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BioC 3.5: BUILD BIN report for EBImage on veracruz2

This page was generated on 2017-08-16 13:27:41 -0400 (Wed, 16 Aug 2017).

Package 381/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBImage 4.18.1
Andrzej OleÅ›
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/EBImage
Last Changed Rev: 131633 / Revision: 131943
Last Changed Date: 2017-07-28 10:18:14 -0400 (Fri, 28 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: EBImage
Version: 4.18.1
Command: rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh EBImage_4.18.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R EBImage.buildbin-libdir
StartedAt: 2017-08-16 10:04:19 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 10:04:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 19.1 seconds
RetCode: 0
Status:  OK 
PackageFile: EBImage_4.18.1.tgz
PackageFileSize: 6.268 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBImage.buildbin-libdir && mkdir EBImage.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh EBImage_4.18.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R EBImage.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=EBImage.buildbin-libdir EBImage_4.18.1.tar.gz'
>>>>>>> 

* installing *source* package ‘EBImage’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c EBImage.c -o EBImage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c clahe.c -o clahe.o
clahe.c:194:13: warning: comparison of constant 256 with expression of type 'kz_pixel_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare]
    if (Max >= uiNR_OF_GREY) return -5;    /* maximum too large */
        ˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c distmap.cpp -o distmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c drawCircle.c -o drawCircle.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c floodFill.cpp -o floodFill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c getFrames.c -o getFrames.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c haralick.c -o haralick.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c medianFilter.c -o medianFilter.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c morphology.cpp -o morphology.o
morphology.cpp:78:32: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                               ^˜
                               .C = 
morphology.cpp:78:41: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                        ^˜˜˜˜˜˜˜
                                        .CLength = 
morphology.cpp:78:53: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                                    ^˜˜˜˜˜˜˜˜˜˜
                                                    .minYoffset = 
morphology.cpp:78:76: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                                                           ^˜˜˜˜˜˜˜˜˜˜
                                                                           .maxYoffset = 
morphology.cpp:78:100: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                                                                                   ^˜˜˜˜˜˜˜˜˜˜
                                                                                                   .minXoffset = 
morphology.cpp:78:123: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                                                                                                          ^˜˜˜˜˜˜˜˜˜˜
                                                                                                                          .maxXoffset = 
morphology.cpp:78:147: warning: use of GNU old-style field designator extension [-Wgnu-designator]
    chordSet set = (chordSet) {C: NULL, CLength: 0, minYoffset: korigin.y, maxYoffset: -korigin.y, minXoffset: korigin.x, maxXoffset: -korigin.x, maxN: 0};
                                                                                                                                                  ^˜˜˜˜
                                                                                                                                                  .maxN = 
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) {
             ^
25 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nativeRaster.c -o nativeRaster.o
nativeRaster.c:38:7: warning: assigning to 'uint32_t *' (aka 'unsigned int *') from 'int *' converts between pointers to integer types with different sign [-Wpointer-sign]
  out = INTEGER(res);
      ^ ˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c normalize.c -o normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -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 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ocontour.c -o ocontour.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c propagate.cpp -o propagate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spatial.c -o spatial.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -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:163:17: warning: unused variable 'tgt' [-Wunused-variable]
  double *src, *tgt;
                ^
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:161:29: warning: unused variable 'y' [-Wunused-variable]
  int nprotect=0, i, j, im, y, iim;
                            ^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tools.c -o tools.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c transpose.cpp -o transpose.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c watershed.cpp -o watershed.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/EBImage.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR EBImage.buildbin-libdir/EBImage/libs//EBImage.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "EBImage.buildbin-libdir/EBImage/libs//EBImage.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "EBImage.buildbin-libdir/EBImage/libs//EBImage.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "EBImage.buildbin-libdir/EBImage/libs//EBImage.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "EBImage.buildbin-libdir/EBImage/libs//EBImage.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "EBImage.buildbin-libdir/EBImage/libs//EBImage.so"