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###
### Running command:
###
### rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh EBImage_4.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R EBImage.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=EBImage.buildbin-libdir EBImage_4.48.0.tar.gz'
>>>>>>>
* installing *source* package ‘EBImage’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EBImage.c -o EBImage.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clahe.c -o clahe.o
clahe.c:223:19: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses]
uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU;
~~~~~~~^~ ~~
clahe.c:223:19: note: place parentheses around the '+' expression to silence this warning
uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU;
^
( )
clahe.c:235:23: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses]
uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL;
~~~~~~~^~ ~~
clahe.c:235:23: note: place parentheses around the '+' expression to silence this warning
uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL;
^
( )
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distmap.cpp -o distmap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c drawCircle.c -o drawCircle.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c floodFill.cpp -o floodFill.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getFrames.c -o getFrames.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c haralick.c -o haralick.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c medianFilter.c -o medianFilter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c morphology.cpp -o morphology.o
morphology.cpp:163:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:166:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:170:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp:196:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:199:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:203:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp:196:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:253:42: note: in instantiation of function template specialization 'compute_lookup_table_for_line_erode<int>' requested here
compute_lookup_table_for_line = &compute_lookup_table_for_line_erode<type>;
^
morphology.cpp:340:9: note: in instantiation of function template specialization 'erode_dilate<int>' requested here
erode_dilate<type>(x, res, size, nz, what, &set, T);
^
morphology.cpp:374:9: note: in instantiation of function template specialization '_morphology<int>' requested here
_morphology<int>(INTEGER(x), INTEGER(res), size, nz, kernel, operation);
^
morphology.cpp:199:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:203:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp:163:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:257:42: note: in instantiation of function template specialization 'compute_lookup_table_for_line_dilate<int>' requested here
compute_lookup_table_for_line = &compute_lookup_table_for_line_dilate<type>;
^
morphology.cpp:340:9: note: in instantiation of function template specialization 'erode_dilate<int>' requested here
erode_dilate<type>(x, res, size, nz, what, &set, T);
^
morphology.cpp:374:9: note: in instantiation of function template specialization '_morphology<int>' requested here
_morphology<int>(INTEGER(x), INTEGER(res), size, nz, kernel, operation);
^
morphology.cpp:166:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:170:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp:196:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:253:42: note: in instantiation of function template specialization 'compute_lookup_table_for_line_erode<double>' requested here
compute_lookup_table_for_line = &compute_lookup_table_for_line_erode<type>;
^
morphology.cpp:340:9: note: in instantiation of function template specialization 'erode_dilate<double>' requested here
erode_dilate<type>(x, res, size, nz, what, &set, T);
^
morphology.cpp:377:9: note: in instantiation of function template specialization '_morphology<double>' requested here
_morphology<double>(REAL(x), REAL(res), size, nz, kernel, operation);
^
morphology.cpp:199:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:203:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp:163:14: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:257:42: note: in instantiation of function template specialization 'compute_lookup_table_for_line_dilate<double>' requested here
compute_lookup_table_for_line = &compute_lookup_table_for_line_dilate<type>;
^
morphology.cpp:340:9: note: in instantiation of function template specialization 'erode_dilate<double>' requested here
erode_dilate<type>(x, res, size, nz, what, &set, T);
^
morphology.cpp:377:9: note: in instantiation of function template specialization '_morphology<double>' requested here
_morphology<double>(REAL(x), REAL(res), size, nz, kernel, operation);
^
morphology.cpp:166:14: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:170:14: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
18 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nativeRaster.c -o nativeRaster.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c normalize.c -o normalize.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objects.c -o objects.o
objects.c:21:30: warning: unused variable 'dp' [-Wunused-variable]
double *obj, *src, *tgt, dp, val;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ocontour.c -o ocontour.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c propagate.cpp -o propagate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spatial.c -o spatial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c thresh.cpp -o thresh.o
thresh.cpp:64:42: warning: unused variable 'i' [-Wunused-variable]
int xi, yi, u, k, l, ou, nu, ov, nv, i;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tile.cpp -o tile.o
tile.cpp:24:17: warning: unused variable 'ims' [-Wunused-variable]
SEXP res, dm, ims;
^
tile.cpp:167:20: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~
.dx =
tile.cpp:167:33: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~
.dy =
tile.cpp:167:46: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~
.nx =
tile.cpp:167:54: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~
.ny =
tile.cpp:167:62: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~~~
.xoff =
tile.cpp:167:71: warning: use of GNU old-style field designator extension [-Wgnu-designator]
Dims d = (Dims) {dx: sdim[0], dy: sdim[1], nx: nx, ny: ny, xoff: 0, yoff: 0};
^~~~~
.yoff =
tile.cpp:163:11: warning: unused variable 'src' [-Wunused-variable]
double *src, *tgt;
^
tile.cpp:162:18: warning: unused variable 'dat' [-Wunused-variable]
SEXP res, dim, dat;
^
tile.cpp:163:17: warning: unused variable 'tgt' [-Wunused-variable]
double *src, *tgt;
^
tile.cpp:161:29: warning: unused variable 'y' [-Wunused-variable]
int nprotect=0, i, j, im, y, iim;
^
11 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tools.c -o tools.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transpose.cpp -o transpose.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c watershed.cpp -o watershed.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o EBImage.so EBImage.o clahe.o distmap.o drawCircle.o floodFill.o getFrames.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o transpose.o watershed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/EBImage.buildbin-libdir/00LOCK-EBImage/00new/EBImage/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘abind’ in package ‘EBImage’
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (EBImage)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR EBImage.buildbin-libdir/EBImage/libs/EBImage.so
>>>>>>>
>>>>>>> Paths before fix:
EBImage.buildbin-libdir/EBImage/libs/EBImage.so:
EBImage.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "EBImage.buildbin-libdir/EBImage/libs/EBImage.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "EBImage.buildbin-libdir/EBImage/libs/EBImage.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "EBImage.buildbin-libdir/EBImage/libs/EBImage.so"
>>>>>>> Paths after fix:
EBImage.buildbin-libdir/EBImage/libs/EBImage.so:
EBImage.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
