* 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++-17 -std=gnu++17 accepts -g... yes checking for clang++-17 -std=gnu++17 option to enable C++11 features... none needed 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 checking for library containing opj_version... -lopenjp2 checking for openjpeg.h... no checking for library containing jas_getversion... no configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Debian clang version 17.0.6 (5)’ clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c main.cpp -o main.o In file included from main.cpp:3: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti.h:50: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage.h:333:33: warning: suggest braces around initialization of subobject [-Wmissing-braces] 333 | Rcomplex rValue = { value.real(), value.imag() }; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | { } 1 warning generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c dcm2niix/nifti1_io_core.cpp -o dcm2niix/nifti1_io_core.o In file included from dcm2niix/nifti1_io_core.cpp:19: In file included from dcm2niix/nifti1_io_core.h:10: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti.h:50: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage.h:333:33: warning: suggest braces around initialization of subobject [-Wmissing-braces] 333 | Rcomplex rValue = { value.real(), value.imag() }; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | { } 1 warning generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -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:10: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti.h:50: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage.h:333:33: warning: suggest braces around initialization of subobject [-Wmissing-braces] 333 | Rcomplex rValue = { value.real(), value.imag() }; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | { } dcm2niix/nii_dicom.cpp:1912:6: warning: variable 'patientPositionNumPhilips' set but not used [-Wunused-but-set-variable] 1912 | int patientPositionNumPhilips = 0; | ^ 2 warnings generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o In file included from dcm2niix/nii_dicom_batch.cpp:31: In file included from dcm2niix/nifti1_io_core.h:10: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti.h:50: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage.h:333:33: warning: suggest braces around initialization of subobject [-Wmissing-braces] 333 | Rcomplex rValue = { value.real(), value.imag() }; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | { } dcm2niix/nii_dicom_batch.cpp:2505:7: warning: variable 'isIsotropic' set but not used [-Wunused-but-set-variable] 2505 | bool isIsotropic = false; | ^ dcm2niix/nii_dicom_batch.cpp:3268:4: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 3268 | fprintf(fp, kDCMdate); | ^ dcm2niix/nii_dicom_batch.cpp:3266:3: note: previous statement is here 3266 | if (fp != NULL) | ^ dcm2niix/nii_dicom_batch.cpp:6334:9: warning: unused variable 'pf' [-Wunused-variable] 6334 | float pf = 1.0f; //partial fourier | ^~ dcm2niix/nii_dicom_batch.cpp:6597:7: warning: variable 'isDirLabel' set but not used [-Wunused-but-set-variable] 6597 | bool isDirLabel = false; //report phase encoding direction | ^ dcm2niix/nii_dicom_batch.cpp:6768:6: warning: variable 'nVol' set but not used [-Wunused-but-set-variable] 6768 | int nVol = 1; | ^ dcm2niix/nii_dicom_batch.cpp:7728:11: warning: variable 'slicePositionRepeats' set but not used [-Wunused-but-set-variable] 7728 | int slicePositionRepeats = 1; //how many times is first position repeated | ^ dcm2niix/nii_dicom_batch.cpp:8022:10: warning: unused variable 'shearMat' [-Wunused-variable] 8022 | mat33 shearMat; | ^~~~~~~~ 8 warnings generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -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:10: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti.h:50: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include/RNifti/NiftiImage.h:333:33: warning: suggest braces around initialization of subobject [-Wmissing-braces] 333 | Rcomplex rValue = { value.real(), value.imag() }; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | { } 1 warning generated. clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG -DUSING_R -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RNifti/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-17/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 -L/home/hornik/tmp/R-d-clang-17/lib -lR installing to /srv/hornik/tmp/CRAN/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)