused 75 (delta 32), pack-reused 23518
Receiving objects: 100% (23666/23666), 20.34 MiB | 4.71 MiB/s, done.
Resolving deltas: 100% (16708/16708), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
Already up to date.
Note: checking out '7ea9f7441bf2415478814fa0ff4e47941e68fd03'.

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 7ea9f744 Merge pull request #875 from gdevenyi/verbose_ninja
-- The C compiler identification is GNU 7.3.1
-- The CXX compiler identification is GNU 7.3.1
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-7/root/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: /opt/rh/devtoolset-7/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- 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 C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Performing Test have_gold
-- Performing Test have_gold - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /usr/local/bin/git (found version "2.18.0")
-- SuperBuild - ANTS => Requires ITKv5,
-- SuperBuild -   ITKv5[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    COPY_SCRIPT_FILES_TO_BIN_DIR

-- Build files have been written to: /tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageArith.cpp -o antsImageArith.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageClone.cpp -o antsImageClone.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageComparison.cpp -o antsImageComparison.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageHeaderInfo.cpp -o antsImageHeaderInfo.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageIterator.cpp -o antsImageIterator.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageLogic.cpp -o antsImageLogic.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMath.cpp -o antsImageMath.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMutualInformation.cpp -o antsImageMutualInformation.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageRead.cpp -o antsImageRead.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageStats.cpp -o antsImageStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageWrite.cpp -o antsImageWrite.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsJointFusion.cpp -o antsJointFusion.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsMatrix.cpp -o antsMatrix.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsRegistration.cpp -o antsRegistration.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrMetric.cpp -o antsrMetric.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform1.cpp -o antsrTransform1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform2.cpp -o antsrTransform2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c cropImage.cpp -o cropImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface.cpp -o iMathInterface.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface1.cpp -o iMathInterface1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface2.cpp -o iMathInterface2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c imagesToMatrix.cpp -o imagesToMatrix.o
gcc -std=gnu99 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c labelStats.cpp -o labelStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c makeImage.cpp -o makeImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c mergeChannels.cpp -o mergeChannels.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c patchAnalysis.cpp -o patchAnalysis.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c smoothImage.cpp -o smoothImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Utilities -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c splitChannels.cpp -o splitChannels.o
cd /tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb && make -j 2 &&  cd /tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build && make all install && rm -rf /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/libs/bin && cd /tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src
make[1]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[2]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[3]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
Scanning dependencies of target ITKv5
make[3]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[3]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
[  5%] Creating directories for 'ITKv5'
[ 11%] No download step for 'ITKv5'
[ 17%] No patch step for 'ITKv5'
[ 23%] No update step for 'ITKv5'
[ 29%] No configure step for 'ITKv5'
[ 35%] No build step for 'ITKv5'
[ 41%] No install step for 'ITKv5'
[ 47%] Completed 'ITKv5'
make[3]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
[ 47%] Built target ITKv5
make[3]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
Scanning dependencies of target ANTS
make[3]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[3]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
[ 52%] Creating directories for 'ANTS'
[ 58%] No download step for 'ANTS'
[ 64%] No patch step for 'ANTS'
[ 70%] No update step for 'ANTS'
[ 76%] Performing configure step for 'ANTS'
Not searching for unused variables given on the command line.
-- The CXX compiler identification is GNU 7.3.1
-- The C compiler identification is GNU 7.3.1
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- 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 C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Performing Test have_gold
-- Performing Test have_gold - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Building ANTS version ""
-- antsAffineInitializer
-- antsJointFusion
-- DenoiseImage
-- SurfaceBasedSmoothing
-- ThresholdImage
-- ResampleImage
-- sccan
-- N4BiasFieldCorrection
-- N3BiasFieldCorrection
-- KellyKapowski
-- antsRegistration
-- antsMotionCorrStats
-- antsMotionCorr
-- antsApplyTransforms
-- LabelGeometryMeasures
-- LabelClustersUniquely
-- Atropos
-- antsApplyTransformsToPoints
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build
[ 82%] Performing forcebuild step for 'ANTS'
[ 88%] Performing build step for 'ANTS'
make[4]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[5]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
Scanning dependencies of target antsUtilities
make[6]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
[  1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistrationTemplateHeader.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DDouble.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DFloat.cxx.o

[  5%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DDouble.cxx.o
[  6%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o
[  7%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o
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[ 10%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o
[ 11%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o
[ 12%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o
[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:43:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MAJOR;
     ^~~~~~
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:47:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MINOR;
     ^~~~~~
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:
/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/ants/Examples/ANTsVersion.cxx:51:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_PATCH;
     ^~~~~~
make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[5]: *** [Examples/CMakeFiles/antsUtilities.dir/all] Error 2
make[5]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb/ANTS-build'
make[3]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
make[3]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[2]: *** [CMakeFiles/ANTS.dir/all] Error 2
make[2]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/tmp/RtmpGGgQKP/devtools7da022665166/ANTsX-ANTsRCore-ac85804/src/antb'
make: *** [libs] Error 2
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
* restoring previous ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
Installation failed: Command failed (1)
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpGGgQKP/devtools7da04fb2ac4a/ANTsX-ANTsR-c9fe959'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

* installing *source* package ‘ANTsR’ ...
linux-gnu 0
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpGGgQKP/devtools7da04fb2ac4a/ANTsX-ANTsR-c9fe959/src    -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/   -I../inst/include/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include" -I/usr/local/include   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
In file included from /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0,
                 from CreateJacobianDeterminantImage.cpp:8:
/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:10: fatal error: itkVectorCastImageFilter.h: No such file or directory
 #include "itkVectorCastImageFilter.h"
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package ‘ANTsR’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR’
Installation failed: Command failed (1)
gdevenyi commented 4 years ago

Antsr core has an old ants version hard coded antstag=7ea9f7441bf2415478814fa0ff4e47941e68fd03

stnava commented 4 years ago

Correct, I have not updated the tag yet, pull request welcome

On Sun, Oct 20, 2019 at 5:03 PM Gabriel A. Devenyi notifications@github.com wrote:

Antsr core has an old ants version hard coded antstag=7ea9f7441bf2415478814fa0ff4e47941e68fd03

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/282?email_source=notifications&email_token=AACPE7TAMAIMAXNN45SQQJ3QPTBRZA5CNFSM4I7F6UMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBYT4HA#issuecomment-544292380, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACPE7XYMAK7O3JMT5BOUK3QPTBRZANCNFSM4I7F6UMA .

--

brian

dorianps commented 4 years ago

The tag is ok now:

Note: checking out 'ea8af5f2bc2bd5eaef9f6e944bf76c76bf29e62d'.

but the error persists.

Not sure if this means anything, but the build log shows an empty ANTs version, too:

-- Building ANTS version ""

Full log here:

> devtools::install_github('ANTsX/ANTsR')
Downloading GitHub repo ANTsX/ANTsR@master
from URL https://api.github.com/repos/ANTsX/ANTsR/zipball/master
Installing ANTsR
Downloading GitHub repo ANTsX/ANTsRCore@master
from URL https://api.github.com/repos/ANTsX/ANTsRCore/zipball/master
Installing ANTsRCore
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

* installing *source* package ‘ANTsRCore’ ...
linux-gnu 0
fatal: not a git repository (or any of the parent directories): .git
Cloning into 'ants'...
remote: Enumerating objects: 148, done.
remote: Counting objects: 100% (148/148), done.
remote: Compressing objects: 100% (116/116), done.
remote: Total 23666 (delta 53), reused 75 (delta 32), pack-reused 23518
Receiving objects: 100% (23666/23666), 20.34 MiB | 5.64 MiB/s, done.
Resolving deltas: 100% (16708/16708), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
Already up to date.
Note: checking out 'ea8af5f2bc2bd5eaef9f6e944bf76c76bf29e62d'.

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 ea8af5f2 WIP: try to resolve undefined version issues
-- The C compiler identification is GNU 7.3.1
-- The CXX compiler identification is GNU 7.3.1
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-7/root/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: /opt/rh/devtoolset-7/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- 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 C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Performing Test have_gold
-- Performing Test have_gold - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Found Git: /usr/local/bin/git (found version "2.18.0")
-- SuperBuild - ANTS => Requires ITKv5,
-- SuperBuild -   ITKv5[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    COPY_SCRIPT_FILES_TO_BIN_DIR

-- Build files have been written to: /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageArith.cpp -o antsImageArith.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageClone.cpp -o antsImageClone.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageComparison.cpp -o antsImageComparison.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageHeaderInfo.cpp -o antsImageHeaderInfo.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageIterator.cpp -o antsImageIterator.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageLogic.cpp -o antsImageLogic.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMath.cpp -o antsImageMath.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMutualInformation.cpp -o antsImageMutualInformation.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageRead.cpp -o antsImageRead.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageStats.cpp -o antsImageStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageWrite.cpp -o antsImageWrite.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsJointFusion.cpp -o antsJointFusion.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsMatrix.cpp -o antsMatrix.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsRegistration.cpp -o antsRegistration.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrMetric.cpp -o antsrMetric.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform1.cpp -o antsrTransform1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform2.cpp -o antsrTransform2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c cropImage.cpp -o cropImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface.cpp -o iMathInterface.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface1.cpp -o iMathInterface1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface2.cpp -o iMathInterface2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c imagesToMatrix.cpp -o imagesToMatrix.o
gcc -std=gnu99 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c labelStats.cpp -o labelStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c makeImage.cpp -o makeImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c mergeChannels.cpp -o mergeChannels.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c patchAnalysis.cpp -o patchAnalysis.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c smoothImage.cpp -o smoothImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c splitChannels.cpp -o splitChannels.o
cd /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb && make -j 2 &&  cd /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build && make all install && rm -rf /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/libs/bin && cd /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src
make[1]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make[2]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make[3]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
Scanning dependencies of target ITKv5
make[3]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make[3]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
[  5%] Creating directories for 'ITKv5'
[ 11%] No download step for 'ITKv5'
[ 17%] No patch step for 'ITKv5'
[ 23%] No update step for 'ITKv5'
[ 29%] No configure step for 'ITKv5'
[ 35%] No build step for 'ITKv5'
[ 41%] No install step for 'ITKv5'
[ 47%] Completed 'ITKv5'
make[3]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
[ 47%] Built target ITKv5
make[3]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
Scanning dependencies of target ANTS
make[3]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make[3]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
[ 52%] Creating directories for 'ANTS'
[ 58%] No download step for 'ANTS'
[ 64%] No patch step for 'ANTS'
[ 70%] No update step for 'ANTS'
[ 76%] Performing configure step for 'ANTS'
Not searching for unused variables given on the command line.
-- The CXX compiler identification is GNU 7.3.1
-- The C compiler identification is GNU 7.3.1
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- 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 C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Performing Test have_gold
-- Performing Test have_gold - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
-- Building ANTS version ""
-- antsAffineInitializer
-- antsJointFusion
-- DenoiseImage
-- SurfaceBasedSmoothing
-- ThresholdImage
-- ResampleImage
-- sccan
-- N4BiasFieldCorrection
-- N3BiasFieldCorrection
-- KellyKapowski
-- antsRegistration
-- antsMotionCorrStats
-- antsMotionCorr
-- antsApplyTransforms
-- LabelGeometryMeasures
-- LabelClustersUniquely
-- Atropos
-- antsApplyTransformsToPoints
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build
[ 82%] Performing forcebuild step for 'ANTS'
[ 88%] Performing build step for 'ANTS'
make[4]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
make[5]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
Scanning dependencies of target antsUtilities
make[6]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
make[6]: Entering directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
[  1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o
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[ 13%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MajorVersion()’:
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx:53:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MAJOR;
     ^~~~~~
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::MinorVersion()’:
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx:57:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_MINOR;
     ^~~~~~
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx: In static member function ‘static unsigned int ANTs::Version::PatchVersion()’:
/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ANTsVersion.cxx:61:5: error: return-statement with no value, in function returning ‘unsigned int’ [-fpermissive]
     return ANTS_VERSION_PATCH;
     ^~~~~~
make[6]: *** [Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
make[5]: *** [Examples/CMakeFiles/antsUtilities.dir/all] Error 2
make[5]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb/ANTS-build'
make[4]: *** [all] Error 2
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make[3]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
make[3]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make[2]: *** [CMakeFiles/ANTS.dir/all] Error 2
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make[1]: *** [all] Error 2
make[1]: Leaving directory `/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb'
make: *** [libs] Error 2
ERROR: compilation failed for package ‘ANTsRCore’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
* restoring previous ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore’
Installation failed: Command failed (1)
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpdKbqoS/devtoolsac1570d1a34e/ANTsX-ANTsR-c9fe959'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

* installing *source* package ‘ANTsR’ ...
linux-gnu 0
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac1570d1a34e/ANTsX-ANTsR-c9fe959/src    -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/   -I../inst/include/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include" -I/usr/local/include   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
In file included from /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0,
                 from CreateJacobianDeterminantImage.cpp:8:
/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:10: fatal error: itkVectorCastImageFilter.h: No such file or directory
 #include "itkVectorCastImageFilter.h"
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package ‘ANTsR’
* removing ‘/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR’
Installation failed: Command failed (1)
stnava commented 4 years ago

Need to make antsrcore release before change propagates to antsr.

On Sun, Oct 20, 2019 at 8:56 PM dorianps notifications@github.com wrote:

The tag is ok now:

Note: checking out 'ea8af5f2bc2bd5eaef9f6e944bf76c76bf29e62d'.

but the error persists.

Not sure if this means anything, but the build log shows an empty ANTs version, too:

-- Building ANTS version ""

Full log here:

devtools::install_github('ANTsX/ANTsR') Downloading GitHub repo ANTsX/ANTsR@master from URL https://api.github.com/repos/ANTsX/ANTsR/zipball/master Installing ANTsR Downloading GitHub repo ANTsX/ANTsRCore@master from URL https://api.github.com/repos/ANTsX/ANTsRCore/zipball/master Installing ANTsRCore '/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save \

--no-restore --quiet CMD INSTALL \

'/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200' \

--library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests

  • installing source package ‘ANTsRCore’ ... linux-gnu 0 fatal: not a git repository (or any of the parent directories): .git Cloning into 'ants'... remote: Enumerating objects: 148, done. remote: Counting objects: 100% (148/148), done. remote: Compressing objects: 100% (116/116), done. remote: Total 23666 (delta 53), reused 75 (delta 32), pack-reused 23518 Receiving objects: 100% (23666/23666), 20.34 MiB | 5.64 MiB/s, done. Resolving deltas: 100% (16708/16708), done. Already on 'master' Your branch is up to date with 'origin/master'. Already up to date. Note: checking out 'ea8af5f2bc2bd5eaef9f6e944bf76c76bf29e62d'.

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 ea8af5f2 WIP: try to resolve undefined version issues

-- The C compiler identification is GNU 7.3.1 -- The CXX compiler identification is GNU 7.3.1 -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- Check for working C compiler: /opt/rh/devtoolset-7/root/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: /opt/rh/devtoolset-7/root/usr/bin/c++ -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Not using CCache -- 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-Wno-long-double -- Performing Test C_HAS_WARNING-Wno-long-double - Failed -- 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-Wno-long-double -- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed -- 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-Wno-undefined-var-template -- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed -- 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 C_HAS_WARNING-mtune_native -- Performing Test C_HAS_WARNING-mtune_native - Success -- Performing Test C_HAS_WARNING-march_corei7 -- Performing Test C_HAS_WARNING-march_corei7 - Success -- Performing Test CXX_HAS_WARNING-mtune_native -- Performing Test CXX_HAS_WARNING-mtune_native - Success -- Performing Test CXX_HAS_WARNING-march_corei7 -- Performing Test CXX_HAS_WARNING-march_corei7 - Success -- Performing Test have_gold -- Performing Test have_gold - Success -- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG -- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed -- Found Git: /usr/local/bin/git (found version "2.18.0") -- SuperBuild - ANTS => Requires ITKv5, -- SuperBuild - ITKv5[OK] -- SuperBuild - ANTS[OK] -- Configuring done -- Generating done CMake Warning:

Manually-specified variables were not used by the project:

COPY_SCRIPT_FILES_TO_BIN_DIR

-- Build files have been written to: /tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/antb ** libs g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c Atropos.cpp -o Atropos.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c antsImage.cpp -o antsImage.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Utilities -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Examples/ -I../inst/include/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore-9318200/src/ants/Tensor/ -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include -fpic -g -O2 -c antsImageArith.cpp -o antsImageArith.o g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpdKbqoS/devtoolsac154f1a17ed/ANTsX-ANTsRCore

--

brian

stnava commented 4 years ago

@gdevenyi do you know the minimum gcc requirements?

gdevenyi commented 4 years ago

Travis currently passes with >gcc5, but @nutusion did a bunch of c++ warnings and fixes so I was going to re add earlier 4.x serious in a Travis PR today to see if anything passes

gdevenyi commented 4 years ago

'>=gcc5'

muschellij2 commented 4 years ago

I believe I saw a GCc requirement of 5 in the cmake lists

On Mon, Oct 21, 2019 at 8:11 AM Gabriel A. Devenyi notifications@github.com wrote:

=gcc5

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gdevenyi commented 4 years ago

@muschellij2 yes, we added a >=gcc5 requirement to avoid complaints of compilation failures. I'm going to do some checks now to see if we incidentally fixed it.

muschellij2 commented 4 years ago

It'd be helpful if you could allow gcc 4.9 for trying Windows builds with R toolchain (https://cran.r-project.org/bin/windows/Rtools/) which has gcc 4.9.3.

On Mon, Oct 21, 2019 at 10:31 AM Gabriel A. Devenyi < notifications@github.com> wrote:

@muschellij2 https://github.com/muschellij2 yes, we added a >=gcc5 requirement to avoid complaints of compilation failures. I'm going to do some checks now to see if we incidentally fixed it.

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dorianps commented 4 years ago

What's the plan with ANTsRCore, does someone need to make a release or are we waiting for ANTs changes as well?

Dorian

On Mon, Oct 21, 2019, 12:03 PM John Muschelli notifications@github.com wrote:

It'd be helpful if you could allow gcc 4.9 for trying Windows builds with R toolchain (https://cran.r-project.org/bin/windows/Rtools/) which has gcc 4.9.3.

On Mon, Oct 21, 2019 at 10:31 AM Gabriel A. Devenyi < notifications@github.com> wrote:

@muschellij2 https://github.com/muschellij2 yes, we added a >=gcc5 requirement to avoid complaints of compilation failures. I'm going to do some checks now to see if we incidentally fixed it.

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gdevenyi commented 4 years ago

Initial tests indicate that we can build again on 4.8: https://travis-ci.org/ANTsX/ANTs/jobs/600796948

I can no longer find a packaged version of gcc-4.9 on ubuntu bionic though, so I can't test on travis.

stnava commented 4 years ago

I made a release and tested via remotes::... and no luck - need a way to reproduce the error locally / trying another approach.

muschellij2 commented 4 years ago

Does "no luck" mean you cannot install or you cannot reproduce the error and can install Best, John

On Mon, Oct 21, 2019 at 1:51 PM stnava notifications@github.com wrote:

I made a release and tested via remotes::... and no luck - need a way to reproduce the error locally / trying another approach.

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stnava commented 4 years ago

I cannot reproduce the error So should have a real fix soon

On Mon, Oct 21, 2019 at 2:33 PM John Muschelli notifications@github.com wrote:

Does "no luck" mean you cannot install or you cannot reproduce the error and can install Best, John

On Mon, Oct 21, 2019 at 1:51 PM stnava notifications@github.com wrote:

I made a release and tested via remotes::... and no luck - need a way to reproduce the error locally / trying another approach.

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brian

stnava commented 4 years ago

Meant can reproduce

On Mon, Oct 21, 2019 at 2:41 PM brian avants stnava@gmail.com wrote:

I cannot reproduce the error So should have a real fix soon

On Mon, Oct 21, 2019 at 2:33 PM John Muschelli notifications@github.com wrote:

Does "no luck" mean you cannot install or you cannot reproduce the error and can install Best, John

On Mon, Oct 21, 2019 at 1:51 PM stnava notifications@github.com wrote:

I made a release and tested via remotes::... and no luck - need a way to reproduce the error locally / trying another approach.

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--

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--

brian

stnava commented 4 years ago

just pushed a commit - I am short on time but need to propagate to ANTsRCore + test etc.

stnava commented 4 years ago

possible this is fixed now.

dorianps commented 4 years ago

Success now, but with gcc 7.3.1, not with gcc < 5 due to this error

CMake Error at CMake/ITKSetStandardCompilerFlags.cmake:330 (message):
  Minimum GCC version is 5.0

likely coming from here

Fail log for ANTsRCore with gcc 4.8.5

installing to /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ITKR)
Downloading GitHub repo ANTsX/ANTsRCore@master
from URL https://api.github.com/repos/ANTsX/ANTsRCore/zipball/master
Installing ANTsRCore
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests 

* installing *source* package ?ANTsRCore? ...
linux-gnu 0
fatal: not a git repository (or any of the parent directories): .git
Cloning into 'ants'...
Already on 'master'
Your branch is up to date with 'origin/master'.
Already up to date.
Note: checking out '1c421a5853f343a020aaae861a751545112e0807'.

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 1c421a58 BUG: setting a default 0 0 0 version when version undefined.
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- 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
-- Not using CCache
-- 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-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- 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-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- 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 C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
CMake Error at CMake/ITKSetStandardCompilerFlags.cmake:330 (message):
  Minimum GCC version is 5.0
Call Stack (most recent call first):
  CMake/ITKSetStandardCompilerFlags.cmake:471 (check_compiler_platform_flags)
  Common.cmake:111 (include)
  SuperBuild.cmake:15 (include)
  CMakeLists.txt:67 (include)

-- Configuring incomplete, errors occurred!
See also "/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb/CMakeFiles/CMakeOutput.log".
See also "/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb/CMakeFiles/CMakeError.log".
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c Atropos.cpp -o Atropos.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c DenoiseImage.cpp -o DenoiseImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c LabelClustersUniquely.cpp -o LabelClustersUniquely.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N3BiasFieldCorrection.cpp -o N3BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c N4BiasFieldCorrection.cpp -o N4BiasFieldCorrection.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c ThresholdImage.cpp -o ThresholdImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransforms.cpp -o antsApplyTransforms.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsApplyTransformsToPoints.cpp -o antsApplyTransformsToPoints.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImage.cpp -o antsImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageArith.cpp -o antsImageArith.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageClone.cpp -o antsImageClone.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageComparison.cpp -o antsImageComparison.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageHeaderInfo.cpp -o antsImageHeaderInfo.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageIterator.cpp -o antsImageIterator.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageLogic.cpp -o antsImageLogic.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMath.cpp -o antsImageMath.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageMutualInformation.cpp -o antsImageMutualInformation.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageRead.cpp -o antsImageRead.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageStats.cpp -o antsImageStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsImageWrite.cpp -o antsImageWrite.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsJointFusion.cpp -o antsJointFusion.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsMatrix.cpp -o antsMatrix.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsRegistration.cpp -o antsRegistration.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrMetric.cpp -o antsrMetric.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform1.cpp -o antsrTransform1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c antsrTransform2.cpp -o antsrTransform2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c cropImage.cpp -o cropImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface.cpp -o iMathInterface.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface1.cpp -o iMathInterface1.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c iMathInterface2.cpp -o iMathInterface2.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c imagesToMatrix.cpp -o imagesToMatrix.o
gcc -std=gnu99 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c labelStats.cpp -o labelStats.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c makeImage.cpp -o makeImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c mergeChannels.cpp -o mergeChannels.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c patchAnalysis.cpp -o patchAnalysis.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c smoothImage.cpp -o smoothImage.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Utilities -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Examples/ -I../inst/include/   -I/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/ants/Tensor/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I/usr/local/include   -fpic  -g -O2 -c splitChannels.cpp -o splitChannels.o
cd /tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb && make -j 2 &&  cd /tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb/ANTS-build && make all install && rm -rf /home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore/libs/bin && cd /tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src
make[1]: Entering directory `/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb'
make[1]: Leaving directory `/tmp/RtmpCfz6VL/devtools3a0279853652/ANTsX-ANTsRCore-6464142/src/antb'
make[1]: *** No targets specified and no makefile found.  Stop.
make: *** [libs] Error 2
ERROR: compilation failed for package ?ANTsRCore?
* removing ?/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsRCore?
Installation failed: Command failed (1)
'/opt/R/3.5.0/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpCfz6VL/devtools3a023d5a372a/ANTsX-ANTsR-c9fe959'  \
  --library='/home/dorian/R/x86_64-pc-linux-gnu-library/3.5' --install-tests 

* installing *source* package ?ANTsR? ...
linux-gnu 0
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib64/R/include" -DNDEBUG -I/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/libs/include/ITK-5.1/ -I/tmp/RtmpCfz6VL/devtools3a023d5a372a/ANTsX-ANTsR-c9fe959/src    -I/home/APPS/R/3.5.0/lib64/R/library/ANTsRCore/include/   -I../inst/include/  -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ITKR/include" -I"/home/APPS/R/3.5.0/lib64/R/library/ANTsRCore/include" -I/usr/local/include   -fpic  -g -O2 -c CreateJacobianDeterminantImage.cpp -o CreateJacobianDeterminantImage.o
In file included from /home/APPS/R/3.5.0/lib64/R/library/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.h:156:0,
                 from CreateJacobianDeterminantImage.cpp:8:
/home/APPS/R/3.5.0/lib64/R/library/ANTsRCore/include/itkDeformationFieldGradientTensorImageFilter.hxx:21:38: fatal error: itkVectorCastImageFilter.h: No such file or directory
 #include "itkVectorCastImageFilter.h"
                                      ^
compilation terminated.
make: *** [CreateJacobianDeterminantImage.o] Error 1
ERROR: compilation failed for package ?ANTsR?
* removing ?/home/dorian/R/x86_64-pc-linux-gnu-library/3.5/ANTsR?
Installation failed: Command failed (1)
gdevenyi commented 4 years ago

My PR has not been merged yet, waiting for tests https://github.com/ANTsX/ANTs/pull/889

dorianps commented 4 years ago

Ok, thanks. I can test again later with gcc 4.8.5. I am getting some weird segfaults with antsAverageImages, but that might be from other reasons. antsImageRead works though. Will check the version installed with gcc 4.8.5 later.

dorianps commented 4 years ago

Tests are still running for OSx but Linux is finally done and all is green, including gcc 4.8: https://travis-ci.org/ANTsX/ANTs/builds/600949333

Shall we merge https://github.com/ANTsX/ANTs/pull/889 so we can can give it a try?

I am looking to see if using the old gcc 4.8 without devtoolset will fix the segfaults.

gdevenyi commented 4 years ago

I want to see https://travis-ci.org/ANTsX/ANTs/jobs/600949347 first.

dorianps commented 4 years ago

Fyi, I reinstalled all three (ITKR, ANTsRCore, ANTsR) and don't see segfaults anymore. Current ANTsR is at 0.5.4, bumped in the last two days from 0.5.1. Nothing changed on my machine, so not sure why I was getting segfaults when calling antsAverageImages before (one possibility is hard drive errors which has been giving problems before). Current working installation used gcc 7.3.1.

gdevenyi commented 4 years ago

Fixes are likely due to @ntustison 's work on my "gcc9 warn everything" reports, since that also fixed the compile failures on gcc4.8.