* 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++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -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... -ljasper
checking for jasper/jasper.h... yes
configure: Using JasPer for JPEG2000 support
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/divest/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c main.cpp -o main.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dcm2niix/jpg_0XC3.cpp -o dcm2niix/jpg_0XC3.o
dcm2niix/jpg_0XC3.cpp:186: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
186 | #pragma unused(DHTnLi) //we need to increment the input file position, but we do not care what the value is
|
dcm2niix/jpg_0XC3.cpp:260: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
260 | #pragma unused(btS1) //dummy value used to increment file position
|
dcm2niix/jpg_0XC3.cpp:262: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
262 | #pragma unused(btS2) //dummy value used to increment file position
|
dcm2niix/jpg_0XC3.cpp:267: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
267 | #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:135:29: warning: variable 'btS2' set but not used [-Wunused-but-set-variable]
135 | unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; //tag
| ^~~~
dcm2niix/jpg_0XC3.cpp:135:35: warning: variable 'SOSse' set but not used [-Wunused-but-set-variable]
135 | unsigned char btS1, btS2, SOSse, SOSahal, btMarkerType, SOSns = 0x00; //tag
| ^~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dcm2niix/nifti1_io_core.cpp -o dcm2niix/nifti1_io_core.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dcm2niix/nii_dicom.cpp -o dcm2niix/nii_dicom.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dcm2niix/nii_dicom_batch.cpp -o dcm2niix/nii_dicom_batch.o
In file included from dcm2niix/nii_dicom_batch.cpp:22:
dcm2niix/miniz.c:3805: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
3805 | #pragma unused(cur_file_ofs)
|
dcm2niix/miniz.c:3808: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
3808 | #pragma unused(comp_remaining)
|
dcm2niix/miniz.c:4684: warning: ignoring '#pragma unused ' [-Wunknown-pragmas]
4684 | #pragma unused(cur_src_file_ofs)
|
dcm2niix/nii_dicom.cpp: In function 'unsigned char* nii_loadImgCoreJasper(char*, nifti_1_header, TDICOMdata, int)':
dcm2niix/nii_dicom.cpp:3232:66: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
3232 | jas_image_cmptprec(image, cmpts[cmptno]) != prec ||
| ^
dcm2niix/miniz.c: In function 'tinfl_status tinfl_decompress(tinfl_decompressor*, const mz_uint8*, size_t*, mz_uint8*, mz_uint8*, size_t*, mz_uint32)':
dcm2niix/miniz.c:1506:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
1506 | for ( i = 0; i <= 143; ++i) *p++ = 8; for ( ; i <= 255; ++i) *p++ = 9; for ( ; i <= 279; ++i) *p++ = 7; for ( ; i <= 287; ++i) *p++ = 8;
| ^~~
dcm2niix/miniz.c:1506:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
1506 | for ( i = 0; i <= 143; ++i) *p++ = 8; for ( ; i <= 255; ++i) *p++ = 9; for ( ; i <= 279; ++i) *p++ = 7; for ( ; i <= 287; ++i) *p++ = 8;
| ^~~
dcm2niix/miniz.c: In function 'void tdefl_start_dynamic_block(tdefl_compressor*)':
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1987:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1987 | TDEFL_PUT_BITS(2, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1987:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1987 | TDEFL_PUT_BITS(2, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1989:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1989 | TDEFL_PUT_BITS(num_lit_codes - 257, 5);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1989:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1989 | TDEFL_PUT_BITS(num_lit_codes - 257, 5);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1990:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1990 | TDEFL_PUT_BITS(num_dist_codes - 1, 5);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1990:3: note: in expansion of macro 'TDEFL_PUT_BITS'
1990 | TDEFL_PUT_BITS(num_dist_codes - 1, 5);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1993:55: note: in expansion of macro 'TDEFL_PUT_BITS'
1993 | num_bit_lengths = MZ_MAX(4, (num_bit_lengths + 1)); TDEFL_PUT_BITS(num_bit_lengths - 4, 4);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1993:55: note: in expansion of macro 'TDEFL_PUT_BITS'
1993 | num_bit_lengths = MZ_MAX(4, (num_bit_lengths + 1)); TDEFL_PUT_BITS(num_bit_lengths - 4, 4);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1994:46: note: in expansion of macro 'TDEFL_PUT_BITS'
1994 | for (i = 0; (int)i < num_bit_lengths; i++) TDEFL_PUT_BITS(d->m_huff_code_sizes[2][s_tdefl_packed_code_size_syms_swizzle[i]], 3);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1994:46: note: in expansion of macro 'TDEFL_PUT_BITS'
1994 | for (i = 0; (int)i < num_bit_lengths; i++) TDEFL_PUT_BITS(d->m_huff_code_sizes[2][s_tdefl_packed_code_size_syms_swizzle[i]], 3);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:1999:5: note: in expansion of macro 'TDEFL_PUT_BITS'
1999 | TDEFL_PUT_BITS(d->m_huff_codes[2][code], d->m_huff_code_sizes[2][code]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:1999:5: note: in expansion of macro 'TDEFL_PUT_BITS'
1999 | TDEFL_PUT_BITS(d->m_huff_codes[2][code], d->m_huff_code_sizes[2][code]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2000:21: note: in expansion of macro 'TDEFL_PUT_BITS'
2000 | if (code >= 16) TDEFL_PUT_BITS(packed_code_sizes[packed_code_sizes_index++], "\02\03\07"[code - 16]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2000:21: note: in expansion of macro 'TDEFL_PUT_BITS'
2000 | if (code >= 16) TDEFL_PUT_BITS(packed_code_sizes[packed_code_sizes_index++], "\02\03\07"[code - 16]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c: In function 'void tdefl_start_static_block(tdefl_compressor*)':
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2019:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2019 | TDEFL_PUT_BITS(1, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2019:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2019 | TDEFL_PUT_BITS(1, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c: In function 'mz_bool tdefl_compress_lz_codes(tdefl_compressor*)':
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2130:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2130 | TDEFL_PUT_BITS(d->m_huff_codes[0][s_tdefl_len_sym[match_len]], d->m_huff_code_sizes[0][s_tdefl_len_sym[match_len]]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2130:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2130 | TDEFL_PUT_BITS(d->m_huff_codes[0][s_tdefl_len_sym[match_len]], d->m_huff_code_sizes[0][s_tdefl_len_sym[match_len]]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2131:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2131 | TDEFL_PUT_BITS(match_len & mz_bitmasks[s_tdefl_len_extra[match_len]], s_tdefl_len_extra[match_len]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2131:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2131 | TDEFL_PUT_BITS(match_len & mz_bitmasks[s_tdefl_len_extra[match_len]], s_tdefl_len_extra[match_len]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2142:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2142 | TDEFL_PUT_BITS(d->m_huff_codes[1][sym], d->m_huff_code_sizes[1][sym]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2142:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2142 | TDEFL_PUT_BITS(d->m_huff_codes[1][sym], d->m_huff_code_sizes[1][sym]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2143:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2143 | TDEFL_PUT_BITS(match_dist & mz_bitmasks[num_extra_bits], num_extra_bits);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2143:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2143 | TDEFL_PUT_BITS(match_dist & mz_bitmasks[num_extra_bits], num_extra_bits);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2149:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2149 | TDEFL_PUT_BITS(d->m_huff_codes[0][lit], d->m_huff_code_sizes[0][lit]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2149:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2149 | TDEFL_PUT_BITS(d->m_huff_codes[0][lit], d->m_huff_code_sizes[0][lit]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2153:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2153 | TDEFL_PUT_BITS(d->m_huff_codes[0][256], d->m_huff_code_sizes[0][256]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2153:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2153 | TDEFL_PUT_BITS(d->m_huff_codes[0][256], d->m_huff_code_sizes[0][256]);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c: In function 'int tdefl_flush_block(tdefl_compressor*, int)':
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2188:5: note: in expansion of macro 'TDEFL_PUT_BITS'
2188 | TDEFL_PUT_BITS(0x78, 8); TDEFL_PUT_BITS(0x01, 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2188:5: note: in expansion of macro 'TDEFL_PUT_BITS'
2188 | TDEFL_PUT_BITS(0x78, 8); TDEFL_PUT_BITS(0x01, 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2188:30: note: in expansion of macro 'TDEFL_PUT_BITS'
2188 | TDEFL_PUT_BITS(0x78, 8); TDEFL_PUT_BITS(0x01, 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2188:30: note: in expansion of macro 'TDEFL_PUT_BITS'
2188 | TDEFL_PUT_BITS(0x78, 8); TDEFL_PUT_BITS(0x01, 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2191:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2191 | TDEFL_PUT_BITS(flush == TDEFL_FINISH, 1);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2191:3: note: in expansion of macro 'TDEFL_PUT_BITS'
2191 | TDEFL_PUT_BITS(flush == TDEFL_FINISH, 1);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2203:5: note: in expansion of macro 'TDEFL_PUT_BITS'
2203 | TDEFL_PUT_BITS(0, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2203:5: note: in expansion of macro 'TDEFL_PUT_BITS'
2203 | TDEFL_PUT_BITS(0, 2);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2204:25: note: in expansion of macro 'TDEFL_PUT_BITS'
2204 | if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2204:25: note: in expansion of macro 'TDEFL_PUT_BITS'
2204 | if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2207:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2207 | TDEFL_PUT_BITS(d->m_total_lz_bytes & 0xFFFF, 16);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2207:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2207 | TDEFL_PUT_BITS(d->m_total_lz_bytes & 0xFFFF, 16);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2211:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2211 | TDEFL_PUT_BITS(d->m_dict[(d->m_lz_code_buf_dict_pos + i) & TDEFL_LZ_DICT_SIZE_MASK], 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2211:7: note: in expansion of macro 'TDEFL_PUT_BITS'
2211 | TDEFL_PUT_BITS(d->m_dict[(d->m_lz_code_buf_dict_pos + i) & TDEFL_LZ_DICT_SIZE_MASK], 8);
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2225:27: note: in expansion of macro 'TDEFL_PUT_BITS'
2225 | if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2225:27: note: in expansion of macro 'TDEFL_PUT_BITS'
2225 | if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2226:106: note: in expansion of macro 'TDEFL_PUT_BITS'
2226 | if (d->m_flags & TDEFL_WRITE_ZLIB_HEADER) { mz_uint i, a = d->m_adler32; for (i = 0; i < 4; i++) { TDEFL_PUT_BITS((a >> 24) & 0xFF, 8); a <<= 8; } }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2226:106: note: in expansion of macro 'TDEFL_PUT_BITS'
2226 | if (d->m_flags & TDEFL_WRITE_ZLIB_HEADER) { mz_uint i, a = d->m_adler32; for (i = 0; i < 4; i++) { TDEFL_PUT_BITS((a >> 24) & 0xFF, 8); a <<= 8; } }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2230:25: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2230:25: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2230:67: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2230:67: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1916:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1916 | if (d->m_pOutput_buf < d->m_pOutput_buf_end) \
| ^~
dcm2niix/miniz.c:2230:141: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c:1918:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1918 | d->m_bit_buffer >>= 8; \
| ^
dcm2niix/miniz.c:2230:141: note: in expansion of macro 'TDEFL_PUT_BITS'
2230 | mz_uint i, z = 0; TDEFL_PUT_BITS(0, 3); if (d->m_bits_in) { TDEFL_PUT_BITS(0, 8 - d->m_bits_in); } for (i = 2; i; --i, z ^= 0xFFFF) { TDEFL_PUT_BITS(z & 0xFFFF, 16); }
| ^~~~~~~~~~~~~~
dcm2niix/miniz.c: In function 'void tdefl_find_match(tdefl_compressor*, mz_uint, mz_uint, mz_uint, mz_uint*, mz_uint*)':
dcm2niix/miniz.c:2324:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2324 | if (!dist) break; p = s; q = d->m_dict + probe_pos; for (probe_len = 0; probe_len < max_match_len; probe_len++) if (*p++ != *q++) break;
| ^~
dcm2niix/miniz.c:2324:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2324 | if (!dist) break; p = s; q = d->m_dict + probe_pos; for (probe_len = 0; probe_len < max_match_len; probe_len++) if (*p++ != *q++) break;
| ^
dcm2niix/nii_dicom_batch.cpp: In function 'int* nii_saveDTI(char*, int, TDCMsort*, TDICOMdata*, TDCMopts, int, TDTI4D*, int*, int)':
dcm2niix/nii_dicom_batch.cpp:2505:14: warning: variable 'isIsotropic' set but not used [-Wunused-but-set-variable]
2505 | bool isIsotropic = false;
| ^~~~~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function 'void createDummyBidsBoilerplate(char*, bool)':
dcm2niix/nii_dicom_batch.cpp:3266:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
3266 | if (fp != NULL)
| ^~
dcm2niix/nii_dicom_batch.cpp:3268:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
3268 | fprintf(fp, kDCMdate);
| ^~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function 'void setBidsSiemens(TDICOMdata*, int, int, const char*)':
dcm2niix/nii_dicom_batch.cpp:6334:23: warning: unused variable 'pf' [-Wunused-variable]
6334 | float pf = 1.0f; //partial fourier
| ^~
dcm2niix/nii_dicom_batch.cpp: In function 'void setBidsPhilips(TDICOMdata*, int, int)':
dcm2niix/nii_dicom_batch.cpp:6597:14: warning: variable 'isDirLabel' set but not used [-Wunused-but-set-variable]
6597 | 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:6768:13: warning: variable 'nVol' set but not used [-Wunused-but-set-variable]
6768 | int nVol = 1;
| ^~~~
dcm2niix/nii_dicom_batch.cpp: In function 'int saveDcm2NiiCore(int, TDCMsort*, TDICOMdata*, TSearchList*, TDCMopts, TDTI4D*, int)':
dcm2niix/nii_dicom_batch.cpp:8022:31: warning: unused variable 'shearMat' [-Wunused-variable]
8022 | mat33 shearMat;
| ^~~~~~~~
dcm2niix/nii_dicom_batch.cpp: In function 'int nii_loadDirCore(char*, TDCMopts*)':
dcm2niix/nii_dicom_batch.cpp:9115:35: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
9115 | for (int i = 0; i < nameList.numItems; i++)
| ~~^~~~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp: In function 'TDICOMdata readDICOMx(char*, TDCMprefs*, TDTI4D*)':
dcm2niix/nii_dicom.cpp:5105:66: warning: 'vr[1]' may be used uninitialized [-Wmaybe-uninitialized]
5105 | if ((groupElement == kItemTag) && (vr[0] == 'O') && (vr[1] == 'B') && (isIconImageSequence))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp:4731:14: note: 'vr[1]' was declared here
4731 | char vr[2];
| ^~
dcm2niix/nii_dicom.cpp:5105:48: warning: 'vr[0]' may be used uninitialized [-Wmaybe-uninitialized]
5105 | if ((groupElement == kItemTag) && (vr[0] == 'O') && (vr[1] == 'B') && (isIconImageSequence))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
dcm2niix/nii_dicom.cpp:4731:14: note: 'vr[0]' was declared here
4731 | char vr[2];
| ^~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dcm2niix/nii_ortho.cpp -o dcm2niix/nii_ortho.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DUSING_R -DmyEnableJasper -DmyDisableOpenJPEG -DHAVE_FMEMOPEN -I. -Idcm2niix -Iujpeg -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RNifti/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ujpeg/ujpeg.cpp -o ujpeg/ujpeg.o
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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 -ljasper
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/divest/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/divest/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/divest/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)