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BioC 3.5: CHECK 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 Oleś
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.18.1.tar.gz
StartedAt: 2017-08-16 02:17:02 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:18:27 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 85.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘4.18.1’
* 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  8.6Mb
  sub-directories of 1Mb or more:
    doc      6.4Mb
    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 4.602   0.54   7.331
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...351,352c351
< checking 'localCurvature' ..................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpjzgwWy/365570df8eaa/display.html.
< PASS (80236128c43c5c64) aa70763bde359b48
---
> checking 'localCurvature' ..................... PASS (80236128c43c5c64) aa70763bde359b48
509c508
< checking 'computeFeatures' .................... PASS (2f1272bf9a3428b3) 3989786
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
588c587
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
591,592c590
< checking 'localCurvature' ..................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpjzgwWy/3655532e9385/display.html.
< PASS (9ddeedd40b4e5c7b) a2c60afaa6d43988
---
> checking 'localCurvature' ..................... PASS (9ddeedd40b4e5c7b) a2c60afaa6d43988
676c674
< checking 'filter2' ............................ PASS (f63788502234dbd7) 26149148
---
> checking 'filter2' ............................ PASS (e5a3d2e924e050fe) 26149148
750c748
< checking 'computeFeatures' .................... PASS (5eaf503a54600569) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
830c828
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
910,911c908
< LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpjzgwWy/365545e109fe/display.html.
< 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-3.5-bioc/meat/EBImage.Rcheck/00check.log’
for details.

EBImage.Rcheck/00install.out:

* 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: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;
                ^
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.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
EBImage4.6020.5407.331
Image0.3760.0780.461
bwlabel0.9200.1351.090
channel0.6970.2300.960
clahe0.1450.0320.179
colorLabels0.0760.0550.134
colormap0.4360.2510.707
combine0.7710.4031.230
computeFeatures0.8930.1751.102
display1.0220.3631.432
distmap0.1910.0280.225
drawCircle0.0870.0090.097
equalize1.2260.4491.712
fillHull0.2270.0300.266
filter22.3460.3652.828
floodFill0.2260.0440.277
gblur0.3510.0350.401
io0.6250.1432.152
localCurvature0.9380.2021.165
medianFilter0.7220.1070.844
morphology0.1570.0430.205
normalize0.0200.0070.027
ocontour0.0150.0080.028
otsu0.1730.0430.224
paintObjects1.6210.2471.924
propagate1.1370.0781.257
rmObjects0.0750.0120.098
spatial0.6710.0550.754
stackObjects3.0281.2244.375
thresh0.1340.0320.172
tile0.3330.3800.723
transpose0.1470.0340.189
watershed0.0940.0070.101