* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘divest’ ...
** 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 g++-14 -std=gnu++17 accepts -g... yes
checking for g++-14 -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: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/tmp/RtmpMEyBHv/R.INSTALL1a2a669c709ab/divest/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c main.cpp -o main.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/niftilib/nifti1_io.h:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti.h:43,
from main.cpp:3:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o
dcm2niix/jpg_0XC3.cpp:191: warning: ignoring ‘#pragma unused ’ [-Wunknown-pragmas]
191 | #pragma unused(DHTnLi) // we need to increment the input file position, but we do not care what the value is
dcm2niix/jpg_0XC3.cpp:265: warning: ignoring ‘#pragma unused ’ [-Wunknown-pragmas]
265 | #pragma unused(btS1) // dummy value used to increment file position
dcm2niix/jpg_0XC3.cpp:267: warning: ignoring ‘#pragma unused ’ [-Wunknown-pragmas]
267 | #pragma unused(btS2) // dummy value used to increment file position
dcm2niix/jpg_0XC3.cpp:272: warning: ignoring ‘#pragma unused ’ [-Wunknown-pragmas]
272 | #pragma unused(SOSse) // dummy value used to increment file position
dcm2niix/jpg_0XC3.cpp: In function ‘unsigned char* decode_JPEG_SOF_0XC3(const char*, int, bool, int*, int*, int*, int*, int)’:
dcm2niix/jpg_0XC3.cpp:140:29: warning: variable ‘btS2’ set but not used [-Wunused-but-set-variable]
140 | unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; // tag
| ^~~~
dcm2niix/jpg_0XC3.cpp:140:35: warning: variable ‘SOSse’ set but not used [-Wunused-but-set-variable]
140 | unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; // tag
| ^~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dcm2niix/nifti1_io_core.cpp -o dcm2niix/nifti1_io_core.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/niftilib/nifti1_io.h:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti.h:43,
from dcm2niix/nifti1_io_core.h:9,
from dcm2niix/nifti1_io_core.cpp:18:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dcm2niix/nii_dicom.cpp -o dcm2niix/nii_dicom.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/niftilib/nifti1_io.h:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti.h:43,
from dcm2niix/nifti1_io_core.h:9,
from dcm2niix/nii_dicom.cpp:27:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
dcm2niix/nii_dicom.cpp: In function ‘unsigned char* nii_loadImgCoreOpenJPEG(char*, nifti_1_header, TDICOMdata, int)’:
dcm2niix/nii_dicom.cpp:230:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
230 | if (sz < size)
| ~~~^~~~~~
dcm2niix/nii_dicom.cpp: In function ‘TDICOMdata readDICOMx(char*, TDCMprefs*, TDTI4D*)’:
dcm2niix/nii_dicom.cpp:4876:26: warning: unused variable ‘realGroupElement’ [-Wunused-variable]
4876 | uint32_t realGroupElement = groupElement;
| ^~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp:5160:66: warning: ‘vr[1]’ may be used uninitialized [-Wmaybe-uninitialized]
5160 | if ((groupElement == kItemTag) && (vr[0] == 'O') && (vr[1] == 'B') && (isIconImageSequence))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp:4764:14: note: ‘vr[1]’ was declared here
4764 | char vr[2];
| ^~
dcm2niix/nii_dicom.cpp:5160:48: warning: ‘vr[0]’ may be used uninitialized [-Wmaybe-uninitialized]
5160 | if ((groupElement == kItemTag) && (vr[0] == 'O') && (vr[1] == 'B') && (isIconImageSequence))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp:4764:14: note: ‘vr[0]’ was declared here
4764 | char vr[2];
| ^~
dcm2niix/nii_dicom.cpp:7732:21: warning: ‘lLength’ may be used uninitialized [-Wmaybe-uninitialized]
7732 | int imgBytes = (int)(lLength);
| ^~~~~~~~
dcm2niix/nii_dicom.cpp:4743:18: note: ‘lLength’ was declared here
4743 | uint32_t lLength;
| ^~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/niftilib/nifti1_io.h:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti.h:43,
from dcm2niix/nifti1_io_core.h:9,
from dcm2niix/nii_dicom_batch.cpp:30:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
dcm2niix/nii_dicom_batch.cpp: In function ‘int* nii_saveDTI(char*, int, TDCMsort*, TDICOMdata*, TDCMopts, int, TDTI4D*, int*, int)’:
dcm2niix/nii_dicom_batch.cpp:2727:14: warning: variable ‘isIsotropic’ set but not used [-Wunused-but-set-variable]
2727 | bool isIsotropic = false;
| ^~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘void heudiconvStr(char*)’:
dcm2niix/nii_dicom_batch.cpp:3485:20: warning: unused variable ‘kTempPathSeparator’ [-Wunused-variable]
3485 | const char kTempPathSeparator = '\a';
| ^~~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp:3486:14: warning: unused variable ‘hasCaret’ [-Wunused-variable]
3486 | bool hasCaret = false;
| ^~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘void setBidsSiemens(TDICOMdata*, int, int, const char*)’:
dcm2niix/nii_dicom_batch.cpp:6833:23: warning: unused variable ‘pf’ [-Wunused-variable]
6833 | float pf = 1.0f; // partial fourier
| ^~
dcm2niix/nii_dicom_batch.cpp: In function ‘void setBidsPhilips(TDICOMdata*, int, int)’:
dcm2niix/nii_dicom_batch.cpp:7118:14: warning: variable ‘isDirLabel’ set but not used [-Wunused-but-set-variable]
7118 | bool isDirLabel = false; // report phase encoding direction
| ^~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘void setBidsGE(TDICOMdata*, int, int, const char*)’:
dcm2niix/nii_dicom_batch.cpp:7296:13: warning: variable ‘nVol’ set but not used [-Wunused-but-set-variable]
7296 | int nVol = 1;
| ^~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘int saveDcm2NiiCore(int, TDCMsort*, TDICOMdata*, TSearchList*, TDCMopts, TDTI4D*, int)’:
dcm2niix/nii_dicom_batch.cpp:8566:31: warning: unused variable ‘shearMat’ [-Wunused-variable]
8566 | mat33 shearMat;
| ^~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘int nii_loadDirCore(char*, TDCMopts*)’:
dcm2niix/nii_dicom_batch.cpp:9690:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
9690 | for (int i = 0; i < nameList.numItems; i++)
| ~~^~~~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function ‘int searchDirForDICOM(char*, TSearchList*, int, int, TDCMopts*)’:
dcm2niix/nii_dicom_batch.cpp:9264:20: warning: ‘dir.tinydir_dir::has_next’ may be used uninitialized [-Wmaybe-uninitialized]
9264 | while (dir.has_next) {
| ~~~~^~~~~~~~
dcm2niix/nii_dicom_batch.cpp:9262:21: note: ‘dir’ declared here
9262 | tinydir_dir dir;
| ^~~
dcm2niix/nii_dicom_batch.cpp:9264:20: warning: ‘dir.tinydir_dir::has_next’ may be used uninitialized [-Wmaybe-uninitialized]
9264 | while (dir.has_next) {
| ~~~~^~~~~~~~
dcm2niix/nii_dicom_batch.cpp:9262:21: note: ‘dir’ declared here
9262 | tinydir_dir dir;
| ^~~
dcm2niix/nii_dicom_batch.cpp: In function ‘int nii_loadDirOneDirAtATime(char*, TDCMopts*, int, int)’:
dcm2niix/nii_dicom_batch.cpp:9982:20: warning: ‘dir.tinydir_dir::has_next’ may be used uninitialized [-Wmaybe-uninitialized]
9982 | while (dir.has_next) {
| ~~~~^~~~~~~~
dcm2niix/nii_dicom_batch.cpp:9980:21: note: ‘dir’ declared here
9980 | tinydir_dir dir;
| ^~~
dcm2niix/nii_dicom_batch.cpp:9982:20: warning: ‘dir.tinydir_dir::has_next’ may be used uninitialized [-Wmaybe-uninitialized]
9982 | while (dir.has_next) {
| ~~~~^~~~~~~~
dcm2niix/nii_dicom_batch.cpp:9980:21: note: ‘dir’ declared here
9980 | tinydir_dir dir;
| ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dcm2niix/nii_ortho.cpp -o dcm2niix/nii_ortho.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/niftilib/nifti1_io.h:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti.h:43,
from dcm2niix/nifti1_io_core.h:9,
from dcm2niix/nii_ortho.cpp:4:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include/RNifti/NiftiImage_print.h:6:9: warning: "R_NO_REMAP" redefined
6 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -DUSING_R -DmyDisableMiniZ -I/usr/include/openjpeg-2.5 -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RNifti/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/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.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpMEyBHv/R.INSTALL1a2a669c709ab/divest/src'
make[1]: Entering directory '/tmp/RtmpMEyBHv/R.INSTALL1a2a669c709ab/divest/src'
make[1]: Leaving directory '/tmp/RtmpMEyBHv/R.INSTALL1a2a669c709ab/divest/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)