* installing *source* package ‘divest’ ... ** 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++-18 -std=gnu++17 accepts -g... yes checking for clang++-18 -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: ‘Debian clang version 18.1.8 (12)’ clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c main.cpp -o main.o In file included from main.cpp:3: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti.h:43: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/niftilib/nifti1_io.h:24: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 6 | #define R_NO_REMAP | ^ :7:9: note: previous definition is here 7 | #define R_NO_REMAP 1 | ^ In file included from main.cpp:6: ./ImageList.h:6:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 6 | #define STRICT_R_HEADERS | ^ :6:9: note: previous definition is here 6 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -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: dcm2niix/nifti1_io_core.h:8:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 8 | #define STRICT_R_HEADERS | ^ :6:9: note: previous definition is here 6 | #define STRICT_R_HEADERS 1 | ^ In file included from dcm2niix/nifti1_io_core.cpp:18: In file included from dcm2niix/nifti1_io_core.h:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti.h:43: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/niftilib/nifti1_io.h:24: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 6 | #define R_NO_REMAP | ^ :7:9: note: previous definition is here 7 | #define R_NO_REMAP 1 | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c dcm2niix/nii_dicom.cpp -o dcm2niix/nii_dicom.o In file included from dcm2niix/nii_dicom.cpp:27: dcm2niix/nifti1_io_core.h:8:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 8 | #define STRICT_R_HEADERS | ^ :6:9: note: previous definition is here 6 | #define STRICT_R_HEADERS 1 | ^ In file included from dcm2niix/nii_dicom.cpp:27: In file included from dcm2niix/nifti1_io_core.h:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti.h:43: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/niftilib/nifti1_io.h:24: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 6 | #define R_NO_REMAP | ^ :7:9: note: previous definition is here 7 | #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:4901:12: warning: unused variable 'realGroupElement' [-Wunused-variable] 4901 | uint32_t realGroupElement = groupElement; | ^~~~~~~~~~~~~~~~ 4 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o In file included from dcm2niix/nii_dicom_batch.cpp:30: dcm2niix/nifti1_io_core.h:8:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 8 | #define STRICT_R_HEADERS | ^ :6:9: note: previous definition is here 6 | #define STRICT_R_HEADERS 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 /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti.h:43: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/niftilib/nifti1_io.h:24: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 6 | #define R_NO_REMAP | ^ :7:9: note: previous definition is here 7 | #define R_NO_REMAP 1 | ^ dcm2niix/nii_dicom_batch.cpp:2721:7: warning: variable 'isIsotropic' set but not used [-Wunused-but-set-variable] 2721 | bool isIsotropic = false; | ^ dcm2niix/nii_dicom_batch.cpp:3479:13: warning: unused variable 'kTempPathSeparator' [-Wunused-variable] 3479 | const char kTempPathSeparator = '\a'; | ^~~~~~~~~~~~~~~~~~ dcm2niix/nii_dicom_batch.cpp:3480:7: warning: unused variable 'hasCaret' [-Wunused-variable] 3480 | bool hasCaret = false; | ^~~~~~~~ dcm2niix/nii_dicom_batch.cpp:6818:9: warning: unused variable 'pf' [-Wunused-variable] 6818 | float pf = 1.0f; // partial fourier | ^~ dcm2niix/nii_dicom_batch.cpp:7103:7: warning: variable 'isDirLabel' set but not used [-Wunused-but-set-variable] 7103 | bool isDirLabel = false; // report phase encoding direction | ^ dcm2niix/nii_dicom_batch.cpp:7281:6: warning: variable 'nVol' set but not used [-Wunused-but-set-variable] 7281 | int nVol = 1; | ^ dcm2niix/nii_dicom_batch.cpp:8252:11: warning: variable 'slicePositionRepeats' set but not used [-Wunused-but-set-variable] 8252 | int slicePositionRepeats = 1; // how many times is first position repeated | ^ dcm2niix/nii_dicom_batch.cpp:8551:10: warning: unused variable 'shearMat' [-Wunused-variable] 8551 | mat33 shearMat; | ^~~~~~~~ 10 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c dcm2niix/nii_ortho.cpp -o dcm2niix/nii_ortho.o In file included from dcm2niix/nii_ortho.cpp:4: dcm2niix/nifti1_io_core.h:8:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 8 | #define STRICT_R_HEADERS | ^ :6:9: note: previous definition is here 6 | #define STRICT_R_HEADERS 1 | ^ In file included from dcm2niix/nii_ortho.cpp:4: In file included from dcm2niix/nifti1_io_core.h:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti.h:43: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/niftilib/nifti1_io.h:24: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 6 | #define R_NO_REMAP | ^ :7:9: note: previous definition is here 7 | #define R_NO_REMAP 1 | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -DUSING_R -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-18/lib -Wl,-O1 -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 -L/home/hornik/tmp/R-d-clang-18/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/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)