############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL EBImage ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘EBImage’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c EBImage.c -o EBImage.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clahe.c -o clahe.o clahe.c: In function ‘CLAHE’: clahe.c:223:19: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 223 | uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; | ~~~~~~~^~ clahe.c:235:23: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 235 | uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; | ~~~~~~~^~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distmap.cpp -o distmap.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c drawCircle.c -o drawCircle.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c floodFill.cpp -o floodFill.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c getFrames.c -o getFrames.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c haralick.c -o haralick.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c medianFilter.c -o medianFilter.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c morphology.cpp -o morphology.o morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = int]’: morphology.cpp:253:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]’ morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]’ morphology.cpp:374:79: required from here morphology.cpp:196:14: warning: statement has no effect [-Wunused-value] 196 | for (i; i < 0; ++i) { | ^ morphology.cpp:199:14: warning: statement has no effect [-Wunused-value] 199 | for (i; i < maxX; ++i) { | ^ morphology.cpp:203:14: warning: statement has no effect [-Wunused-value] 203 | for (i; i < size.x + set->maxXoffset; ++i) { | ^ morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = int]’: morphology.cpp:257:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]’ morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]’ morphology.cpp:374:79: required from here morphology.cpp:163:14: warning: statement has no effect [-Wunused-value] 163 | for (i; i < 0; ++i) { | ^ morphology.cpp:166:14: warning: statement has no effect [-Wunused-value] 166 | for (i; i < maxX; ++i) { | ^ morphology.cpp:170:14: warning: statement has no effect [-Wunused-value] 170 | for (i; i < size.x + set->maxXoffset; ++i) { | ^ morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = double]’: morphology.cpp:253:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]’ morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]’ morphology.cpp:377:76: required from here morphology.cpp:196:14: warning: statement has no effect [-Wunused-value] 196 | for (i; i < 0; ++i) { | ^ morphology.cpp:199:14: warning: statement has no effect [-Wunused-value] 199 | for (i; i < maxX; ++i) { | ^ morphology.cpp:203:14: warning: statement has no effect [-Wunused-value] 203 | for (i; i < size.x + set->maxXoffset; ++i) { | ^ morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = double]’: morphology.cpp:257:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]’ morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]’ morphology.cpp:377:76: required from here morphology.cpp:163:14: warning: statement has no effect [-Wunused-value] 163 | for (i; i < 0; ++i) { | ^ morphology.cpp:166:14: warning: statement has no effect [-Wunused-value] 166 | for (i; i < maxX; ++i) { | ^ morphology.cpp:170:14: warning: statement has no effect [-Wunused-value] 170 | for (i; i < size.x + set->maxXoffset; ++i) { | ^ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nativeRaster.c -o nativeRaster.o nativeRaster.c: In function ‘nativeRaster’: nativeRaster.c:38:7: warning: pointer targets in assignment from ‘int *’ to ‘uint32_t *’ {aka ‘unsigned int *’} differ in signedness [-Wpointer-sign] 38 | out = INTEGER(res); | ^ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c normalize.c -o normalize.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objects.c -o objects.o objects.c: In function ‘paintObjects’: objects.c:21:30: warning: unused variable ‘dp’ [-Wunused-variable] 21 | double *obj, *src, *tgt, dp, val; | ^~ objects.c: In function ‘stackObjects’: objects.c:295:10: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized] 295 | return res; | ^~~ In file included from objects.h:5, from objects.c:1: /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:154:28: warning: ‘dim’ may be used uninitialized in this function [-Wmaybe-uninitialized] 154 | #define SET_DIM(x, n) Rf_setAttrib(x, R_DimSymbol, n) | ^~~~~~~~~~~~ objects.c:192:13: note: ‘dim’ was declared here 192 | SEXP res, dim, xys, img; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ocontour.c -o ocontour.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c propagate.cpp -o propagate.o propagate.cpp: In function ‘SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)’: propagate.cpp:174:31: warning: ‘mask’ may be used uninitialized in this function [-Wmaybe-uninitialized] 174 | if (! mask_in[IJ(p.i, p.j)]) continue; | ^ propagate.cpp:197:8: note: ‘mask’ was declared here 197 | int *mask; | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spatial.c -o spatial.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c thresh.cpp -o thresh.o thresh.cpp: In instantiation of ‘void _thresh(T*, int*, int, int, int, int, double) [with T = int]’: thresh.cpp:50:76: required from here thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable] 64 | int xi, yi, u, k, l, ou, nu, ov, nv, i; | ^ thresh.cpp: In instantiation of ‘void _thresh(T*, int*, int, int, int, int, double) [with T = double]’: thresh.cpp:53:76: required from here thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable] g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tile.cpp -o tile.o tile.cpp: In function ‘SEXPREC* tile(SEXP, SEXP, SEXP)’: tile.cpp:24:17: warning: unused variable ‘ims’ [-Wunused-variable] 24 | SEXP res, dm, ims; | ^~~ tile.cpp: In function ‘SEXPREC* untile(SEXP, SEXP, SEXP)’: tile.cpp:161:29: warning: unused variable ‘y’ [-Wunused-variable] 161 | int nprotect=0, i, j, im, y, iim; | ^ tile.cpp:162:18: warning: unused variable ‘dat’ [-Wunused-variable] 162 | SEXP res, dim, dat; | ^~~ tile.cpp:163:11: warning: unused variable ‘src’ [-Wunused-variable] 163 | double *src, *tgt; | ^~~ tile.cpp:163:17: warning: unused variable ‘tgt’ [-Wunused-variable] 163 | double *src, *tgt; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tools.c -o tools.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c transpose.cpp -o transpose.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c watershed.cpp -o watershed.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/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)