############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EBImage_4.34.0.tar.gz && rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBImage.buildbin-libdir EBImage_4.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EBImage_4.34.0.zip && rm EBImage_4.34.0.tar.gz EBImage_4.34.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1878k 100 1878k 0 0 3774k 0 --:--:-- --:--:-- --:--:-- 3780k install for i386 * installing *source* package 'EBImage' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EBImage.c -o EBImage.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c clahe.c -o clahe.o clahe.c: In function 'CLAHE': clahe.c:223:19: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; ~~~~~~~^~ clahe.c:235:23: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; ~~~~~~~^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distmap.cpp -o distmap.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c drawCircle.c -o drawCircle.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c floodFill.cpp -o floodFill.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFrames.c -o getFrames.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c haralick.c -o haralick.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c medianFilter.c -o medianFilter.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:196:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:199:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:203:15: warning: statement has no effect [-Wunused-value] 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:163:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:166:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:170:15: warning: statement has no effect [-Wunused-value] 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:196:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:199:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:203:15: warning: statement has no effect [-Wunused-value] 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:163:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:166:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:170:15: warning: statement has no effect [-Wunused-value] for (i; i < size.x + set->maxXoffset; ++i) { ^ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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] out = INTEGER(res); ^ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normalize.c -o normalize.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c objects.c -o objects.o objects.c: In function 'paintObjects': objects.c:21:30: warning: unused variable 'dp' [-Wunused-variable] 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] return res; ^~~ In file included from objects.h:5, from objects.c:1: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:154:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_DIM(x, n) Rf_setAttrib(x, R_DimSymbol, n) ^~~~~~~~~~~~ objects.c:192:13: note: 'dim' was declared here SEXP res, dim, xys, img; ^~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ocontour.c -o ocontour.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] if (! mask_in[IJ(p.i, p.j)]) continue; ^ propagate.cpp:197:8: note: 'mask' was declared here int *mask; ^~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c spatial.c -o spatial.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 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] "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] SEXP res, dm, ims; ^~~ tile.cpp: In function 'SEXPREC* untile(SEXP, SEXP, SEXP)': tile.cpp:161:29: warning: unused variable 'y' [-Wunused-variable] int nprotect=0, i, j, im, y, iim; ^ tile.cpp:162:18: warning: unused variable 'dat' [-Wunused-variable] SEXP res, dim, dat; ^~~ tile.cpp:163:11: warning: unused variable 'src' [-Wunused-variable] double *src, *tgt; ^~~ tile.cpp:163:17: warning: unused variable 'tgt' [-Wunused-variable] double *src, *tgt; ^~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tools.c -o tools.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transpose.cpp -o transpose.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c watershed.cpp -o watershed.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o EBImage.dll tmp.def 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 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBImage.buildbin-libdir/00LOCK-EBImage/00new/EBImage/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'abind' in package 'EBImage' ** help *** installing help indices converting help for package 'EBImage' finding HTML links ... done EBImage-defunct html EBImage html Image html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/EBImage.buildbin-libdir/00LOCK-EBImage/00new/EBImage/help/colormode.html abind html bwlabel html channel html clahe html colorLabels html colormap html combine html computeFeatures html display-shiny html display html finding level-2 HTML links ... done distmap html drawCircle html equalize html fillHull html filter2 html floodFill html gblur html io html localCurvature html medianFilter html morphology html normalize html ocontour html otsu html paintObjects html propagate html rmObjects html spatial html stackObjects html thresh html tile html transpose html watershed html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'EBImage' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EBImage.c -o EBImage.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c clahe.c -o clahe.o clahe.c: In function 'CLAHE': clahe.c:223:19: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; ~~~~~~~^~ clahe.c:235:23: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; ~~~~~~~^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distmap.cpp -o distmap.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c drawCircle.c -o drawCircle.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c floodFill.cpp -o floodFill.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getFrames.c -o getFrames.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c haralick.c -o haralick.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c medianFilter.c -o medianFilter.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:196:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:199:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:203:15: warning: statement has no effect [-Wunused-value] 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:163:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:166:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:170:15: warning: statement has no effect [-Wunused-value] 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:196:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:199:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:203:15: warning: statement has no effect [-Wunused-value] 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:163:15: warning: statement has no effect [-Wunused-value] for (i; i < 0; ++i) { ^ morphology.cpp:166:15: warning: statement has no effect [-Wunused-value] for (i; i < maxX; ++i) { ^ morphology.cpp:170:15: warning: statement has no effect [-Wunused-value] for (i; i < size.x + set->maxXoffset; ++i) { ^ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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] out = INTEGER(res); ^ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c normalize.c -o normalize.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c objects.c -o objects.o objects.c: In function 'paintObjects': objects.c:21:30: warning: unused variable 'dp' [-Wunused-variable] 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] return res; ^~~ In file included from objects.h:5, from objects.c:1: C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:154:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized] #define SET_DIM(x, n) Rf_setAttrib(x, R_DimSymbol, n) ^~~~~~~~~~~~ objects.c:192:13: note: 'dim' was declared here SEXP res, dim, xys, img; ^~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ocontour.c -o ocontour.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] if (! mask_in[IJ(p.i, p.j)]) continue; ^ propagate.cpp:197:8: note: 'mask' was declared here int *mask; ^~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c spatial.c -o spatial.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 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] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] SEXP res, dm, ims; ^~~ tile.cpp: In function 'SEXPREC* untile(SEXP, SEXP, SEXP)': tile.cpp:161:29: warning: unused variable 'y' [-Wunused-variable] int nprotect=0, i, j, im, y, iim; ^ tile.cpp:162:18: warning: unused variable 'dat' [-Wunused-variable] SEXP res, dim, dat; ^~~ tile.cpp:163:11: warning: unused variable 'src' [-Wunused-variable] double *src, *tgt; ^~~ tile.cpp:163:17: warning: unused variable 'tgt' [-Wunused-variable] double *src, *tgt; ^~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tools.c -o tools.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transpose.cpp -o transpose.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c watershed.cpp -o watershed.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o EBImage.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'EBImage' as EBImage_4.34.0.zip * DONE (EBImage) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'EBImage' successfully unpacked and MD5 sums checked