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### Running command:
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### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL EBImage
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘EBImage’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c EBImage.c -o EBImage.o
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distmap.cpp -o distmap.o
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c floodFill.cpp -o floodFill.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c getFrames.c -o getFrames.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c haralick.c -o haralick.o
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-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-3.15-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-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c normalize.c -o normalize.o
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include/Rdefines.h:143:28: warning: ‘dim’ may be used uninitialized in this function [-Wmaybe-uninitialized]
143 | #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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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)
