* installing *source* package ‘divest’ ...
** package ‘divest’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... yes
checking for /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 option to enable C++11 features... none needed
checking for pkg-config... /usr/bin/pkg-config
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for fmemopen... yes
configure: Using OpenJPEG for JPEG2000 support
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/divest/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c main.cpp -o main.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dcm2niix/nifti1_io_core.cpp -o dcm2niix/nifti1_io_core.o
In file included from dcm2niix/nifti1_io_core.cpp:18:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/RNifti.h:43:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/niftilib/nifti1_io.h:24:
/data/gannet/ripley/R/test-clang/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
6 | #define R_NO_REMAP
| ^
<command line>:5:9: note: previous definition is here
5 | #define R_NO_REMAP 1
| ^
In file included from main.cpp:3:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/RNifti.h:43:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/niftilib/nifti1_io.h:24:
/data/gannet/ripley/R/test-clang/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
6 | #define R_NO_REMAP
| ^
<command line>:5:9: note: previous definition is here
5 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dcm2niix/nii_dicom.cpp -o dcm2niix/nii_dicom.o
In file included from dcm2niix/nii_dicom.cpp:27:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/RNifti.h:43:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/niftilib/nifti1_io.h:24:
/data/gannet/ripley/R/test-clang/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
6 | #define R_NO_REMAP
| ^
<command line>:5:9: note: previous definition is here
5 | #define R_NO_REMAP 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dcm2niix/nii_ortho.cpp -o dcm2niix/nii_ortho.o
In file included from dcm2niix/nii_ortho.cpp:4:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/RNifti.h:43:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/niftilib/nifti1_io.h:24:
/data/gannet/ripley/R/test-clang/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
6 | #define R_NO_REMAP
| ^
<command line>:5:9: note: previous definition is here
5 | #define R_NO_REMAP 1
| ^
In file included from dcm2niix/nii_dicom_batch.cpp:30:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/RNifti.h:43:
In file included from /data/gannet/ripley/R/test-clang/RNifti/include/niftilib/nifti1_io.h:24:
/data/gannet/ripley/R/test-clang/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
6 | #define R_NO_REMAP
| ^
<command line>:5:9: note: previous definition is here
5 | #define R_NO_REMAP 1
| ^
dcm2niix/nii_dicom.cpp:1922:6: warning: variable 'patientPositionNumPhilips' set but not used [-Wunused-but-set-variable]
1922 | int patientPositionNumPhilips = 0;
| ^
dcm2niix/nii_dicom.cpp:4876:12: warning: unused variable 'realGroupElement' [-Wunused-variable]
4876 | uint32_t realGroupElement = groupElement;
| ^~~~~~~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp:2727:7: warning: variable 'isIsotropic' set but not used [-Wunused-but-set-variable]
2727 | bool isIsotropic = false;
| ^
dcm2niix/nii_dicom_batch.cpp:3485:13: warning: unused variable 'kTempPathSeparator' [-Wunused-variable]
3485 | const char kTempPathSeparator = '\a';
| ^~~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp:3486:7: warning: unused variable 'hasCaret' [-Wunused-variable]
3486 | bool hasCaret = false;
| ^~~~~~~~
dcm2niix/nii_dicom_batch.cpp:6833:9: warning: unused variable 'pf' [-Wunused-variable]
6833 | float pf = 1.0f; // partial fourier
| ^~
dcm2niix/nii_dicom_batch.cpp:7118:7: warning: variable 'isDirLabel' set but not used [-Wunused-but-set-variable]
7118 | bool isDirLabel = false; // report phase encoding direction
| ^
dcm2niix/nii_dicom_batch.cpp:7296:6: warning: variable 'nVol' set but not used [-Wunused-but-set-variable]
7296 | int nVol = 1;
| ^
dcm2niix/nii_dicom_batch.cpp:8267:11: warning: variable 'slicePositionRepeats' set but not used [-Wunused-but-set-variable]
8267 | int slicePositionRepeats = 1; // how many times is first position repeated
| ^
dcm2niix/nii_dicom_batch.cpp:8566:10: warning: unused variable 'shearMat' [-Wunused-variable]
8566 | mat33 shearMat;
| ^~~~~~~~
1 warning generated.
9 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.4 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RNifti/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o divest.so main.o dcm2niix/jpg_0XC3.o dcm2niix/nifti1_io_core.o dcm2niix/nii_dicom.o dcm2niix/nii_dicom_batch.o dcm2niix/nii_ortho.o ujpeg/ujpeg.o -lopenjp2
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/divest/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/divest/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/divest/src'
installing to /data/gannet/ripley/R/packages/tests-clang/divest.Rcheck/00LOCK-divest/00new/divest/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (divest)