* 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:In file included from main.cpp:3:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h:504:
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::
/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]
In file included from 153 | void minmax (voiddcm2niix/nii_dicom.cpp:27:
In file included from 153:14: warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
dcm2niix/nifti1_io_core.h 153 | :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]
*ptr, const size_t le153 | void mninmax (void *ptrgth, double *m, const size_t in, double *mavoid minmaxlx, const bo eonl dropNaN = true)
| ^(gth, double *min, void *ptr, constdouble *max, const
s bool di/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: zeropNaN = true)
| ^_note:
t lengin instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44th, do
uble : note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
207 | 207 | c *min, double *max, const case DaT bool dropNas_COMPLEX64: return new ConN = true)creteTypeHandler<complex64_t>e
| ^
DT/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h(); break;
| ^
_/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22COMP: note: :207:hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
LEX64:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here
89 | virtual v return ne207 | w Co noicreteTd minmax (void *ptr, c case DT_COMPonst sLEX6y4: returpeHandlen new ConcreteTr<complex64_t>();ypeHand breize_t lenler<complex64_t>(); gth, doak;
| ^
ub /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 | break;
| ^
l/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h :e 89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)* m
i 89 | n virtual v virtual void minmoid minmax , double *max, con(void sax (v*poid *tptr, const size_tr, lengtht bool d, douropNaN const siIn file included from z dcm2niix/nii_dicom_batch.cpp:ble *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.hmin, dou:= 50:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:b153:14:t warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
le *ma r153 | void minmax (void *ptr,xe_t , const bool d ue)lr enocongst cponst sN{ith, doa *min Nub le *min, double = R_PosInf; *max = R_NegInf;* }
z=m| In file included from ax, cdcm2niix/nifti1_io_core.cppe ^o
_t lenngth, doubl: t18:
In file included from dcm2niix/nifti1_io_core.h:9:
In file included from rsue)et bool dropN/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti.h/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:: aN = true) const { *min = R_const 50153:Pos:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: In warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
f ;{153 | 14: *warning: m'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual] i*min*
m 153 | nv = R, douax_PosInf; o ble *max, *mic vod oid min= R_axnmNax (vsmtegi b oooInlnf=id m dax (rop vR; }
| ^o_idNNa
N = true*ptr,) ec
| ^
gIn*/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.honst size_t length, double *min,/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hptr, : :fd; 153:14:coublo ewarning: n'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]207}st :44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested heres
i 207z
| *max, const be_t le ^ |
o153 c | nol 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 | ropNaN = tgta void minmax sruh(e)
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hvoi e:208:44: note: d in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
, doubD*v oTple *min_it208 | d r , c, d aoconst sminmax (void *ptr, coCOMPLEX64:iseuze_ nble Dst sizT_COMPLEX12 e_t8*m raeturn neltx,:w Concrete ength, clTo double *minry,neenpgthetsHandler<complex64_t>( u); double *max, const,t bool rbndou new C brobdropNaN = trueln)
eceool dr reteTypeHandler<compla | keo*p;x ^min, do
Nu
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:aN = true)
| ^
1/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:207:44: note: 2208:44:ble *8 max, co note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89 208 | in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<float>>' requested here_c
207 | :an22s stet DT_ bool drCOMPLopN:>E (); break;
a NX note: 128: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified) = true )
| ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22:c| ase DT_COMPLEX64: r 89 | return enew ConcreteTypeHandler<complex64_ t v turn new Concretnote: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified) ^eTyp
e/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hir:>208:t(44:
unote: Handler<complex)189;in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here | virtual void minmax al void2 minmax(
v 8 _(t>(); b 208 | voor i br de ieak;
| ^
ak;d
| ^
cas/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:89:22: e DT note: */Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hptr, const si*:89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)ze_t leng
p tr, t_consv ht sirtua,l void minmax (void *ptr,Ci89 | Oze_t leng th, c d doublo e oubl nst MPL *em size iEn, doub_Xvirt1 *lu28e *min, dmouble : return*maaax, x, t lengthconst boocn, dolo dl unropNasewtbN = tvl boorue) id minmax (vCcool dnropNaN = trueoonise *min,ct {)r *mied n = Rtc_onst {P *odm*ptr, constoe TypeisInf; *n = R_usble ize_t length, douH*maxbPomaxle *min, d, c sInf;=a *max = R_NegI nRn_dof; }
| ^
Nler<compoubnst bool egInf;dropNaN = true) le *l/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153:14: warning: mex12'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
} 153 | 8ax, con c voido
st mnst { bool dropN_t>(); inma aN| *mi ^
xn = b (void *ptr,= R_PosInf; t re*max arconst s= ue) cok;
nRiz| e_t lengts_hN, double *min, t { *min = R_PosInfdo; ^
e *gInfm/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hauble; }: *max, con
89:22: note: hidden overloaded virtual function 'RNifti::NiftiImageData::TypeHandler::minmax' declared here: different qualifiers ('const' vs unqualified)
89 | virtual st bool dv| ropNaN =x o id minmax (void *ptr, con ^
=strue)
| ^
R_/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.hNegInf; :t si}
| ^
ze_t length, double *min, do/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:153208:44: note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
: 20814u: | warning: 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>::minmax' hides overloaded virtual function [-Woverloaded-virtual]
ble *max, const bool d r153 o | void minpNaN = tr ue) co nmaxst { *min = R _PosInf; ( case DT_COMPLEX128: return new ConcreteType*max = R_HNegInf; }
| andler ^
<complex128_t>(void *ptr, const size_t length, double *min, do); breakuble *max, con;
| ^
s/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)
t bool dr 89 | virtuopNaN = true)
| ^
al void min/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RNifti/include/RNifti/NiftiImage.h:208:44:max (void *ptr, con note: in instantiation of template class 'RNifti::NiftiImageData::ConcreteTypeHandler<std::complex<double>>' requested here
st size_208 | t length, double case DT_COMPLEX*min, 128: doureturn new Cbleoncre *mteTypeHandler<complex128_t>(); ax, const bool br dropNaN = truee)ak;
| ^
const { *m/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)
i 89 | n = R_P vosIirtnf; *max = R_ualNegInf; }
| ^
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)