Andrzej Oleś
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) |
| URL: https://git.bioconductor.org/packages/EBImage |
| Branch: RELEASE_3_5 |
| Last Commit: 57f6a1e |
| Last Changed Date: 2017-10-05 07:53:10 -0400 (Thu, 05 Oct 2017) |
| Back to the "Multiple platform build/check report" | A B C D [E] F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:19:21 -0400 (Wed, 18 Oct 2017).
| Package 381/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EBImage 4.18.3 Andrzej Oleś
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: EBImage |
| Version: 4.18.3 |
| 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_4.18.3.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_4.18.3.tar.gz |
| StartedAt: 2017-10-17 23:29:39 -0400 (Tue, 17 Oct 2017) |
| EndedAt: 2017-10-17 23:32:48 -0400 (Tue, 17 Oct 2017) |
| EllapsedTime: 189.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBImage.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_4.18.3.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_4.18.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '4.18.3'
* 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 7.22 0.83 9.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EBImage 5.61 0.81 8.43
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
Comparing 'test.Rout' to 'test.Rout.save' ...223,226c223,226
< 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
333c333
< checking 'rotate' ............................. PASS (088dd8b96f88132b) 483.6843
---
> checking 'rotate' ............................. PASS (6fef9b3e4085e72c) 483.6843
355d354
< checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
356a356
> checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
392c392
< checking 'hist' ............................... PASS (6f582e57b9d39351) 7574da3879d26bc5
---
> checking 'hist' ............................... PASS (758d77d39292aceb) 22261eb2334cd65e
413,414c413,414
< checking 'resize' ............................. PASS (58a1e87fc7f80a75) 1419476
< checking 'rotate' ............................. PASS (85dbbdd76b94062f) 2493977
---
> checking 'resize' ............................. PASS (00fab9ec40eb5e2f) 1419476
> checking 'rotate' ............................. PASS (447c32314cc4e9d7) 2493977
418c418
< checking 'affine' ............................. PASS (ca5cb529f9bc5201) 54171.17
---
> checking 'affine' ............................. PASS (1ed86f465543429e) 54171.17
435,436c435,436
< checking 'normalize' .......................... PASS (c52f0e1b5f71ed30) 1431381
< checking 'normalize' .......................... PASS (00ce67aad1fc8cc2) 1266798
---
> checking 'normalize' .......................... PASS (dd024957ed9be970) 1431381
> checking 'normalize' .......................... PASS (327914cc2a95292d) 1266798
494,495c494,495
< checking 'resize' ............................. PASS (09d631cf6bbbe045) 2941770
< checking 'rotate' ............................. PASS (76b31508bb82fc43) 1247487
---
> checking 'resize' ............................. PASS (3e691caece9a23f3) 2941770
> checking 'rotate' ............................. PASS (8445c36b57d60c5d) 1247487
499c499
< checking 'affine' ............................. PASS (a9d3083b4b79134f) 22238.15
---
> checking 'affine' ............................. PASS (3aca89b692c9110c) 22238.15
512c512
< checking 'computeFeatures' .................... PASS (445b221e24c87b72) 3990189
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
517c517
< checking 'normalize' .......................... PASS (1e6214ed61d5da98) 809649.2
---
> checking 'normalize' .......................... PASS (4b1f8e1c8e2f7bf3) 809649.2
574,575c574,575
< checking 'resize' ............................. PASS (d84d391c48e19630) 15155777
< checking 'rotate' ............................. PASS (0e682da4c2d3fc08) 4525312
---
> checking 'resize' ............................. PASS (75a7216227f8dbfa) 15155777
> checking 'rotate' ............................. PASS (cba5275a49d1c025) 4525312
579c579
< checking 'affine' ............................. PASS (b991742daa634d98) 226067.6
---
> checking 'affine' ............................. PASS (091470a40c4fba44) 226067.6
592c592
< checking 'computeFeatures' .................... PASS (4a081a1eefd4acc9) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
597c597
< checking 'normalize' .......................... PASS (aefb38d29f78b9f4) 1858155
---
> checking 'normalize' .......................... PASS (95a2f0d3d09f9593) 1858155
656,657c656,657
< checking 'resize' ............................. PASS (b50a31835364c09e) 9108608
< checking 'rotate' ............................. PASS (7b2ebfe00d3a3a42) 1600126
---
> checking 'resize' ............................. PASS (b189246d26913306) 9108608
> checking 'rotate' ............................. PASS (a4a84e73999cd629) 1600126
661c661
< checking 'affine' ............................. PASS (05fc5cb10e082fd3) 133467.8
---
> checking 'affine' ............................. PASS (4a6b1cf59de37216) 133467.8
674c674
< checking 'computeFeatures' .................... PASS (ff70e8e7d5c1f3ed) 416154745
---
> checking 'computeFeatures' .................... PASS (1d847743be56e5a7) 416164140
680,681c680,681
< checking 'gblur' .............................. PASS (458650b37f0343dd) 1037581
< checking 'filter2' ............................ PASS (bd3a768b0d187c23) 26149148
---
> checking 'gblur' .............................. PASS (f499c36c42da96ae) 1037581
> checking 'filter2' ............................ PASS (e5a3d2e924e050fe) 26149148
737,738c737,738
< checking 'resize' ............................. PASS (5ad3e43560133426) 76725662
< checking 'rotate' ............................. PASS (c00f3179a9298754) 4140744
---
> checking 'resize' ............................. PASS (19f045e2a12c3dcd) 76725662
> checking 'rotate' ............................. PASS (5ca7d358dc5f6cb8) 4140744
742c742
< checking 'affine' ............................. PASS (fbf2f25eade0659a) 301692.6
---
> checking 'affine' ............................. PASS (8490fa9d387d7f22) 301692.6
755c755
< checking 'computeFeatures' .................... PASS (cd365d27117f6c14) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
759,760c759,760
< checking 'normalize' .......................... PASS (7dda630cba451455) 2693244
< checking 'normalize' .......................... PASS (bcc1a8e152bb4b7a) 2315924
---
> checking 'normalize' .......................... PASS (6f82aae3b180c153) 2693244
> checking 'normalize' .......................... PASS (27441d4baba7c727) 2315924
818,819c818,819
< checking 'resize' ............................. PASS (13c670f51a30c923) 72772706
< checking 'rotate' ............................. PASS (e9f525591f2229cf) 3978266
---
> checking 'resize' ............................. PASS (c2412da2d423bb4c) 72772706
> checking 'rotate' ............................. PASS (e88e2e93ce61d959) 3978266
823c823
< checking 'affine' ............................. PASS (af56a3e7ebac2881) 219714.6
---
> checking 'affine' ............................. PASS (987d2bf7d6243ac5) 219714.6
836c836
< checking 'computeFeatures' .................... PASS (8f8affb55724e2fe) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
840,841c840,841
< checking 'normalize' .......................... PASS (0e05442ba3086ec5) 2526618
< checking 'normalize' .......................... PASS (5eaa50b45138e9cd) 2163958
---
> checking 'normalize' .......................... PASS (c6700c53a770f4dc) 2526618
> checking 'normalize' .......................... PASS (321165d27d376355) 2163958
899,900c899,900
< checking 'resize' ............................. PASS (7b3beb675b6c79c3) 72772706
< checking 'rotate' ............................. PASS (5cccffa37dd92aa2) 3978266
---
> checking 'resize' ............................. PASS (d4439ccaddffedbf) 72772706
> checking 'rotate' ............................. PASS (49bab3d36db066a3) 3978266
904c904
< checking 'affine' ............................. PASS (0909fbeb314a51f1) 219714.6
---
> checking 'affine' ............................. PASS (6f88949e9ca0500f) 219714.6
917c917
< checking 'computeFeatures' .................... PASS (8f8affb55724e2fe) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
921,922c921,922
< checking 'normalize' .......................... PASS (5b0492833b6f1cf5) 2526618
< checking 'normalize' .......................... PASS (c3ad7ad72e6c0b63) 2163958
---
> checking 'normalize' .......................... PASS (c864fc347d3e1eec) 2526618
> checking 'normalize' .......................... PASS (b924aa1ced88d0b0) 2163958
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpkBXTRs\Rdiffa10204525781b" "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpkBXTRs\Rdiffb102029ea7283"' had status 1
OK
** running tests for arch 'x64' ...
Running 'test.R'
Comparing 'test.Rout' to 'test.Rout.save' ...355d354
< checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
356a356
> checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
392c392
< checking 'hist' ............................... PASS (25c2c5f6936c4cc3) 6cce517eeddbb6cd
---
> checking 'hist' ............................... PASS (758d77d39292aceb) 22261eb2334cd65e
592c592
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
755c755
< checking 'computeFeatures' .................... PASS (5eaf503a54600569) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
836c836
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
917c917
< 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\RtmpMz1I5A\Rdiffa23c8244879fc" "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\RtmpMz1I5A\Rdiffb23c849271a36"' 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
clahe.c: In function 'CLAHE':
clahe.c:219:19: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU;
^
clahe.c:231:23: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL;
^
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
clahe.c: In function 'CLAHE':
clahe.c:219:19: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU;
^
clahe.c:231:23: warning: suggest parentheses around '+' inside '>>' [-Wparentheses]
uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL;
^
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_4.18.3.zip
* DONE (EBImage)
EBImage.Rcheck/examples_i386/EBImage-Ex.timings:
| name | user | system | elapsed | |
| EBImage | 7.22 | 0.83 | 9.31 | |
| Image | 0.55 | 0.12 | 0.67 | |
| bwlabel | 2.65 | 0.14 | 2.80 | |
| channel | 0.85 | 0.35 | 1.19 | |
| clahe | 0.34 | 0.03 | 0.37 | |
| colorLabels | 0.11 | 0.01 | 0.13 | |
| colormap | 0.64 | 0.30 | 0.94 | |
| combine | 1.23 | 0.38 | 1.60 | |
| computeFeatures | 1.32 | 0.15 | 1.47 | |
| display | 1.78 | 0.39 | 2.17 | |
| distmap | 0.36 | 0.00 | 0.36 | |
| drawCircle | 0.14 | 0.00 | 0.14 | |
| equalize | 1.64 | 0.47 | 2.11 | |
| fillHull | 0.43 | 0.05 | 0.47 | |
| filter2 | 2.40 | 0.65 | 3.06 | |
| floodFill | 0.28 | 0.07 | 0.35 | |
| gblur | 0.46 | 0.04 | 0.50 | |
| io | 1.11 | 0.19 | 2.26 | |
| localCurvature | 1.14 | 0.19 | 1.33 | |
| medianFilter | 2.42 | 0.11 | 2.53 | |
| morphology | 0.16 | 0.01 | 0.17 | |
| normalize | 0.03 | 0.02 | 0.05 | |
| ocontour | 0.01 | 0.01 | 0.03 | |
| otsu | 0.24 | 0.07 | 0.30 | |
| paintObjects | 2.00 | 0.23 | 2.23 | |
| propagate | 1.86 | 0.08 | 1.94 | |
| rmObjects | 0.08 | 0.03 | 0.11 | |
| spatial | 1.06 | 0.08 | 1.14 | |
| stackObjects | 3.35 | 1.17 | 4.52 | |
| thresh | 0.18 | 0.01 | 0.20 | |
| tile | 0.43 | 0.27 | 0.69 | |
| transpose | 0.26 | 0.01 | 0.28 | |
| watershed | 0.14 | 0.00 | 0.14 | |
EBImage.Rcheck/examples_x64/EBImage-Ex.timings:
| name | user | system | elapsed | |
| EBImage | 5.61 | 0.81 | 8.43 | |
| Image | 0.35 | 0.11 | 0.47 | |
| bwlabel | 1.68 | 0.14 | 1.82 | |
| channel | 0.92 | 0.43 | 1.34 | |
| clahe | 0.20 | 0.01 | 0.22 | |
| colorLabels | 0.15 | 0.03 | 0.17 | |
| colormap | 0.35 | 0.22 | 0.58 | |
| combine | 0.65 | 0.44 | 1.08 | |
| computeFeatures | 0.79 | 0.17 | 0.97 | |
| display | 0.94 | 0.33 | 1.26 | |
| distmap | 0.19 | 0.02 | 0.21 | |
| drawCircle | 0.14 | 0.00 | 0.14 | |
| equalize | 1.62 | 0.49 | 2.11 | |
| fillHull | 0.28 | 0.00 | 0.28 | |
| filter2 | 2.61 | 0.45 | 3.07 | |
| floodFill | 0.21 | 0.06 | 0.26 | |
| gblur | 0.34 | 0.03 | 0.38 | |
| io | 0.72 | 0.21 | 1.87 | |
| localCurvature | 0.91 | 0.17 | 1.08 | |
| medianFilter | 0.85 | 0.06 | 0.92 | |
| morphology | 0.10 | 0.02 | 0.11 | |
| normalize | 0.01 | 0.01 | 0.03 | |
| ocontour | 0.02 | 0.00 | 0.02 | |
| otsu | 0.19 | 0.03 | 0.22 | |
| paintObjects | 1.76 | 0.24 | 2.00 | |
| propagate | 1.35 | 0.04 | 1.39 | |
| rmObjects | 0.06 | 0.03 | 0.10 | |
| spatial | 0.61 | 0.08 | 0.68 | |
| stackObjects | 2.67 | 1.36 | 4.04 | |
| thresh | 0.14 | 0.03 | 0.17 | |
| tile | 0.33 | 0.12 | 0.45 | |
| transpose | 0.16 | 0.02 | 0.17 | |
| watershed | 0.09 | 0.02 | 0.11 | |