* installing *source* package ‘divest’ ...
** this is package ‘divest’ version ‘1.2.0’
** 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 clang++ -arch arm64 -std=gnu++20 accepts -g... yes
checking for clang++ -arch arm64 -std=gnu++20 option to enable C++11 features... -std=gnu++11
checking for pkg-config... /opt/R/arm64/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: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dcm2niix/nifti1_io_core.cpp -o dcm2niix/nifti1_io_core.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dcm2niix/nii_dicom.cpp -o dcm2niix/nii_dicom.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dcm2niix/nii_ortho.cpp -o dcm2niix/nii_ortho.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/opt/R/arm64/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o
In file included from dcm2niix/nii_ortho.cpp:4:
In file included from dcm2niix/nifti1_io_core.hIn file included from dcm2niix/nii_dicom_batch.cpp:30:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
:9:
153 | void minmax (vIn file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153oid *ptr:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
, con 153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNst size_t lengthaN = true, double *min, dou)
| ^
ble *max, co/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
nst bool dropNaN 207 | case DT_COMPLEX64: return new = true)
| ^
ConcreteTyp/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: eHandlein instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
207 | case DT_COMPLEr<complexX64: return64_t>(); new Concre break;
teTypeHandler<comp| ^
lex64_t>(); /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | 89 | virtual void minm virtual ax (voidvoid minma *ptr, const size_t length, dox (void *ptr, const size_t length, douuble *min,ble *min double , double *max, c*max, const bool dropNaN = true) const { *min = onst bool dropNaNR_PosInf; * = true) consmax = R_t { *min = R_PosInNegInf; }
f; *max = R_| ^
NegInf; }
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool d/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void ropNaN = true)
| ^
minmax (void *ptr, const size_t length, doubl/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: e *min, dnote: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
oub 208 | case DT_le *max, COMPLEX1const bool dropNaN = true)
| ^
28: retur/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
208 | case DT_COMPLEX128n new Con: returncreteTy new ConcreteTypeHandler<complepeHandler<complex128_t>(); break;
| ^
x128_t>(); /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: break;
| ^
hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virt 89 | virtual void minmax (void *ptr, const size_t lual void minmax (void *ptr, const size_t lengength, doth, double *min, doubluble *mine *max, const bool dropNaN , double *max, const bool dropNaN = true) con= true) const { *mst { *min = R_PosInf; *in = R_PosInf; *max = R_NegInf; }
| ^
max = R_NegInf; }
| ^
In file included from dcm2niix/nifti1_io_core.cpp:18:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
207 | case DT_COMPLEX64: return new ConcreteTypeHandler<complex64_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
208 | case DT_COMPLEX128: return new ConcreteTypeHandler<complex128_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
In file included from dcm2niix/nii_dicom.cpp:27:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
207 | case DT_COMPLEX64: return new ConcreteTypeHandler<complex64_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
208 | case DT_COMPLEX128: return new ConcreteTypeHandler<complex128_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
In file included from main.cpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
207 | case DT_COMPLEX64: return new ConcreteTypeHandler<complex64_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
208 | case DT_COMPLEX128: return new ConcreteTypeHandler<complex128_t>(); break;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual void minmax (void *ptr, const size_t length, double *min, double *max, const bool dropNaN = true) const { *min = R_PosInf; *max = R_NegInf; }
| ^
dcm2niix/nii_dicom.cpp:1922:6: warning: variable 'patientPositionNumPhilips' set but not used [-Wunused-but-set-variable]
1922 | int patientPositionNumPhilips = 0;
| ^
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.cpp:4876:12: warning: unused variable 'realGroupElement' [-Wunused-variable]
4876 | uint32_t realGroupElement = groupElement;
| ^~~~~~~~~~~~~~~~
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;
| ^~~~~~~~
2 warnings generated.
2 warnings generated.
2 warnings generated.
10 warnings generated.
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -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 -L/opt/R/arm64/lib -lopenjp2 -lm -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/divest.Rcheck/00LOCK-divest/00new/divest/libs
** generating debug symbols (dSYM)
** 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)