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Package 199/671HostnameOS / ArchBUILDCHECKBUILD BIN
EBImage 4.2.1
Andrzej Oles
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/EBImage
Last Changed Rev: 75776 / Revision: 76155
Last Changed Date: 2013-04-18 05:16:43 -0700 (Thu, 18 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: EBImage
Version: 4.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBImage_4.2.1.tar.gz
StartedAt: 2013-05-01 04:57:54 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:00:49 -0700 (Wed, 01 May 2013)
EllapsedTime: 175.4 seconds
RetCode: 0
Status:  OK 
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/EBImage.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'EBImage/DESCRIPTION' ... OK
* this is package 'EBImage' version '4.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'EBImage' can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [108s/114s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
EBImage      20.836  2.294  25.200
stackObjects 16.122  3.065  19.739
paintObjects 11.183  1.249  13.416
propagate    10.955  0.313  11.786
medianFilter  5.685  0.719   6.531
display       4.449  1.010   5.609
io            3.040  1.154   5.748
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [6s/6s]
  Comparing 'test.Rout' to 'test.Rout.save' ...202,205c202,205
< checking 'erodeGreyScale' ... OK (hash=2720750)
< checking 'dilateGreyScale' ... OK (hash=3113874)
< checking 'whiteTopHatGreyScale' ... OK (hash=73793.25)
< checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=145920.1)
---
> checking 'erodeGreyScale' ... OK (hash=2693268)
> checking 'dilateGreyScale' ... OK (hash=3097664)
> checking 'whiteTopHatGreyScale' ... OK (hash=91389.01)
> checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=148854.6)
254,257c254,257
< checking 'erodeGreyScale' ... OK (hash=5256840)
< checking 'dilateGreyScale' ... OK (hash=5764880)
< checking 'whiteTopHatGreyScale' ... OK (hash=136404.6)
< checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=280896.1)
---
> checking 'erodeGreyScale' ... OK (hash=5123645)
> checking 'dilateGreyScale' ... OK (hash=5764578)
> checking 'whiteTopHatGreyScale' ... OK (hash=140101.3)
> checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=144311.9)
 [6s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

EBImage.Rcheck/00install.out:

* installing *source* package 'EBImage' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c EBImage.c -o EBImage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c distmap.c -o distmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c drawCircle.c -o drawCircle.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c floodFill.cpp -o floodFill.o
In file included from floodFill.cpp:1:
./floodFill.h:16:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from floodFill.cpp:2:
./tools.h:37:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c greyscale_morphology.c -o greyscale_morphology.o
greyscale_morphology.c:136:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                CHECK_BUFFER(set.R, set.RLength, RBufLength, int)
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
greyscale_morphology.c:23:34: note: expanded from macro 'CHECK_BUFFER'
    pointer = R_Realloc(pointer, buffer, type);\
                                 ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:67:70: note: expanded from macro 'R_Realloc'
#define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                     ^
greyscale_morphology.c:142:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                CHECK_BUFFER(set.C, set.CLength, CBufLength, chord)
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
greyscale_morphology.c:23:34: note: expanded from macro 'CHECK_BUFFER'
    pointer = R_Realloc(pointer, buffer, type);\
                                 ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:67:70: note: expanded from macro 'R_Realloc'
#define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                     ^
greyscale_morphology.c:157:25: warning: implicit conversion turns floating-point number into integer: 'numeric' (aka 'double') to 'int' [-Wconversion]
            prevValue = kern[index];
                      ˜ ^˜˜˜˜˜˜˜˜˜˜
greyscale_morphology.c:168:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        CHECK_BUFFER(set.R, set.RLength, RBufLength, int)
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
greyscale_morphology.c:23:34: note: expanded from macro 'CHECK_BUFFER'
    pointer = R_Realloc(pointer, buffer, type);\
                                 ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:67:70: note: expanded from macro 'R_Realloc'
#define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                     ^
greyscale_morphology.c:178:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            CHECK_BUFFER(set.R, set.RLength, RBufLength, int)
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
greyscale_morphology.c:23:34: note: expanded from macro 'CHECK_BUFFER'
    pointer = R_Realloc(pointer, buffer, type);\
                                 ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:67:70: note: expanded from macro 'R_Realloc'
#define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
                                                                     ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c haralick.c -o haralick.o
haralick.c:45:40: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      if ( data[index] > nobj ) nobj = floor( data[index] );
                                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:69:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    ncomp = (int *) R_alloc (nobj, sizeof(int) );
                    ˜˜˜˜˜˜˜  ^˜˜˜
haralick.c:76:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        index = floor( data[x + y * nx] ); /* index of the object, R-style = 1-based */
              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:80:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        colthis = floor(refdata[x + y * nx] * (nc - 1));
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:83:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          colthat = floor(refdata[x+1 + y * nx] * (nc - 1));
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:89:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          colthat = floor(refdata[x + (y+1) * nx] * (nc - 1));
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:95:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          colthat = floor(refdata[x+1 + (y+1) * nx] * (nc - 1));
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:101:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          colthat = floor(refdata[x-1 + (y+1) * nx] * (nc - 1));
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
haralick.c:170:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  px   = (double *) R_alloc (nc, sizeof(double) );
                    ˜˜˜˜˜˜˜  ^˜
haralick.c:171:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  Pxpy = (double *) R_alloc(2 * nc + 10, sizeof(double) ); // +10 is to be safe with limits
                    ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜
haralick.c:172:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  Pxmy = (double *) R_alloc(2 * nc + 10, sizeof(double) ); // +10 is to be safe with limits
                    ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c medianFilter.c -o medianFilter.o
medianFilter.c:240:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    h_coarse = (uint16_t*) _mm_malloc(  1 * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t), 16 );
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
medianFilter.c:241:80: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    h_fine   = (uint16_t*) _mm_malloc( SQRT_BUCKET_SIZE * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t), 16 );
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
medianFilter.c:242:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset( h_coarse, 0,  1 * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
medianFilter.c:242:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset( h_coarse, 0,  1 * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
medianFilter.c:243:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset( h_fine,   0, SQRT_BUCKET_SIZE * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t) );
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
medianFilter.c:243:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset( h_fine,   0, SQRT_BUCKET_SIZE * SQRT_BUCKET_SIZE * n * cn * sizeof(uint16_t) );
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
medianFilter.c:283:23: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset( H, 0, cn*sizeof(H[0]) );
                      ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
medianFilter.c:283:23: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset( H, 0, cn*sizeof(H[0]) );
                      ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
medianFilter.c:284:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset( luc, 0, cn*sizeof(luc[0]) );
                        ^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
medianFilter.c:284:25: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memset( luc, 0, cn*sizeof(luc[0]) );
                        ^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
medianFilter.c:287:35: warning: implicit conversion loses integer precision: 'const int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                histogram_muladd( r, &h_coarse[SQRT_BUCKET_SIZE*n*c], H[c].coarse );
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^
medianFilter.c:297:38: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                histogram_muladd( 2*r+1, &h_fine[SQRT_BUCKET_SIZE*n*(SQRT_BUCKET_SIZE*c+k)], &H[c].fine[k][0] );
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜˜˜^˜
medianFilter.c:303:42: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                const uint16_t t = 2*r*r + 2*r;
                               ˜   ˜˜˜˜˜˜^˜˜˜˜
medianFilter.c:322:40: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                    for ( luc[c][k] = j-r; luc[c][k] < MIN(j+r+1,n); ++luc[c][k] ) {
                                    ˜ ˜^˜
medianFilter.c:326:49: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        histogram_muladd( j+r+1 - n, &h_fine[SQRT_BUCKET_SIZE*(n*(SQRT_BUCKET_SIZE*c+k)+(n-1))], &H[c].fine[k][0] );
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜^˜˜
medianFilter.c:327:40: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        luc[c][k] = j+r+1;
                                  ˜ ˜˜˜^˜
medianFilter.c:344:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
                        dst[dst_step*i+cn*j+c] = SQRT_BUCKET_SIZE*k + b;
                                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
medianFilter.c:436:88: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    int stripes = (int) ceil( (double) (width - 2*r) / (memsize / sizeof(Histogram) - 2*r) );
                                                                                    ˜ ˜^˜
medianFilter.c:474:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
 px = (uint16_t *) R_alloc(size.x*size.y*(*cn), sizeof(uint16_t));
                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
medianFilter.c:475:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
 py = (uint16_t *) R_alloc(size.x*size.y*(*cn), sizeof(uint16_t));
                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
medianFilter.c:479:78: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
 ctmf(px, py, size.x, size.y, size.x*(*cn), size.x*(*cn), *r, *cn, (*memsize)*1024);
 ˜˜˜˜                                                              ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
21 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c morphology.c -o morphology.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c normalize.c -o normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c objects.c -o objects.o
objects.c:102:42: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
            if ( data[i] > nobj ) nobj = data[i];
                                       ˜ ^˜˜˜˜˜˜
objects.c:142:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int ext = floor(REAL(extension)[0]);
      ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
objects.c:173:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    for (i = 0; i < nx * ny; i++) if (dobj[i] > nobj) nobj = dobj[i];
                                                           ˜ ^˜˜˜˜˜˜
objects.c:240:29: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
          index = dobj[x + y * nx] - 1; // background index 0 is not kept
                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
objects.c:249:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
            pxi = xx + yy * snx;
                ˜ ˜˜˜^˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ocontour.c -o ocontour.o
ocontour.c:82:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(INTEGER(_oc), octemp, nboc*2*sizeof(int));
                                 ˜˜˜˜^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
ocontour.c:82:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(INTEGER(_oc), octemp, nboc*2*sizeof(int));
                                 ˜˜˜˜^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c propagate.cpp -o propagate.o
In file included from propagate.cpp:32:
./propagate.h:14:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from propagate.cpp:34:
./tools.h:37:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
propagate.cpp:81:75: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pixel_diff += fabs(clamped_fetch(image, i1 + delta_i, j1 + delta_j, m, n) - 
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜                                    ^
propagate.cpp:81:78: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pixel_diff += fabs(clamped_fetch(image, i1 + delta_i, j1 + delta_j, m, n) - 
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^
propagate.cpp:82:75: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                         clamped_fetch(image, i2 + delta_i, j2 + delta_j, m, n));
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜                                    ^
propagate.cpp:82:78: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                         clamped_fetch(image, i2 + delta_i, j2 + delta_j, m, n));
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜                                       ^
propagate.cpp:104:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j, m, n, lambda), i-1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:104:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j, m, n, lambda), i-1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:104:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j, m, n, lambda), i-1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:104:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j, m, n, lambda), i-1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ^
propagate.cpp:108:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j-1, m, n, lambda), i, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:108:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j-1, m, n, lambda), i, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:108:52: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j-1, m, n, lambda), i, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ^
propagate.cpp:108:56: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j-1, m, n, lambda), i, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜                 ˜^˜
propagate.cpp:112:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j, m, n, lambda), i+1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:112:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j, m, n, lambda), i+1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:112:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j, m, n, lambda), i+1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:112:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j, m, n, lambda), i+1, j, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ^
propagate.cpp:116:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j+1, m, n, lambda), i, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:116:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j+1, m, n, lambda), i, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:116:52: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j+1, m, n, lambda), i, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ^
propagate.cpp:116:56: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i, j+1, m, n, lambda), i, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜                 ˜^˜
propagate.cpp:122:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j-1, m, n, lambda), i-1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:122:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j-1, m, n, lambda), i-1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:122:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j-1, m, n, lambda), i-1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:122:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j-1, m, n, lambda), i-1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ˜^˜
propagate.cpp:126:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j-1, m, n, lambda), i+1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:126:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j-1, m, n, lambda), i+1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:126:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j-1, m, n, lambda), i+1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:126:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j-1, m, n, lambda), i+1, j-1, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ˜^˜
propagate.cpp:130:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j+1, m, n, lambda), i-1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:130:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j+1, m, n, lambda), i-1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:130:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j+1, m, n, lambda), i-1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:130:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i-1, j+1, m, n, lambda), i-1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ˜^˜
propagate.cpp:134:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j+1, m, n, lambda), i+1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜        ^
propagate.cpp:134:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j+1, m, n, lambda), i+1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜           ^
propagate.cpp:134:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j+1, m, n, lambda), i+1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜              ˜^˜
propagate.cpp:134:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      pq.push(Pixel(dist + Difference(image, i, j, i+1, j+1, m, n, lambda), i+1, j+1, label));
                           ˜˜˜˜˜˜˜˜˜˜                   ˜^˜
propagate.cpp:209:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    _propagate(seeds, x, imask, tgt, dists, nx, ny, lambda); 
    ˜˜˜˜˜˜˜˜˜˜                              ^˜
propagate.cpp:209:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    _propagate(seeds, x, imask, tgt, dists, nx, ny, lambda); 
    ˜˜˜˜˜˜˜˜˜˜                                  ^˜
40 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c spatial.c -o spatial.o
spatial.c:46:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int ftx = floor(tx);
            ˜˜˜   ^˜˜˜˜˜˜˜˜
spatial.c:47:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int fty = floor(ty);
            ˜˜˜   ^˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c thresh.c -o thresh.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c tile.c -o tile.o
tile.c:38:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  ndy = ceil( nz * onetondx ); // number of tiles in y-dir
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tile.c:78:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      y = lwd + floor(index * onetondx) * (ny + lwd) + j;
        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
tile.c:79:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
      x = lwd + (index - floor(index * onetondx) * ndx) * (nx + lwd);
        ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tile.c:85:91: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (oredstride!=-1)   memcpy( &(dim[i+rredstride]), &(REAL(obj)[j* nx+oredstride]), nx * sizeof(double));
                                                                                          ^˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:85:91: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (oredstride!=-1)   memcpy( &(dim[i+rredstride]), &(REAL(obj)[j* nx+oredstride]), nx * sizeof(double));
                                                                                          ^˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:86:95: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (ogreenstride!=-1) memcpy( &(dim[i+rgreenstride]), &(REAL(obj)[j* nx+ogreenstride]), nx * sizeof(double));
                                                                                              ^˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:86:95: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (ogreenstride!=-1) memcpy( &(dim[i+rgreenstride]), &(REAL(obj)[j* nx+ogreenstride]), nx * sizeof(double));
                                                                                              ^˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:87:93: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (obluestride!=-1)  memcpy( &(dim[i+rbluestride]), &(REAL(obj)[j* nx+obluestride]), nx * sizeof(double));
                                                                                            ^˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:87:93: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if (obluestride!=-1)  memcpy( &(dim[i+rbluestride]), &(REAL(obj)[j* nx+obluestride]), nx * sizeof(double));
                                                                                            ^˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:175:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:175:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:180:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:180:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:185:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
tile.c:185:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tgt, src, nx*sizeof(double));
                         ^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
tile.c:129:37: warning: unused variable 'id' [-Wunused-variable]
  void *src, *tgt; double *dd; int *id;
                                    ^
16 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c tools.c -o tools.o
tools.c:8:19: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
    return sqrt ( (long double)( (pt1.x - pt2.x) * (pt1.x - pt2.x) + (pt1.y - pt2.y) * (pt1.y - pt2.y) ) );
           ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tools.c:14:19: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
    return sqrt ( (long double)( (x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) ) );
           ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tools.c:21:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    res.y = floor (index / xsize);
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c watershed.cpp -o watershed.o
In file included from watershed.cpp:1:
./watershed.h:14:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from watershed.cpp:9:
./tools.h:37:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o EBImage.so EBImage.o distmap.o drawCircle.o floodFill.o greyscale_morphology.o haralick.o medianFilter.o morphology.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o watershed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/EBImage.Rcheck/EBImage/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBImage)

EBImage.Rcheck/EBImage-Ex.timings:

nameusersystemelapsed
EBImage20.836 2.29425.200
Image0.5410.3630.928
bwlabel2.9720.7313.811
channel2.4510.8833.390
combine0.0050.0080.013
computeFeatures2.2930.8063.138
display4.4491.0105.609
distmap0.1460.0470.197
drawCircle0.1070.1010.212
fillHull0.7980.2691.071
filter22.4310.4062.993
floodFill0.3930.2240.618
gblur0.4830.1060.589
io3.0401.1545.748
localCurvature2.2771.0043.329
medianFilter5.6850.7196.531
morphology0.0620.0310.096
normalize0.0690.0770.149
ocontour0.0460.0190.067
paintObjects11.183 1.24913.416
propagate10.955 0.31311.786
rmObjects0.1290.0530.196
spatial0.2550.1980.470
stackObjects16.122 3.06519.739
thresh0.5930.2900.896
tile0.7040.5991.310
transpose0.3270.2440.575
watershed0.1720.0390.212