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BioC 3.5: CHECK report for EBImage on tokay2

This page was generated on 2017-08-16 13:19:11 -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 EBImage.Rcheck && mkdir EBImage.buildbin-libdir EBImage.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBImage.buildbin-libdir EBImage_4.18.1.tar.gz >EBImage.Rcheck\00install.out 2>&1 && cp EBImage.Rcheck\00install.out EBImage-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=EBImage.buildbin-libdir --install="check:EBImage-install.out" --force-multiarch --no-vignettes --timings EBImage_4.18.1.tar.gz
StartedAt: 2017-08-15 23:25:53 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:29:18 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 205.1 seconds
RetCode: 0
Status:  OK  
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBImage.buildbin-libdir EBImage.Rcheck && mkdir EBImage.buildbin-libdir EBImage.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBImage.buildbin-libdir EBImage_4.18.1.tar.gz >EBImage.Rcheck\00install.out 2>&1 && cp EBImage.Rcheck\00install.out EBImage-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=EBImage.buildbin-libdir --install="check:EBImage-install.out" --force-multiarch --no-vignettes --timings EBImage_4.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'EBImage' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc      5.0Mb
    images   1.7Mb
    libs     1.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/i386/EBImage.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
EBImage  7.3   0.82   13.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
EBImage 5.78   0.78     8.7
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
  Comparing 'test.Rout' to 'test.Rout.save' ...222,225c222,225
< checking IO for 'sample' ... FAIL
< checking IO for 'sample.color' ... FAIL
< checking IO for 'nuclei' ... FAIL
< checking IO for 'logo' ... FAIL
---
> checking IO for 'sample' ... PASS
> checking IO for 'sample.color' ... PASS
> checking IO for 'nuclei' ... PASS
> checking IO for 'logo' ... PASS
331c331
< checking 'rotate' ............................. PASS (088dd8b96f88132b) 483.6843
---
> checking 'rotate' ............................. PASS (6fef9b3e4085e72c) 483.6843
389c389
< checking 'hist' ............................... PASS (6f582e57b9d39351) 7574da3879d26bc5
---
> checking 'hist' ............................... PASS (758d77d39292aceb) 22261eb2334cd65e
410,411c410,411
< checking 'resize' ............................. PASS (58a1e87fc7f80a75) 1419476
< checking 'rotate' ............................. PASS (85dbbdd76b94062f) 2493977
---
> checking 'resize' ............................. PASS (00fab9ec40eb5e2f) 1419476
> checking 'rotate' ............................. PASS (447c32314cc4e9d7) 2493977
415c415
< checking 'affine' ............................. PASS (ca5cb529f9bc5201) 54171.17
---
> checking 'affine' ............................. PASS (1ed86f465543429e) 54171.17
432c432
< checking 'normalize' .......................... PASS (c52f0e1b5f71ed30) 1431381
---
> checking 'normalize' .......................... PASS (dd024957ed9be970) 1431381
490,491c490,491
< checking 'resize' ............................. PASS (09d631cf6bbbe045) 2941770
< checking 'rotate' ............................. PASS (76b31508bb82fc43) 1247487
---
> checking 'resize' ............................. PASS (3e691caece9a23f3) 2941770
> checking 'rotate' ............................. PASS (8445c36b57d60c5d) 1247487
495c495
< checking 'affine' ............................. PASS (a9d3083b4b79134f) 22238.15
---
> checking 'affine' ............................. PASS (3aca89b692c9110c) 22238.15
508c508
< checking 'computeFeatures' .................... PASS (445b221e24c87b72) 3990189
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
569,570c569,570
< checking 'resize' ............................. PASS (d84d391c48e19630) 15155777
< checking 'rotate' ............................. PASS (0e682da4c2d3fc08) 4525312
---
> checking 'resize' ............................. PASS (75a7216227f8dbfa) 15155777
> checking 'rotate' ............................. PASS (cba5275a49d1c025) 4525312
574c574
< checking 'affine' ............................. PASS (b991742daa634d98) 226067.6
---
> checking 'affine' ............................. PASS (091470a40c4fba44) 226067.6
587c587
< checking 'computeFeatures' .................... PASS (4a081a1eefd4acc9) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
650,651c650,651
< checking 'resize' ............................. PASS (b50a31835364c09e) 9108608
< checking 'rotate' ............................. PASS (7b2ebfe00d3a3a42) 1600126
---
> checking 'resize' ............................. PASS (b189246d26913306) 9108608
> checking 'rotate' ............................. PASS (a4a84e73999cd629) 1600126
655c655
< checking 'affine' ............................. PASS (05fc5cb10e082fd3) 133467.8
---
> checking 'affine' ............................. PASS (4a6b1cf59de37216) 133467.8
668c668
< checking 'computeFeatures' .................... PASS (ff70e8e7d5c1f3ed) 416154745
---
> checking 'computeFeatures' .................... PASS (1d847743be56e5a7) 416164140
673,674c673,674
< checking 'gblur' .............................. PASS (458650b37f0343dd) 1037581
< checking 'filter2' ............................ PASS (bd3a768b0d187c23) 26149148
---
> checking 'gblur' .............................. PASS (f499c36c42da96ae) 1037581
> checking 'filter2' ............................ PASS (e5a3d2e924e050fe) 26149148
730,731c730,731
< checking 'resize' ............................. PASS (5ad3e43560133426) 76725662
< checking 'rotate' ............................. PASS (c00f3179a9298754) 4140744
---
> checking 'resize' ............................. PASS (19f045e2a12c3dcd) 76725662
> checking 'rotate' ............................. PASS (5ca7d358dc5f6cb8) 4140744
735c735
< checking 'affine' ............................. PASS (fbf2f25eade0659a) 301692.6
---
> checking 'affine' ............................. PASS (8490fa9d387d7f22) 301692.6
748c748
< checking 'computeFeatures' .................... PASS (cd365d27117f6c14) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
752c752
< checking 'normalize' .......................... PASS (7dda630cba451455) 2693244
---
> checking 'normalize' .......................... PASS (6f82aae3b180c153) 2693244
810,811c810,811
< checking 'resize' ............................. PASS (13c670f51a30c923) 72772706
< checking 'rotate' ............................. PASS (e9f525591f2229cf) 3978266
---
> checking 'resize' ............................. PASS (c2412da2d423bb4c) 72772706
> checking 'rotate' ............................. PASS (e88e2e93ce61d959) 3978266
815c815
< checking 'affine' ............................. PASS (af56a3e7ebac2881) 219714.6
---
> checking 'affine' ............................. PASS (987d2bf7d6243ac5) 219714.6
828c828
< checking 'computeFeatures' .................... PASS (8f8affb55724e2fe) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
832c832
< checking 'normalize' .......................... PASS (0e05442ba3086ec5) 2526618
---
> checking 'normalize' .......................... PASS (c6700c53a770f4dc) 2526618
890,891c890,891
< checking 'resize' ............................. PASS (7b3beb675b6c79c3) 72772706
< checking 'rotate' ............................. PASS (5cccffa37dd92aa2) 3978266
---
> checking 'resize' ............................. PASS (d4439ccaddffedbf) 72772706
> checking 'rotate' ............................. PASS (49bab3d36db066a3) 3978266
895c895
< checking 'affine' ............................. PASS (0909fbeb314a51f1) 219714.6
---
> checking 'affine' ............................. PASS (6f88949e9ca0500f) 219714.6
908c908
< checking 'computeFeatures' .................... PASS (8f8affb55724e2fe) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
912c912
< checking 'normalize' .......................... PASS (5b0492833b6f1cf5) 2526618
---
> checking 'normalize' .......................... PASS (c864fc347d3e1eec) 2526618
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpUFMP6K\Rdiffa9604e6e4807" "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpUFMP6K\Rdiffb9603a994fb5"' had status 1 
 OK
** running tests for arch 'x64' ...
  Running 'test.R'
  Comparing 'test.Rout' to 'test.Rout.save' ...389c389
< checking 'hist' ............................... PASS (25c2c5f6936c4cc3) 6cce517eeddbb6cd
---
> checking 'hist' ............................... PASS (758d77d39292aceb) 22261eb2334cd65e
587c587
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
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
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmp2LbvSD\Rdiffac28c20302d" "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmp2LbvSD\Rdiffbc281a4a68e0"' had status 1 
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck/00check.log'
for details.


EBImage.Rcheck/00install.out:


install for i386

* installing *source* package 'EBImage' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c clahe.c -o clahe.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distmap.cpp -o distmap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c getFrames.c -o getFrames.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c morphology.cpp -o morphology.o
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = int]':
morphology.cpp:253:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]'
morphology.cpp:374:79:   required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = int]':
morphology.cpp:257:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]'
morphology.cpp:374:79:   required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = double]':
morphology.cpp:253:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]'
morphology.cpp:377:76:   required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = double]':
morphology.cpp:257:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]'
morphology.cpp:377:76:   required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:38:7: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
   out = INTEGER(res);
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
objects.c: In function 'paintObjects':
objects.c:21:30: warning: unused variable 'dp' [-Wunused-variable]
     double *obj, *src, *tgt, dp, val;
                              ^
In file included from objects.h:5:0,
                 from objects.c:1:
objects.c: In function 'stackObjects':
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rdefines.h:152:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_DIM(x, n)      Rf_setAttrib(x, R_DimSymbol, n)
                            ^
objects.c:192:13: note: 'dim' was declared here
   SEXP res, dim, xys, img;
             ^
objects.c:291:10: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
     else SET_VECTOR_ELT(res, im, img);
          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
propagate.cpp: In function 'SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)':
propagate.cpp:174:31: warning: 'mask' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (! mask_in[IJ(p.i, p.j)]) continue;
                               ^
propagate.cpp:197:8: note: 'mask' was declared here
   int *mask;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c thresh.cpp -o thresh.o
thresh.cpp: In instantiation of 'void _thresh(T*, int*, int, int, int, int, double) [with T = int]':
thresh.cpp:50:76:   required from here
thresh.cpp:64:42: warning: unused variable 'i' [-Wunused-variable]
     int xi, yi, u, k, l, ou, nu, ov, nv, i;
                                          ^
thresh.cpp: In instantiation of 'void _thresh(T*, int*, int, int, int, int, double) [with T = double]':
thresh.cpp:53:76:   required from here
thresh.cpp:64:42: warning: unused variable 'i' [-Wunused-variable]
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tile.cpp -o tile.o
tile.cpp: In function 'SEXPREC* tile(SEXP, SEXP, SEXP)':
tile.cpp:24:17: warning: unused variable 'ims' [-Wunused-variable]
   SEXP res, dm, ims;
                 ^
tile.cpp: In function 'SEXPREC* untile(SEXP, SEXP, SEXP)':
tile.cpp:161:29: warning: unused variable 'y' [-Wunused-variable]
   int nprotect=0, i, j, im, y, iim;
                             ^
tile.cpp:162:18: warning: unused variable 'dat' [-Wunused-variable]
   SEXP res, dim, dat;
                  ^
tile.cpp:163:11: warning: unused variable 'src' [-Wunused-variable]
   double *src, *tgt;
           ^
tile.cpp:163:17: warning: unused variable 'tgt' [-Wunused-variable]
   double *src, *tgt;
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c tools.c -o tools.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c transpose.cpp -o transpose.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o EBImage.dll tmp.def EBImage.o clahe.o distmap.o drawCircle.o floodFill.o getFrames.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o transpose.o watershed.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'EBImage' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c clahe.c -o clahe.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c distmap.cpp -o distmap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c getFrames.c -o getFrames.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c morphology.cpp -o morphology.o
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = int]':
morphology.cpp:253:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]'
morphology.cpp:374:79:   required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = int]':
morphology.cpp:257:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]'
morphology.cpp:374:79:   required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = double]':
morphology.cpp:253:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]'
morphology.cpp:377:76:   required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
morphology.cpp: In instantiation of 'void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = double]':
morphology.cpp:257:39:   required from 'void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]'
morphology.cpp:340:59:   required from 'void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]'
morphology.cpp:377:76:   required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
         for (i; i < 0; ++i) {
               ^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
         for (i; i < maxX; ++i) {
               ^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
         for (i; i < size.x + set->maxXoffset; ++i) {
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:38:7: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
   out = INTEGER(res);
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
objects.c: In function 'paintObjects':
objects.c:21:30: warning: unused variable 'dp' [-Wunused-variable]
     double *obj, *src, *tgt, dp, val;
                              ^
In file included from objects.h:5:0,
                 from objects.c:1:
objects.c: In function 'stackObjects':
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rdefines.h:152:28: warning: 'dim' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_DIM(x, n)      Rf_setAttrib(x, R_DimSymbol, n)
                            ^
objects.c:192:13: note: 'dim' was declared here
   SEXP res, dim, xys, img;
             ^
objects.c:291:10: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
     else SET_VECTOR_ELT(res, im, img);
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
propagate.cpp: In function 'SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)':
propagate.cpp:174:31: warning: 'mask' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (! mask_in[IJ(p.i, p.j)]) continue;
                               ^
propagate.cpp:197:8: note: 'mask' was declared here
   int *mask;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c thresh.cpp -o thresh.o
thresh.cpp: In instantiation of 'void _thresh(T*, int*, int, int, int, int, double) [with T = int]':
thresh.cpp:50:76:   required from here
thresh.cpp:64:42: warning: unused variable 'i' [-Wunused-variable]
     int xi, yi, u, k, l, ou, nu, ov, nv, i;
                                          ^
thresh.cpp: In instantiation of 'void _thresh(T*, int*, int, int, int, int, double) [with T = double]':
thresh.cpp:53:76:   required from here
thresh.cpp:64:42: warning: unused variable 'i' [-Wunused-variable]
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c tile.cpp -o tile.o
tile.cpp: In function 'SEXPREC* tile(SEXP, SEXP, SEXP)':
tile.cpp:24:17: warning: unused variable 'ims' [-Wunused-variable]
   SEXP res, dm, ims;
                 ^
tile.cpp: In function 'SEXPREC* untile(SEXP, SEXP, SEXP)':
tile.cpp:161:29: warning: unused variable 'y' [-Wunused-variable]
   int nprotect=0, i, j, im, y, iim;
                             ^
tile.cpp:162:18: warning: unused variable 'dat' [-Wunused-variable]
   SEXP res, dim, dat;
                  ^
tile.cpp:163:11: warning: unused variable 'src' [-Wunused-variable]
   double *src, *tgt;
           ^
tile.cpp:163:17: warning: unused variable 'tgt' [-Wunused-variable]
   double *src, *tgt;
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c tools.c -o tools.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c transpose.cpp -o transpose.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o EBImage.dll tmp.def EBImage.o clahe.o distmap.o drawCircle.o floodFill.o getFrames.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o transpose.o watershed.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBImage' as EBImage_4.18.1.zip
* DONE (EBImage)

EBImage.Rcheck/examples_i386/EBImage-Ex.timings:

nameusersystemelapsed
EBImage 7.30 0.8213.54
Image0.650.090.75
bwlabel2.300.282.58
channel1.030.331.36
clahe0.310.050.36
colorLabels0.110.040.15
colormap0.640.381.02
combine1.410.361.77
computeFeatures1.090.261.35
display1.800.392.19
distmap0.390.020.41
drawCircle0.190.000.19
equalize2.010.502.51
fillHull0.500.010.52
filter23.310.683.98
floodFill0.380.010.39
gblur0.480.000.49
io1.080.192.37
localCurvature1.000.391.39
medianFilter2.500.142.64
morphology0.170.000.17
normalize0.050.000.05
ocontour0.000.010.01
otsu0.310.050.36
paintObjects2.220.262.49
propagate2.270.072.33
rmObjects0.120.030.15
spatial0.990.081.06
stackObjects3.361.314.68
thresh0.280.010.29
tile0.440.250.69
transpose0.280.040.31
watershed0.220.000.22

EBImage.Rcheck/examples_x64/EBImage-Ex.timings:

nameusersystemelapsed
EBImage5.780.788.70
Image0.550.110.72
bwlabel1.810.232.05
channel0.780.251.03
clahe0.140.020.15
colorLabels0.060.020.08
colormap0.380.310.69
combine0.630.451.08
computeFeatures0.780.130.91
display0.890.371.26
distmap0.190.020.21
drawCircle0.080.000.08
equalize1.250.481.73
fillHull0.290.090.39
filter22.640.503.14
floodFill0.200.050.25
gblur0.300.080.37
io0.750.121.90
localCurvature0.910.271.17
medianFilter0.810.130.94
morphology0.090.000.09
normalize0.020.010.03
ocontour0.030.000.03
otsu0.160.050.21
paintObjects1.510.281.79
propagate1.160.081.24
rmObjects0.110.000.11
spatial0.650.080.73
stackObjects2.802.144.94
thresh0.160.030.19
tile0.310.220.53
transpose0.160.030.19
watershed0.090.010.11