BioC 3.6: CHECK report for EBImage on veracruz1

Package: EBImage

Version: 4.19.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.19.8.tar.gz

StartedAt: 2017-08-16 02:30:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:32:14 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 77.5 seconds

RetCode: 0

Status:  OK

CheckDir: EBImage.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.19.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/EBImage.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.19.8’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc      6.7Mb
    images   1.7Mb
* checking package directory ... OK
* checking ‘build’ 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
EBImage 4.468  0.505   7.027
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...508c508
< checking 'computeFeatures' .................... PASS (2f1272bf9a3428b3) 3989786
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
587c587
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
674c674
< checking 'filter2' ............................ PASS (f63788502234dbd7) 26149148
---
> checking 'filter2' ............................ PASS (e5a3d2e924e050fe) 26149148
748c748
< checking 'computeFeatures' .................... PASS (5eaf503a54600569) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
828c828
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
908c908
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/EBImage.Rcheck/00check.log’
for details.

* 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:219:19: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses]
                uiSubY = uiYSize+1 >> 1;        uiYU = uiNrY-1;  uiYB = uiYU;
                         ˜˜˜˜˜˜˜^˜ ˜˜
clahe.c:219:19: note: place parentheses around the '+' expression to silence this warning
                uiSubY = uiYSize+1 >> 1;        uiYU = uiNrY-1;  uiYB = uiYU;
                                ^
                         (        )
clahe.c:231:23: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses]
                    uiSubX = uiXSize+1 >> 1;  uiXL = uiNrX - 1; uiXR = uiXL;
                             ˜˜˜˜˜˜˜^˜ ˜˜
clahe.c:231:23: note: place parentheses around the '+' expression to silence this warning
                    uiSubX = uiXSize+1 >> 1;  uiXL = uiNrX - 1; uiXR = uiXL;
                                    ^
                             (        )
clahe.c:183:13: warning: comparison of constant 65536 with expression of type 'kz_pixel_t' (aka 'unsigned short') is always false [-Wtautological-constant-out-of-range-compare]
    if (Max >= uiNR_OF_GREY) return -5;    /* maximum too large */
        ˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings 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:163:11: 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:163:17: warning: unused variable 'tgt' [-Wunused-variable]
  double *src, *tgt;
                ^
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-3.6-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)

name	user	system	elapsed
EBImage	4.468	0.505	7.027
Image	0.347	0.068	0.420
bwlabel	1.147	0.202	1.388
channel	0.623	0.215	0.854
clahe	0.142	0.026	0.180
colorLabels	0.063	0.027	0.090
colormap	0.450	0.254	0.715
combine	0.829	0.360	1.219
computeFeatures	0.769	0.143	0.927
display-shiny	0.009	0.000	0.010
display	0.973	0.270	1.278
distmap	0.190	0.013	0.208
drawCircle	0.073	0.010	0.084
equalize	1.210	0.330	1.574
fillHull	0.205	0.028	0.242
filter2	1.998	0.351	2.384
floodFill	0.514	0.130	0.650
gblur	0.289	0.036	0.333
io	0.478	0.104	1.885
localCurvature	0.667	0.194	0.864
medianFilter	0.541	0.087	0.630
morphology	0.081	0.015	0.096
normalize	0.013	0.003	0.016
ocontour	0.011	0.006	0.016
otsu	0.144	0.019	0.162
paintObjects	1.243	0.172	1.423
propagate	0.838	0.048	0.893
rmObjects	0.067	0.021	0.088
spatial	0.538	0.045	0.589
stackObjects	2.604	0.988	3.664
thresh	0.125	0.051	0.179
tile	0.313	0.312	0.639
transpose	0.136	0.031	0.167
watershed	0.089	0.005	0.100