* 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++17 accepts -g... yes
checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed
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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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 main.cpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:50:
In 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]
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h 153 | :153: void 14: minmax warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
(voi 153 | d *ptr, co vnst sizoide_t mi lenmangtx (h, doubvoile *mind *ptr,, doubl const e *max,siz coe_tnst le bool dngth, dropNaN ouble *= tminrue)
| ^
/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
, doub 207 | le *max, const boo l d ropNaN case D= tT_Crue)
| ^
OMPLEX64: retu/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207rn new :44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
Con 207 | creteTy peHandler<comp case Dlex64_tT_COMPL>(); EX64: return breanew Conk;
| ^
creteTypeHandler<comp/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89lex:22:64_ note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)t>();
89 | brea virk;
tua | ^l v
oid minmax (voi/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89d *:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
ptr 89 | , c ons t s vizeirt_t uallength, void m double *min, inmdouax ble(vo *mid *ptr, constax, si coze_nstt lengt bool dh, doubrople NaN*mi = n, doubtrue) const { le *max, const*min = bool dR_PosInropNaN f; = t*maruex =) const R_NegInf; }
| ^
{ *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 */Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14:max warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual], const
153 | bool dropNaN = t rue vo)
id minm| ^
ax (/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208voi:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
208d *ptr, const | size_t length, double *min, double * casemaIn file included from dcm2niix/nii_dicom.cpp:27:
In file included from dcm2niix/nifti1_io_core.h:9x, DT_COMPLE const bool dropNaN = true)
| ^
X128: return new/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
:
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]
ConcreteTy153 208 | peHa case DT_Cndler<complOMPLEex12 | 8X_t>(); 128: return new Concr void minmax e(vo id *ptr, const si break;
| ^
ze_t lengthteTypeHand,/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h double *min, double *max, conler<cosIn file included from dcm2niix/nii_ortho.cpp:4:
In file included from dcm2niix/nifti1_io_core.ht bool dro:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
mplex128p _t>()89: | ; 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: 153:14N aN = true)
| ^
: b warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
r 153 | e /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44:a kIn file included from ;
| ^
vdcm2niix/nifti1_io_core.cpp:/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hoid m:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
i 207 | 89 | 18 n vir :
vi In file included from tmdcm2niix/nifti1_io_core.h:9 :
rIn 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: cax 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]a(void
se DT_COMPLEX6*pttuu ar4: 153a rleturn new ConcreteTypeHandler<co | , constlmv o si void mid mi plex64_t>(); breavoid miniknnzmax (voima;d *pmax (vtr, const sizeox
id *pt_( void *ptr, const rt length, des_t | ol,ength, double *min ^
i uczoe/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h, doublnst sizb_ee:89_le *:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)t length, dm
in, do*uble *m 89 | mata x, coouble * length, doubx n , cmin, dlvirtual vose t bool *omdroponsNaN id minmax (voi=it n, douubd *ptro oltrue),ble *
blmax, econst si *max, const d boolconst br| zopNaN = true) cooe_t lengonst { *minl dropNaNt ^
=/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: dh ,ropNaNnote: = true)
R_PosIin instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested herenf |
double ^; *max =
=* tr/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:m 207 | 44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here Rue) cons
_ 207t { *miNin, doun ble e =* case DT | gInR max, cons __ casPosInffe DCOMPLE;; *max =t bool dropNX R_NegTa_64:COM Inf; NPLEX64: = tr}
| }
| ^
^
ue) const { *min = R_PosInf; *m return neaxw Coreturn new Concren = R_NegInf; cteTypeHandler<complex64_t}
| ^
>(); ret breakeTypeHandler<complex64_;
t>(); brea| ^
k;
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22:/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)
note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified) 89 |
vi 89 | rtual v oid min virtual void minmax (void *ptr, const size_t lengthmax (void *ptr, const size_t/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]
l, double *mineng 153 | th, double *min, , douvoble *double *max, const max, const booid minmax (vlbooo dropNaid *ptr, consl dropNaN = true) const { t *minsize_t length, double *min, = R_Pos doublN = true) Inconst { *f; *max = R_me *max, coiNnst ben gInf= R_PosIn;ool dropNaN = true)
| ^
}f; *max =
| ^
R_NegInf; }/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_COMPLE
| ^
X128: return new ConcreteTypeHandler<complex1/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]28_t>(); break
153 | ;
| ^
/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)
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h: void m89 | virtual inmax (void *ptr, const si153:14:void minma warning: xz'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
153 | e_t length, void mi double *min, do(void *ptnmax (voird *ptr,uble *max, co c,o const size_t length, double *min, double *max, connst boolnst size_t st bool dropNaN = true) const { dropNaN = t *min = R_PosInf; *maxlrue)
| ^
e/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44: note: ngth, doub = lin instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
e *min, double *max, cons 208 | t casbool dropNaNe DT_CO = R_NegInf; }
| ^
true)
| ^
M/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
PLEX128: 208 | case DT return ne_COMPLEX128: return new ConcreteTypeHaw ConcreteTypendler<complex128_t>();Handler<comp break;
| ^
lex128_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)
); br 89 | eak;
| ^
virtual voi/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)d minmax (void
89 | *ptr, const size_t length, doublvirtual void me *mininmax (vo, doubleid *ptr, *max, const bool dro const sizpNaN = true) const { *min =e_ R_Pt leosInf; *ngthmax, double *min, do = R_NegIublnf; }
e *max, | ^ const boo
l 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++17 -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)