Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 626/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EBImage 4.48.0 (landing page) Andrzej Oleś
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the EBImage package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBImage.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: EBImage |
Version: 4.48.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBImage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBImage_4.48.0.tar.gz |
StartedAt: 2024-12-20 18:24:53 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 18:26:14 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 80.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EBImage.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBImage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBImage_4.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBImage.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EBImage/DESCRIPTION’ ... OK * this is package ‘EBImage’ version ‘4.48.0’ * 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 * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 code 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed EBImage 4.709 0.312 5.292 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’ Comparing ‘test.Rout’ to ‘test.Rout.save’ ...231c231,234 < checking IO for 'logo' ... FAIL --- > checking IO for 'logo' ... PASS > Warning message: > In readTIFF(x, all = all, ...) : > TIFFReadDirectory: Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples. 238c241 < checking 'hist' ............................... PASS (d722533c4f3f4627) Inf --- > checking 'hist' ............................... PASS (8ef6dc298b72d591) Inf 254c257 < checking 'display' ............................ PASS (68b260509c7ab340) 189.7 --- > checking 'display' ............................ PASS (4c9befc7a9f9f22e) 165.3 313c316 < checking 'hist' ............................... PASS (30119fb81dbf2fbb) Inf --- > checking 'hist' ............................... PASS (c32dc2571db86a0f) Inf 329c332 < checking 'display' ............................ PASS (2b8c45decab7535f) 174.7 --- > checking 'display' ............................ PASS (174250a6d96dee60) 150.3 335c338 < checking 'rotate' ............................. PASS (e342aad091c41434) 483.6843 --- > checking 'rotate' ............................. PASS (3db98677c68c5102) 483.6843 390c393 < checking 'hist' ............................... PASS (c2351b10676ca4d4) 20513.55 --- > checking 'hist' ............................... PASS (e7a708b4f96f88dc) 20513.55 406c409 < checking 'display' ............................ PASS (2f08603669942058) 421.7 --- > checking 'display' ............................ PASS (dada341199e50c3d) 397.3 411,412c414,415 < checking 'resize' ............................. PASS (53079603052afb20) 1419476 < checking 'rotate' ............................. PASS (3a57ba32a333f879) 2493977 --- > checking 'resize' ............................. PASS (7882055c8b670bf4) 1419476 > checking 'rotate' ............................. PASS (559860bb5c99cb82) 2493977 416c419 < checking 'affine' ............................. PASS (b62bb7696f29b3d3) 54171.17 --- > checking 'affine' ............................. PASS (11616142290451c1) 54171.17 483c486 < checking 'display' ............................ PASS (fb5a878c739fdf0a) 357.7 --- > checking 'display' ............................ PASS (bb2b4586191eb980) 333.3 488,489c491,492 < checking 'resize' ............................. PASS (959a9d09fe7ac665) 2941770 < checking 'rotate' ............................. PASS (15e6fc0e7664a911) 1247487 --- > checking 'resize' ............................. PASS (bb1209a84d6b3709) 2941770 > checking 'rotate' ............................. PASS (924fc66d1ec91d44) 1247487 493c496 < checking 'affine' ............................. PASS (b310c82ce2d000ba) 22238.15 --- > checking 'affine' ............................. PASS (7a760844869cec92) 22238.15 506c509 < checking 'computeFeatures' .................... PASS (f164490fb0dee33c) 3989501 --- > checking 'computeFeatures' .................... PASS (c1ff2e62e7bb8eee) 3989786 560c563 < checking 'display' ............................ PASS (38b074e79a93b661) 330.7 --- > checking 'display' ............................ PASS (3d646d4f07d194ba) 306.3 565,566c568,569 < checking 'resize' ............................. PASS (ff7a963b07cc340b) 15155777 < checking 'rotate' ............................. PASS (7a904b4d37503022) 4525312 --- > checking 'resize' ............................. PASS (fe9aa55b037def9d) 15155777 > checking 'rotate' ............................. PASS (2a6f5001ae7d116d) 4525312 570c573 < checking 'affine' ............................. PASS (838cd8c4ef1dc919) 226067.6 --- > checking 'affine' ............................. PASS (517c3559acf97cf4) 226067.6 583c586 < checking 'computeFeatures' .................... PASS (d5abe7093d55440e) 746878.2 --- > checking 'computeFeatures' .................... PASS (a33c53edd3cf8a46) 746878.2 639c642 < checking 'display' ............................ PASS (0f4b8075d5f24755) 309.7 --- > checking 'display' ............................ PASS (2fb2fcab54a4ea5a) 285.3 644,645c647,648 < checking 'resize' ............................. PASS (2e271b3bc9e7a27c) 9108608 < checking 'rotate' ............................. PASS (d16b29b87668867f) 1600126 --- > checking 'resize' ............................. PASS (211e86386b1010af) 9108608 > checking 'rotate' ............................. PASS (d67e39e3cb07d275) 1600126 649c652 < checking 'affine' ............................. PASS (8dc830edbafa5c9b) 133467.8 --- > checking 'affine' ............................. PASS (a6e552f84324fe21) 133467.8 662c665 < checking 'computeFeatures' .................... PASS (2561f1b745b56d57) 416103592 --- > checking 'computeFeatures' .................... PASS (1bf064e6a11f2410) 416164140 668c671 < checking 'gblur' .............................. PASS (fd8945a2f8d02a20) 1037581 --- > checking 'gblur' .............................. PASS (9224b720f9d00006) 1037581 717c720 < checking 'display' ............................ PASS (ef6dce96392bbb6d) 263.7 --- > checking 'display' ............................ PASS (bc877f5317c575b2) 239.3 722,723c725,726 < checking 'resize' ............................. PASS (3127cba298aad55f) 76725662 < checking 'rotate' ............................. PASS (bca3ab9c26f81918) 4140744 --- > checking 'resize' ............................. PASS (dd96ecc9ed75e744) 76725662 > checking 'rotate' ............................. PASS (19319de30582c1d6) 4140744 727c730 < checking 'affine' ............................. PASS (a3eeaaeedbf1f7a2) 301692.6 --- > checking 'affine' ............................. PASS (592877c7d17e1d22) 301692.6 740c743 < checking 'computeFeatures' .................... PASS (4f731e0e205341e5) 749353.1 --- > checking 'computeFeatures' .................... PASS (151a0d98d309d0b1) 749353.1 795c798 < checking 'display' ............................ PASS (4ca607589cc2787e) 280.7 --- > checking 'display' ............................ PASS (d28e3e75eed04056) 256.3 800,801c803,804 < checking 'resize' ............................. PASS (00aef78b69242c90) 72772706 < checking 'rotate' ............................. PASS (f42404ca4cc1e57e) 3978266 --- > checking 'resize' ............................. PASS (5ab5e219e21b7d77) 72772706 > checking 'rotate' ............................. PASS (5ea8cc41d39fe2c4) 3978266 805c808 < checking 'affine' ............................. PASS (9c7b3a7ea964b836) 219714.6 --- > checking 'affine' ............................. PASS (76f6b18d2cb7c9c2) 219714.6 818c821 < checking 'computeFeatures' .................... PASS (6e516e369839bbb1) 734993.9 --- > checking 'computeFeatures' .................... PASS (53798e843cdbfa9f) 734993.9 873c876 < checking 'display' ............................ PASS (4ca607589cc2787e) 280.7 --- > checking 'display' ............................ PASS (d28e3e75eed04056) 256.3 878,879c881,882 < checking 'resize' ............................. PASS (e94d70507c46424a) 72772706 < checking 'rotate' ............................. PASS (bb28d7a739148c1e) 3978266 --- > checking 'resize' ............................. PASS (22d4ff5205c02f14) 72772706 > checking 'rotate' ............................. PASS (3e6dee126668bb5a) 3978266 883c886 < checking 'affine' ............................. PASS (00a69976accd24e7) 219714.6 --- > checking 'affine' ............................. PASS (559df6f741145f7f) 219714.6 896c899 < checking 'computeFeatures' .................... PASS (6e516e369839bbb1) 734993.9 --- > checking 'computeFeatures' .................... PASS (53798e843cdbfa9f) 734993.9 OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/EBImage.Rcheck/00check.log’ for details.
EBImage.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EBImage ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘EBImage’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EBImage.c -o EBImage.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clahe.c -o clahe.o clahe.c:223:19: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses] uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; ~~~~~~~^~ ~~ clahe.c:223:19: note: place parentheses around the '+' expression to silence this warning uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; ^ ( ) clahe.c:235:23: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses] uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; ~~~~~~~^~ ~~ clahe.c:235:23: note: place parentheses around the '+' expression to silence this warning uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; ^ ( ) 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distmap.cpp -o distmap.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c drawCircle.c -o drawCircle.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c floodFill.cpp -o floodFill.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getFrames.c -o getFrames.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c haralick.c -o haralick.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c medianFilter.c -o medianFilter.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c morphology.cpp -o morphology.o 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) { ^ 18 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nativeRaster.c -o nativeRaster.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c normalize.c -o normalize.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ocontour.c -o ocontour.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c propagate.cpp -o propagate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spatial.c -o spatial.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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: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; ^ 11 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tools.c -o tools.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transpose.cpp -o transpose.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c watershed.cpp -o watershed.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-EBImage/00new/EBImage/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘abind’ in package ‘EBImage’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EBImage)
EBImage.Rcheck/tests/test.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## cat tests/test.R | R --vanilla &>tests/test.Rout.save > library("EBImage") > > set.seed(0) # make random color permutations in 'colorLabels' reproducible > .digits = floor(-log10(.Machine$double.eps^.5) - 1) > > ## returns a hashcode given an object > hash = function (x) .Call(digest:::digest_impl, serialize(x, connection=NULL, ascii=FALSE, xdr=FALSE), 7L, -1L, 14L, 0L, 0L, PACKAGE="digest") > > hash.old <- function(x) { + if (is.list(x) && length(x)>0) { + hash.old(sapply(x, hash.old, USE.NAMES=FALSE)) + } + else { + xd <- suppressWarnings(as.numeric(x)) + xd <- xd[!(is.nan(xd)|is.na(xd))] + sx <- sum(xd*(1:length(xd))) + if (is.matrix(xd)) + sx + 0.7 * hash.old(dim(xd)) + else + sx - 0.1 + } + } > > ## try to evaluate fun(x,...) > check <- function(fun, x, ..., capture.output=FALSE, suppressWarnings=FALSE, suppressMessages=FALSE, expectError=FALSE, round=FALSE, debug=FALSE) { + passed <- TRUE + + cat(sprintf("checking \'%s\' %s ", fun, paste(rep(".", 35L-nchar(fun)), collapse = ""))) + + expr = quote(do.call(fun,c(list(x),list(...)))) + if ( isTRUE(capture.output) ) expr = call("capture.output", expr) + if ( isTRUE(suppressWarnings) ) expr = call("suppressWarnings", expr) + if ( isTRUE(suppressMessages) ) expr = call("suppressMessages", expr) + + y <- try(eval(expr), silent=TRUE) + + if ( (inherits(y, "try-error") && !isTRUE(expectError)) || (is.Image(y) && !validObject(y)) ) { + y <- NULL + passed <- FALSE + } + + if (passed) { + if (isTRUE(round) && !inherits(y, "try-error")) + y = if ( is.list(y) ) lapply(y, round, digits=.digits) else round(y, digits = .digits) + cat("PASS (", hash(y), ") ", hash.old(y), "\n", sep="") + } + else cat("FAIL\n") + + if ( isTRUE(debug) ) { + if (is.Image(y)) show(y) + if (is.array(y)) display(y, all=TRUE, interpolate=FALSE) + else if (is.character(y)) cat(y, sep="\n") + } + + y + } > > checkIO <- function(name) { + cat("checking IO for \'", name, "\' ... ", sep="") + x = get(name) + y = FALSE + if ( !is.null(x) ) { + y <- try({ + xx <- readImage(writeImage(x, tempfile("", fileext = ".tif"))) + dimnames(xx) <- dimnames(x) + identical(x, xx) + }, silent=TRUE) + } + if ( isTRUE(y) ) cat("PASS\n") else cat("FAIL\n") + invisible(y) + } > > testIOFunctions <- function(...) invisible(lapply(list(...), function(y) checkIO(y))) > > testEBImageFunctions <- function(x) { + cat("new test (hash=", hash(x), ")\n", sep="") + + z <- check("show", x, capture.output=TRUE) + z <- check("print", x, short=TRUE, capture.output=TRUE) + if ( typeof(x)=="logical" ) + z <- check("hist", EBImage:::castImage(x), breaks = c(0, .5, 1)) + else + z <- check("hist", x) + + ## pixel arithmetic + z <- check(">", x, 0.5) + z <- check("+", x, x) + z <- check("/", x, 2) + z <- check("*", 2L, x) + z <- check("median", x) + z <- check("quantile", x) + + ## image methods + z <- check("Image", x, colormode="Color") + z <- check("as.Image", x) + z <- check("is.Image", x) + z <- check("imageData", x) + z <- check("imageData<-", x, z) + z <- check("as.raster", x) + z <- check("colorMode<-", x, Grayscale, suppressWarnings=TRUE) + y <- check("numberOfFrames", x, type="render") + z <- if ( y==1L ) check("getFrames", x, 1L, "render") else check("getFrames", x) + z <- check("display", x, method = "browser", tempDir = file.path(dirname(tempdir()), "EBImage_tmp")) + if ( y>2L ) { + z <- check("display", x, method = "raster", all = TRUE) + z <- check("image", x, i = 3L) + } + else { + z <- if (y==1L) check("display", x, method = "raster") else check("display", x, method = "raster", frame = 2L, suppressMessages=TRUE) + z <- check("image", x, suppressMessages=TRUE) + } + + ## drawCircle + d <- dim(x) + c.x <- ceiling(d[1L]/2) + c.y <- ceiling(d[2L]/2) + radius <- max(c.x-1, 1) + nf <- numberOfFrames(x, "render") + fill <- nf > 1 + col <- if ( colorMode(x)==Color ) "yellow" else 1 + z <- check("drawCircle", x, c.x, c.x, radius, col, fill, nf) + + ## subset + sub <- list(x, 1:min(10,d[1L]), 1:min(7,d[2L])) + if (length(d)>2) sub <- c(sub, rep(TRUE, length(d)-2)) + z <- do.call("check", c("[", sub)) + + ## spatial transform + z <- check("resize", x, 137, 22) + z <- check("rotate", x, 20) + z <- check("flip", x) + z <- check("flop", x) + z <- check("translate", x, c(-7, 5), bg.col=1) + z <- check("affine", x, matrix(c(-7, 5, 0.1, -0.2, 0.3, 1), ncol=2L)) + z <- check("transpose", x) + + ## segmentation + fd = pmin(5, (d[1:2]-1)/2) + z <- check("thresh", x, w=fd[1L], h=fd[2L]) + y <- check("channel", x, "luminance") + z <- check("otsu", y) + y <- suppressWarnings(normalize(y, separate=FALSE)) + y <- check("bwlabel", y > 0.5) + z <- check("colorLabels", y, suppressWarnings=TRUE) + z <- check("stackObjects", y, x) + z <- check("stackObjects", Image(dim=dim(y)), x) + cls <- if ( colorMode(x)==Color ) TRUE else FALSE + z <- check("paintObjects", y, x, col=c("#ff00ff", "#ffff00"), opac=c(1.0, 0.5), thick=cls, closed=cls) + z <- check("rmObjects", y, as.list(seq_len(numberOfFrames(y))), cls) + z <- check("reenumerate", z) + z <- check("reenumerate", y) + + ## features + x1 <- getFrame(x, 1) + x2 <- list(x=x1, y=2*x1) + y1 <- getFrame(y, 1) + expandRef <- if ( min(dim(x1)) > 31L ) function(ref, refnames) standardExpandRef(ref, refnames, gblob(n=31L)) else NULL + z <- check("computeFeatures", y1, x2, expandRef = expandRef, round = !is.null(expandRef)) + z <- check("computeFeatures", y1, x2, expandRef = expandRef, properties = TRUE) + + ## curvature + y <- check("ocontour", x>0.5) + if (length(y) > 0L ) z <- check("localCurvature", y[[1L]], round=TRUE) + + ## filtering + z <- check("normalize", x, suppressWarnings=TRUE) + z <- check("normalize", x, inputRange=c(0.1, 0.9), suppressWarnings=TRUE) + z <- check("gblur", x, sigma=1, expectError=min(d)<7, round=TRUE) + y <- if (cls) "replicate" else if (nf>1) 0.5 else "circular" + z <- check("filter2", x, array(1, dim=c(5, 5)), y, round=TRUE) + z <- check("medianFilter", x, 2) + z <- check("equalize", x, suppressWarnings=TRUE) + + ## morphological operations + y <- x > 0.5 + z <- check("erode", y) + z <- check("dilate", y, makeBrush(5, 'disc')) + z <- check("opening", y, makeBrush(7, 'line')) + z <- check("closing", y, makeBrush(4, 'line', angle=0), suppressWarnings=TRUE) + z <- check("whiteTopHat", x, makeBrush(3, 'box')) + z <- check("blackTopHat", x, makeBrush(5, 'disc')) + z <- check("selfComplementaryTopHat", x) + z <- check("distmap", y) + z <- check("watershed", z) + z <- check('floodFill', x, c(5, 5), 0.5) + z <- check('fillHull', y) + + ## propagate + y <- thresh(x, w=fd[1L], h=fd[2L], offset=0.02) + y <- fillHull(y) + y <- bwlabel(y) + z <- check("propagate", x, y, x>0.5) + + ## colorspace + z <- check("toRGB", x) + z <- check("rgbImage", x, x>0.5) + z <- check("colormap", channel(x, "luminance"), heat.colors(16L)) + + ## image stacking, combining, tiling + y <- check("combine", list(NULL, x, x, NULL, NULL)) + z <- check("combine", x, y, y) + y <- check("tile", z, nx=3) + z <- check("untile", y, c(3, 2)) + y <- check("abind", list(x, x), along=length(d)+1L) + cat("\n") + } > > > ## check error handling > try.readImage <- function(...) tryCatch(suppressWarnings(readImage(...)), error = function(e) NULL) > mock <- try.readImage(system.file("images", package="EBImage"), type="png") > mock <- try.readImage("http://www.huber.embl.de/EBImage/missing.file ", type="png") > > ## single greyscale and color images > sample <- try.readImage(system.file("images","sample.png", package="EBImage")) > sample.color <- try.readImage(system.file("images","sample-color.png", package="EBImage")) > ## multi-frame image stack > f = system.file("images","nuclei.tif", package="EBImage") > nuclei = try.readImage(c(f, f)) > ## test reading from URL > logo <- try.readImage("http://www.huber.embl.de/EBImage/logo.png") > > ## test: IO operations > testIOFunctions("sample", "sample.color", "nuclei", "logo") checking IO for 'sample' ... PASS checking IO for 'sample.color' ... PASS checking IO for 'nuclei' ... PASS checking IO for 'logo' ... FAIL > > ## test: black image > testEBImageFunctions(Image(0, c(8, 8))) new test (hash=03724aaea0cf64b4) checking 'show' ............................... PASS (5a93d2a87828912b) -0.1 checking 'print' .............................. PASS (0007ac6dee6a14da) -0.1 checking 'hist' ............................... PASS (d722533c4f3f4627) Inf checking '>' .................................. PASS (91517a74c2895221) -0.1 checking '+' .................................. PASS (03724aaea0cf64b4) -0.1 checking '/' .................................. PASS (03724aaea0cf64b4) -0.1 checking '*' .................................. PASS (03724aaea0cf64b4) -0.1 checking 'median' ............................. PASS (8396e8397399bb05) -0.1 checking 'quantile' ........................... PASS (5e6b34b7d87730f0) -0.1 checking 'Image' .............................. PASS (e4b04ad17c704314) -0.1 checking 'as.Image' ........................... PASS (03724aaea0cf64b4) -0.1 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1ba6fa2bac2e6157) -0.1 checking 'imageData<-' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'as.raster' .......................... PASS (e8f1c1057deba532) -0.1 checking 'colorMode<-' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (437d348905e7edea) -0.2 checking 'display' ............................ PASS (68b260509c7ab340) 189.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (76ab1bcd040f633c) 447.9 checking '[' .................................. PASS (3c13b8fa403f3a61) -0.1 checking 'resize' ............................. PASS (59b56ab6bbfb3b98) -0.1 checking 'rotate' ............................. PASS (d9d1aa63f93f02d0) -0.1 checking 'flip' ............................... PASS (03724aaea0cf64b4) -0.1 checking 'flop' ............................... PASS (03724aaea0cf64b4) -0.1 checking 'translate' .......................... PASS (8f2e405bb6973b4a) 1932.9 checking 'affine' ............................. PASS (03724aaea0cf64b4) -0.1 checking 'transpose' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'thresh' ............................. PASS (c13bdaf3a3ddff95) -0.1 checking 'channel' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'otsu' ............................... PASS (e3b39ef666a0ce39) -0.09804688 checking 'bwlabel' ............................ PASS (c13bdaf3a3ddff95) -0.1 checking 'colorLabels' ........................ PASS (73c6f975aa7b9638) -0.1 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (03724aaea0cf64b4) -0.1 checking 'rmObjects' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'reenumerate' ........................ PASS (c13bdaf3a3ddff95) -0.1 checking 'reenumerate' ........................ PASS (c13bdaf3a3ddff95) -0.1 checking 'computeFeatures' .................... PASS (d956c282ac7180e4) -0.1 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (0cbbfbd6c2b5057a) -0.1 checking 'normalize' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'normalize' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'gblur' .............................. PASS (03724aaea0cf64b4) -0.1 checking 'filter2' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'medianFilter' ....................... PASS (03724aaea0cf64b4) -0.1 checking 'equalize' ........................... PASS (03724aaea0cf64b4) -0.1 checking 'erode' .............................. PASS (91517a74c2895221) -0.1 checking 'dilate' ............................. PASS (91517a74c2895221) -0.1 checking 'opening' ............................ PASS (91517a74c2895221) -0.1 checking 'closing' ............................ PASS (91517a74c2895221) -0.1 checking 'whiteTopHat' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'blackTopHat' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'selfComplementaryTopHat' ............ PASS (03724aaea0cf64b4) -0.1 checking 'distmap' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'watershed' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'floodFill' .......................... PASS (b7521415b91cdd6a) 1039.9 checking 'fillHull' ........................... PASS (91517a74c2895221) -0.1 checking 'propagate' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'toRGB' .............................. PASS (73c6f975aa7b9638) -0.1 checking 'rgbImage' ........................... PASS (73c6f975aa7b9638) -0.1 checking 'colormap' ........................... PASS (f55f763f0bce6d0e) 2079.9 checking 'combine' ............................ PASS (7d8cabf23a7147bf) -0.1 checking 'combine' ............................ PASS (dfe23dd6a6fd08b8) -0.1 checking 'tile' ............................... PASS (63b8539b976f10f9) 42140.88 checking 'untile' ............................. PASS (fc2ab5092822346e) 16809.31 checking 'abind' .............................. PASS (7d8cabf23a7147bf) -0.1 > > ## test: white image > testEBImageFunctions(Image(1L, c(5, 5))) new test (hash=5e369a5a8c06ea6e) checking 'show' ............................... PASS (d7ff39dcf34291a7) -0.1 checking 'print' .............................. PASS (423045c171032825) -0.1 checking 'hist' ............................... PASS (30119fb81dbf2fbb) Inf checking '>' .................................. PASS (ab60d77d8694845c) 324.9 checking '+' .................................. PASS (ccb4c957b356b423) 649.9 checking '/' .................................. PASS (e68dd3c4bf42ae06) 162.4 checking '*' .................................. PASS (ccb4c957b356b423) 649.9 checking 'median' ............................. PASS (7c79dea3bfc1415b) 0.9 checking 'quantile' ........................... PASS (03ab24e6a573bd6b) 14.9 checking 'Image' .............................. PASS (e06d5f65342df035) 324.9 checking 'as.Image' ........................... PASS (5e369a5a8c06ea6e) 324.9 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (a72e950dc2c633c4) 324.9 checking 'imageData<-' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'as.raster' .......................... PASS (76158aebe747f7e1) -0.1 checking 'colorMode<-' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (5be9802bf124fe9c) 324.8 checking 'display' ............................ PASS (2b8c45decab7535f) 174.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (a3847050dd15905c) 324.9 checking '[' .................................. PASS (5e369a5a8c06ea6e) 324.9 checking 'resize' ............................. PASS (81601207cc4e4223) 4543605 checking 'rotate' ............................. PASS (e342aad091c41434) 483.6843 checking 'flip' ............................... PASS (5e369a5a8c06ea6e) 324.9 checking 'flop' ............................... PASS (5e369a5a8c06ea6e) 324.9 checking 'translate' .......................... PASS (a3847050dd15905c) 324.9 checking 'affine' ............................. PASS (92683959c9ed97c3) 39.9 checking 'transpose' .......................... PASS (5e369a5a8c06ea6e) 324.9 checking 'thresh' ............................. PASS (dafc92132d191221) -0.1 checking 'channel' ............................ PASS (5e369a5a8c06ea6e) 324.9 checking 'otsu' ............................... PASS (2abebb5cf42f343e) 0.8980469 checking 'bwlabel' ............................ PASS (5e369a5a8c06ea6e) 324.9 checking 'colorLabels' ........................ PASS (a7e8ce686b7c6eec) 2849.9 checking 'stackObjects' ....................... PASS (995b03d1197fdd56) 324.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (fbe94deb2c7c7e12) 270.7333 checking 'rmObjects' .......................... PASS (dafc92132d191221) -0.1 checking 'reenumerate' ........................ PASS (dafc92132d191221) -0.1 checking 'reenumerate' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'computeFeatures' .................... PASS (1e197f38fe3db7df) 950932.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (1ad47b9dc5e279b9) 1087.8 checking 'localCurvature' ..................... PASS (07aef8b9d0c42e30) 1008.955 checking 'normalize' .......................... PASS (a3847050dd15905c) 324.9 checking 'normalize' .......................... PASS (a3847050dd15905c) 324.9 checking 'gblur' .............................. PASS (34be5e3328df689f) -0.1 checking 'filter2' ............................ PASS (046936d9c22a44d3) 8124.9 checking 'medianFilter' ....................... PASS (a3847050dd15905c) 324.9 checking 'equalize' ........................... PASS (5e369a5a8c06ea6e) 324.9 checking 'erode' .............................. PASS (ab60d77d8694845c) 324.9 checking 'dilate' ............................. PASS (ab60d77d8694845c) 324.9 checking 'opening' ............................ PASS (ab60d77d8694845c) 324.9 checking 'closing' ............................ PASS (ab60d77d8694845c) 324.9 checking 'whiteTopHat' ........................ PASS (dafc92132d191221) -0.1 checking 'blackTopHat' ........................ PASS (dafc92132d191221) -0.1 checking 'selfComplementaryTopHat' ............ PASS (ccb4c957b356b423) 649.9 checking 'distmap' ............................ PASS (4620168ff1c2a437) Inf checking 'watershed' .......................... PASS (5e369a5a8c06ea6e) 324.9 checking 'floodFill' .......................... PASS (dafc92132d191221) -0.1 checking 'fillHull' ........................... PASS (ab60d77d8694845c) 324.9 checking 'propagate' .......................... PASS (dafc92132d191221) -0.1 checking 'toRGB' .............................. PASS (f3b87c6a40e54c68) 2849.9 checking 'rgbImage' ........................... PASS (a1c021690e069b07) 1274.9 checking 'colormap' ........................... PASS (948ec87fd2adc7a9) 2652.253 checking 'combine' ............................ PASS (8c39678924e12a09) 1274.9 checking 'combine' ............................ PASS (072d49f53072e43b) 7874.9 checking 'tile' ............................... PASS (16eb65ee8bbcb932) 24420.64 checking 'untile' ............................. PASS (8bcebbd606485233) 10445.49 checking 'abind' .............................. PASS (8c39678924e12a09) 1274.9 > > ## test: 2D Grayscale 64x48 > x <- nuclei[50:113,208:255,2] > testEBImageFunctions(as.array(x)) new test (hash=3e469356855e6210) checking 'show' ............................... PASS (0c6212669ee6288d) -0.1 checking 'print' .............................. PASS (0c6212669ee6288d) -0.1 checking 'hist' ............................... PASS (c2351b10676ca4d4) 20513.55 checking '>' .................................. PASS (0a927a877b0b85eb) 1217568 checking '+' .................................. PASS (2c51607a58b46974) 2940144 checking '/' .................................. PASS (a872fc97379d58f5) 735035.9 checking '*' .................................. PASS (2c51607a58b46974) 2940144 checking 'median' ............................. PASS (d2a8be6a346c3d28) 0.04509804 checking 'quantile' ........................... PASS (645f4aadbce7bdea) 7.331373 checking 'Image' .............................. PASS (923c3911d773eb6e) 1470072 checking 'as.Image' ........................... PASS (b7ae9a016c5a19ec) 1470072 checking 'is.Image' ........................... PASS (69f0cf1cfd5cd8ed) -0.1 checking 'imageData' .......................... PASS (3e469356855e6210) 1470072 checking 'imageData<-' ........................ PASS (3e469356855e6210) 1470072 checking 'as.raster' .......................... PASS (42efa6b3b04694cf) -0.1 checking 'colorMode<-' ........................ PASS (b8d002268bfac3eb) -0.1 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (d38b8f6c1a1504a8) 1470072 checking 'display' ............................ PASS (2f08603669942058) 421.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (872845fa91c628a6) 1607165 checking '[' .................................. PASS (711703fde7cc915e) 48.94314 checking 'resize' ............................. PASS (53079603052afb20) 1419476 checking 'rotate' ............................. PASS (3a57ba32a333f879) 2493977 checking 'flip' ............................... PASS (8834ca70d449207a) 1195977 checking 'flop' ............................... PASS (d73abd773dfc066a) 1462119 checking 'translate' .......................... PASS (5744e19288b9d7f0) 2133961 checking 'affine' ............................. PASS (b62bb7696f29b3d3) 54171.17 checking 'transpose' .......................... PASS (aa87d51a100b139f) 1522055 checking 'thresh' ............................. PASS (c790c6a6872d73d0) 1262811 checking 'channel' ............................ PASS (3e469356855e6210) 1470072 checking 'otsu' ............................... PASS (3aea1e91f3716bcb) 0.3160156 checking 'bwlabel' ............................ PASS (5055cb94d5293a15) 1199387 checking 'colorLabels' ........................ PASS (464d65c8da42be0d) 10021713 checking 'stackObjects' ....................... PASS (c5669f863a2ba20e) 718602.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (19a9fbb907cee1c4) 1447733 checking 'rmObjects' .......................... PASS (365ace8a4657cb08) -0.1 checking 'reenumerate' ........................ PASS (365ace8a4657cb08) -0.1 checking 'reenumerate' ........................ PASS (5055cb94d5293a15) 1199387 checking 'computeFeatures' .................... PASS (f59aa3f08e782acf) 3634215 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (790a5f5b45092d41) 1050552 checking 'localCurvature' ..................... PASS (fb6d4b13b08dcac4) 1049392 checking 'normalize' .......................... PASS (1f79956b7887dd73) 1431381 checking 'normalize' .......................... PASS (13a2d37d997199f9) 1266798 checking 'gblur' .............................. PASS (203a6d72b1fd5eba) 1466231 checking 'filter2' ............................ PASS (c82a1ece6902714d) 36592176 checking 'medianFilter' ....................... PASS (4140c87b3a1db93d) 1454712 checking 'equalize' ........................... PASS (ba175363e5576ad1) 2642794 checking 'erode' .............................. PASS (bee7898f6d8d547b) 759774.9 checking 'dilate' ............................. PASS (ed04adac54c645fd) 1797576 checking 'opening' ............................ PASS (d1c6ca8aafbd90cb) 1152484 checking 'closing' ............................ PASS (b8cf094b52fe1744) 1232737 checking 'whiteTopHat' ........................ PASS (9b53631dd222dd50) 18730.15 checking 'blackTopHat' ........................ PASS (089cd73847d97de5) 27716.23 checking 'selfComplementaryTopHat' ............ PASS (cc378ce1d0553ecd) 2929436 checking 'distmap' ............................ PASS (f98a44bf21faa222) 3826969 checking 'watershed' .......................... PASS (b39c109238f0c74b) 2762113 checking 'floodFill' .......................... PASS (c59341ffade6129a) 1470197 checking 'fillHull' ........................... PASS (0a927a877b0b85eb) 1217568 checking 'propagate' .......................... PASS (cec466bef7a2a81e) 3464201 checking 'toRGB' .............................. PASS (5051d2b131286d46) 12381911 checking 'rgbImage' ........................... PASS (ccc09b31890cd8df) 4859544 checking 'colormap' ........................... PASS (b7020f3851eb7d7c) 11126039 checking 'combine' ............................ PASS (5bda9f75cbc23401) 5597376 checking 'combine' ............................ PASS (306e27bb3ec346e6) 33922678 checking 'tile' ............................... PASS (870e7501fa1f3338) 78718054 checking 'untile' ............................. PASS (868893e062dea032) 72597772 checking 'abind' .............................. PASS (5bda9f75cbc23401) 5597376 > > ## test: 2D Color 32x48x1 > x <- sample[1:32, 1:48] > testEBImageFunctions(Image(as.vector(x), dim(x), Color)) new test (hash=7718e616f411c340) checking 'show' ............................... PASS (1a2c30323dd5a8ee) -0.1 checking 'print' .............................. PASS (e9fad67b70709e2b) -0.1 checking 'hist' ............................... PASS (596b544e7cd6f458) 130241.3 checking '>' .................................. PASS (e72c38d763e5fabf) 988518.9 checking '+' .................................. PASS (e38cf73f1c0c88a2) 1531522 checking '/' .................................. PASS (df4e8bf818fc26fe) 382880.4 checking '*' .................................. PASS (e38cf73f1c0c88a2) 1531522 checking 'median' ............................. PASS (fc60ee4b14ba4a28) 0.5039216 checking 'quantile' ........................... PASS (436f03b8c9c3ad0e) 10.10392 checking 'Image' .............................. PASS (7718e616f411c340) 765760.9 checking 'as.Image' ........................... PASS (7718e616f411c340) 765760.9 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (19c51d4d9d30d60c) 765760.9 checking 'imageData<-' ........................ PASS (7718e616f411c340) 765760.9 checking 'as.raster' .......................... PASS (05c68b3f51ec838b) -0.1 checking 'colorMode<-' ........................ PASS (733871e596e328df) 765760.9 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (681aab4c8a24c6c5) 765760.8 checking 'display' ............................ PASS (fb5a878c739fdf0a) 357.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (a6757bb66994b1f7) 782100.7 checking '[' .................................. PASS (25a626878222798c) 1285.273 checking 'resize' ............................. PASS (959a9d09fe7ac665) 2941770 checking 'rotate' ............................. PASS (15e6fc0e7664a911) 1247487 checking 'flip' ............................... PASS (828db3b8ad878bd6) 661525.2 checking 'flop' ............................... PASS (f69b431f36c97abd) 768451.1 checking 'translate' .......................... PASS (3eb2fe0d22e461ed) 820434.5 checking 'affine' ............................. PASS (b310c82ce2d000ba) 22238.15 checking 'transpose' .......................... PASS (d438f72715d302ed) 652051.4 checking 'thresh' ............................. PASS (8b3a72b493ab8540) 382924.9 checking 'channel' ............................ PASS (3982766c7e1077b3) 162800.7 checking 'otsu' ............................... PASS (ebd9ed7a0cf4831d) 0.03085937 checking 'bwlabel' ............................ PASS (498723eb57bcca48) 832970.9 checking 'colorLabels' ........................ PASS (ecbf282c48506ef2) 3692613 checking 'stackObjects' ....................... PASS (e30de50cc1d8e117) 596493.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (9b5026b178720a80) 919069.9 checking 'rmObjects' .......................... PASS (e0ab50f8e544290a) 565.9 checking 'reenumerate' ........................ PASS (e0ab50f8e544290a) 565.9 checking 'reenumerate' ........................ PASS (498723eb57bcca48) 832970.9 checking 'computeFeatures' .................... PASS (f164490fb0dee33c) 3989501 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (ced9c409ca879dc9) 848253.8 checking 'localCurvature' ..................... PASS (25e900bf67a8cdb0) 847428.3 checking 'normalize' .......................... PASS (b8b2cfe4f431fc83) 747801.4 checking 'normalize' .......................... PASS (3ee0aade2890ed53) 809649.2 checking 'gblur' .............................. PASS (0c28ab262af637d1) 761679.3 checking 'filter2' ............................ PASS (bf01322f9e0aed7a) 19130329 checking 'medianFilter' ....................... PASS (189cf2d04b2316f5) 765141.6 checking 'equalize' ........................... PASS (b525d614a289c5a3) 705546.8 checking 'erode' .............................. PASS (84add15c6fa8ac14) 908526.9 checking 'dilate' ............................. PASS (e99e1ecfd4ef49d3) 1072658 checking 'opening' ............................ PASS (80d457c0bcd57e44) 985798.9 checking 'closing' ............................ PASS (cc9339fed43d2c52) 988727.9 checking 'whiteTopHat' ........................ PASS (25444773943cf26b) 3572.998 checking 'blackTopHat' ........................ PASS (10fae7d8c0f86c96) 7139.473 checking 'selfComplementaryTopHat' ............ PASS (2f97211e82aa8221) 1533178 checking 'distmap' ............................ PASS (218b9e66643db8d3) 12740449 checking 'watershed' .......................... PASS (6edd3aa33ad54089) 988518.9 checking 'floodFill' .......................... PASS (228b47626610f8c9) 765755.4 checking 'fillHull' ........................... PASS (e72c38d763e5fabf) 988518.9 checking 'propagate' .......................... PASS (73d53b87d72f0409) 26630579 checking 'toRGB' .............................. PASS (7718e616f411c340) 765760.9 checking 'rgbImage' ........................... PASS (6df3c3d16757cdd6) 3520680 checking 'colormap' ........................... PASS (8e7f90c18580cd50) 1816912 checking 'combine' ............................ PASS (f156de3e1aff037c) 2960568 checking 'combine' ............................ PASS (1bfd38ce66379070) 18119267 checking 'tile' ............................... PASS (3f8e8f9b949597b4) 33061491 checking 'untile' ............................. PASS (9f839c04542fa7e4) 27788327 checking 'abind' .............................. PASS (a65f1e1e2d249be6) 2960568 > > ## test: 3D Color 65x17x3 > x <- sample.color[1:65, 1:17,] > testEBImageFunctions(x) new test (hash=3884fe38962577a7) checking 'show' ............................... PASS (8331bd653405c3be) -0.1 checking 'print' .............................. PASS (de22d3dc188680fd) -0.1 checking 'hist' ............................... PASS (10b008981f19c77a) 348464.1 checking '>' .................................. PASS (e6c8a64e9fff6055) 1058553 checking '+' .................................. PASS (5bb860f09b56b4d9) 4072301 checking '/' .................................. PASS (17b2c344ff60cf34) 1018075 checking '*' .................................. PASS (5bb860f09b56b4d9) 4072301 checking 'median' ............................. PASS (a9ae52973fed588b) 0.2333333 checking 'quantile' ........................... PASS (e51be80ed6288f06) 7.280392 checking 'Image' .............................. PASS (3884fe38962577a7) 2036151 checking 'as.Image' ........................... PASS (3884fe38962577a7) 2036151 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1456dcb0ab2d690b) 2036151 checking 'imageData<-' ........................ PASS (3884fe38962577a7) 2036151 checking 'as.raster' .......................... PASS (abd1d3d0d6329777) -0.1 checking 'colorMode<-' ........................ PASS (0aa63faa9d4e0838) 2036151 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (2ed277d7e69a05d2) 2036151 checking 'display' ............................ PASS (38b074e79a93b661) 330.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (5175a6622762681a) 2049936 checking '[' .................................. PASS (c60784a663dd1761) 9950.096 checking 'resize' ............................. PASS (ff7a963b07cc340b) 15155777 checking 'rotate' ............................. PASS (7a904b4d37503022) 4525312 checking 'flip' ............................... PASS (192932ac94cae831) 1977928 checking 'flop' ............................... PASS (55c97a05ee9ed805) 2048664 checking 'translate' .......................... PASS (c866b3232cda2c68) 2998417 checking 'affine' ............................. PASS (838cd8c4ef1dc919) 226067.6 checking 'transpose' .......................... PASS (e6349d8cc35ed017) 1907377 checking 'thresh' ............................. PASS (e98d9e4246c476a4) 954376.9 checking 'channel' ............................ PASS (84d92148a5eda650) 257578.5 checking 'otsu' ............................... PASS (6a2131f538a2a53e) 0.3316406 checking 'bwlabel' ............................ PASS (2fa4cf414bbb7787) 230329.9 checking 'colorLabels' ........................ PASS (b71e0c0d93c0ba5d) 1920855 checking 'stackObjects' ....................... PASS (f30668520190ffed) 712799.6 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (6a1ba970169d82ad) 2090128 checking 'rmObjects' .......................... PASS (3705fc84a07dd0cd) -0.1 checking 'reenumerate' ........................ PASS (3705fc84a07dd0cd) -0.1 checking 'reenumerate' ........................ PASS (2fa4cf414bbb7787) 230329.9 checking 'computeFeatures' .................... PASS (d5abe7093d55440e) 746878.2 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (1be2808a87ee437f) 117866.8 checking 'localCurvature' ..................... PASS (ad1fddb421e46506) 116636.2 checking 'normalize' .......................... PASS (edb5f31f14cd540d) 1788995 checking 'normalize' .......................... PASS (6a1005a2ed478c1e) 1858155 checking 'gblur' .............................. PASS (c61849c1f4dc6d25) 2029979 checking 'filter2' ............................ PASS (760ded68d0c55bfa) 50878763 checking 'medianFilter' ....................... PASS (0b06f73d5aecad7d) 2034604 checking 'equalize' ........................... PASS (2d4d0558bb48cbfc) 2942981 checking 'erode' .............................. PASS (94112a39c70cd747) 830816.9 checking 'dilate' ............................. PASS (a9fbe5f3b81787ec) 1339263 checking 'opening' ............................ PASS (957aea2990d2caa1) 1013295 checking 'closing' ............................ PASS (7af64e74f8e80dbb) 1069405 checking 'whiteTopHat' ........................ PASS (d50f6d3e0e26602d) 16585.63 checking 'blackTopHat' ........................ PASS (310953bdffbb07ee) 22039.05 checking 'selfComplementaryTopHat' ............ PASS (dfefa629c102a00d) 4071763 checking 'distmap' ............................ PASS (6c03a6a34b67eec0) 6038778 checking 'watershed' .......................... PASS (61ebc564dd827878) 1058553 checking 'floodFill' .......................... PASS (f537dd1499704563) 2036854 checking 'fillHull' ........................... PASS (e6c8a64e9fff6055) 1058553 checking 'propagate' .......................... PASS (7b81c961226b8218) 7755487 checking 'toRGB' .............................. PASS (3884fe38962577a7) 2036151 checking 'rgbImage' ........................... PASS (43e895266c1b7cae) 7617867 checking 'colormap' ........................... PASS (972e374a8a23c0e1) 1657338 checking 'combine' ............................ PASS (d56bf3140c7cd055) 8350133 checking 'combine' ............................ PASS (b21bd2c702883543) 52959073 checking 'tile' ............................... PASS (4f60a4ae167b4e6e) 107188639 checking 'untile' ............................. PASS (05afb65e638c5769) 97994583 checking 'abind' .............................. PASS (d56bf3140c7cd055) 8350133 > > ## test: 3D Grayscale logical 32x32x2 > x <- sample[32:63, 32:63] > x <- x > otsu(x) > x <- combine(x, x) > testEBImageFunctions(x) new test (hash=db12fa8044d98567) checking 'show' ............................... PASS (75018abdcca926f0) -0.1 checking 'print' .............................. PASS (9bacee8faec96053) -0.1 checking 'hist' ............................... PASS (f0f3640c0aa89c38) 5855.343 checking '>' .................................. PASS (db12fa8044d98567) 1055560 checking '+' .................................. PASS (0b5a21f5cc627e62) 2111120 checking '/' .................................. PASS (bf2545eee0c6aa3e) 527779.9 checking '*' .................................. PASS (0b5a21f5cc627e62) 2111120 checking 'median' ............................. PASS (8396e8397399bb05) -0.1 checking 'quantile' ........................... PASS (130a179fb028f1a7) 8.9 checking 'Image' .............................. PASS (041d3981bcab3129) 1055560 checking 'as.Image' ........................... PASS (db12fa8044d98567) 1055560 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6b02d87cd459ac19) 1055560 checking 'imageData<-' ........................ PASS (db12fa8044d98567) 1055560 checking 'as.raster' .......................... PASS (26cf978328d1a712) -0.1 checking 'colorMode<-' ........................ PASS (db12fa8044d98567) 1055560 checking 'numberOfFrames' ..................... PASS (161e41d6aa749739) 1.9 checking 'getFrames' .......................... PASS (ce29246f73d959c3) 916715.6 checking 'display' ............................ PASS (0f4b8075d5f24755) 309.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (1180c20b46fdaf4e) 1656514 checking '[' .................................. PASS (2a55f6dafc492b42) 1889.9 checking 'resize' ............................. PASS (2e271b3bc9e7a27c) 9108608 checking 'rotate' ............................. PASS (d16b29b87668867f) 1600126 checking 'flip' ............................... PASS (fbb2a6f78f2cc7f1) 714439.9 checking 'flop' ............................... PASS (f6825dda37058381) 1064092 checking 'translate' .......................... PASS (8d027c3127938636) 1105982 checking 'affine' ............................. PASS (8dc830edbafa5c9b) 133467.8 checking 'transpose' .......................... PASS (eeeb148d04107340) 758083.9 checking 'thresh' ............................. PASS (5b7b2d141f385123) 824497.9 checking 'channel' ............................ PASS (db12fa8044d98567) 1055560 checking 'otsu' ............................... PASS (69c60dc99d5066e3) 1.4 checking 'bwlabel' ............................ PASS (10092f8e4256496b) 1597368 checking 'colorLabels' ........................ PASS (ebf6961f64378f97) 5485361 checking 'stackObjects' ....................... PASS (d1d99850ff4d6d38) 8889538 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (8c5ef6f490aa8762) 834266.6 checking 'rmObjects' .......................... PASS (0a1cd72f8d3c03e8) 1303423 checking 'reenumerate' ........................ PASS (df75276eeec5813d) 1244828 checking 'reenumerate' ........................ PASS (10092f8e4256496b) 1597368 checking 'computeFeatures' .................... PASS (2561f1b745b56d57) 416103592 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (9f7d90d6312e32f3) 836958.8 checking 'localCurvature' ..................... PASS (477746e4fee34aeb) 835041.5 checking 'normalize' .......................... PASS (eea76285d45436f7) 1055560 checking 'normalize' .......................... PASS (eea76285d45436f7) 1055560 checking 'gblur' .............................. PASS (fd8945a2f8d02a20) 1037581 checking 'filter2' ............................ PASS (637287a5df76a79d) 26149148 checking 'medianFilter' ....................... PASS (ed8d722e63a36a34) 1030730 checking 'equalize' ........................... PASS (eea76285d45436f7) 1055560 checking 'erode' .............................. PASS (54ccd3aba098da92) 617311.9 checking 'dilate' ............................. PASS (3f0aed5a551e26b5) 1591594 checking 'opening' ............................ PASS (ae3c29b4498904c5) 861145.9 checking 'closing' ............................ PASS (2e26e13058dee387) 1188258 checking 'whiteTopHat' ........................ PASS (28bbffedc1bcb297) 148131.9 checking 'blackTopHat' ........................ PASS (a862285882d4249e) 202411.9 checking 'selfComplementaryTopHat' ............ PASS (92483d40b14844db) 2151192 checking 'distmap' ............................ PASS (766610b2223767b0) 3856630 checking 'watershed' .......................... PASS (eaba5359a5afa00e) 1443978 checking 'floodFill' .......................... PASS (0db2bbd3a6d9a773) 2057384 checking 'fillHull' ........................... PASS (ccded36693237a0e) 1096352 checking 'propagate' .......................... PASS (e3c3ba3dd998f78f) 1613920 checking 'toRGB' .............................. PASS (a594b4f9b88125f1) 8499672 checking 'rgbImage' ........................... PASS (172b07d65c57f496) 4777616 checking 'colormap' ........................... PASS (a6b9bc2f3472cbee) 10283526 checking 'combine' ............................ PASS (f13e4c8ca8445cd0) 3888784 checking 'combine' ............................ PASS (d8a9b6cf082a9146) 23054440 checking 'tile' ............................... PASS (4c3d7086d0c2c786) 48846817 checking 'untile' ............................. PASS (65365043e983ec58) 41221063 checking 'abind' .............................. PASS (af0697002f77c709) 3888784 > > ## test: 4D Color 33x16x3x2 > x <- sample.color[1:33, 1:16,] > x <- combine(x, x) > testEBImageFunctions(x) new test (hash=290d7a45d7468e5f) checking 'show' ............................... PASS (78a7303aa046067b) -0.1 checking 'print' .............................. PASS (9aaf686697ac72be) -0.1 checking 'hist' ............................... PASS (b01a7d139c82f457) 492113.2 checking '>' .................................. PASS (1f65757da86f51b3) 2013322 checking '+' .................................. PASS (86bdea7870f6d0cc) 4709417 checking '/' .................................. PASS (c3533150260f42c4) 1177354 checking '*' .................................. PASS (86bdea7870f6d0cc) 4709417 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (290d7a45d7468e5f) 2354709 checking 'as.Image' ........................... PASS (290d7a45d7468e5f) 2354709 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1936bbf08b457bab) 2354709 checking 'imageData<-' ........................ PASS (290d7a45d7468e5f) 2354709 checking 'as.raster' .......................... PASS (da1c028f359bf00b) -0.1 checking 'colorMode<-' ........................ PASS (7856ef3bde7528ce) 2354709 checking 'numberOfFrames' ..................... PASS (161e41d6aa749739) 1.9 checking 'getFrames' .......................... PASS (f0d9427233f46fbb) 1440422 checking 'display' ............................ PASS (ef6dce96392bbb6d) 263.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (ad8f0dc0cad6885c) 2650006 checking '[' .................................. PASS (144b12c39a99e2bc) 40701.82 checking 'resize' ............................. PASS (3127cba298aad55f) 76725662 checking 'rotate' ............................. PASS (bca3ab9c26f81918) 4140744 checking 'flip' ............................... PASS (91c7918c52fe8718) 2309692 checking 'flop' ............................... PASS (49ae0fb3bef587c5) 2358658 checking 'translate' .......................... PASS (a8fcd75113ffb2d2) 3393923 checking 'affine' ............................. PASS (a3eeaaeedbf1f7a2) 301692.6 checking 'transpose' .......................... PASS (a42245132dbea662) 2303263 checking 'thresh' ............................. PASS (167470821b508c29) 1549362 checking 'channel' ............................ PASS (d4dd2cc593776db0) 287206.2 checking 'otsu' ............................... PASS (2ff953970aa01423) 1.370703 checking 'bwlabel' ............................ PASS (404699231a09f479) 360413.9 checking 'colorLabels' ........................ PASS (4742967f9e3ced6e) 3039066 checking 'stackObjects' ....................... PASS (71587dec63927412) 2472601 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (0daa597dbe10a6cd) 2558300 checking 'rmObjects' .......................... PASS (ea36bf2e51776461) 261782.9 checking 'reenumerate' ........................ PASS (ea36bf2e51776461) 261782.9 checking 'reenumerate' ........................ PASS (404699231a09f479) 360413.9 checking 'computeFeatures' .................... PASS (4f731e0e205341e5) 749353.1 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (20fad83d539e2372) 107408.8 checking 'localCurvature' ..................... PASS (469cd750daa03946) 106275.7 checking 'normalize' .......................... PASS (4484b1dbbf34c675) 2693244 checking 'normalize' .......................... PASS (27680837000f1ded) 2315924 checking 'gblur' .............................. PASS (fc2147343f5faed5) 2349701 checking 'filter2' ............................ PASS (958b84b9c0054384) 58841710 checking 'medianFilter' ....................... PASS (8ccc036255fe88d9) 2352447 checking 'equalize' ........................... PASS (e7f99b2a8483f2d3) 2616480 checking 'erode' .............................. PASS (16554ca32b165307) 1547948 checking 'dilate' ............................. PASS (560c069e5292fdc9) 2604996 checking 'opening' ............................ PASS (592d8ab4156490aa) 1919386 checking 'closing' ............................ PASS (c57a6175329f5e45) 2038196 checking 'whiteTopHat' ........................ PASS (6938d64e59a77fe1) 12437.36 checking 'blackTopHat' ........................ PASS (8fbaad8a000d91c5) 19780.97 checking 'selfComplementaryTopHat' ............ PASS (b11bd64d03fe29b9) 4711722 checking 'distmap' ............................ PASS (708df2d4560d23a7) 10836360 checking 'watershed' .......................... PASS (4aa1432f01914277) 2013322 checking 'floodFill' .......................... PASS (02926422d15cf3c2) 2355706 checking 'fillHull' ........................... PASS (1f65757da86f51b3) 2013322 checking 'propagate' .......................... PASS (1656991af484107e) 11618104 checking 'toRGB' .............................. PASS (290d7a45d7468e5f) 2354709 checking 'rgbImage' ........................... PASS (98de7e0def0bab8b) 12071186 checking 'colormap' ........................... PASS (0798dea20c907720) 2273276 checking 'combine' ............................ PASS (579971440faf3f11) 9516503 checking 'combine' ............................ PASS (fb7944257dfefb91) 59844403 checking 'tile' ............................... PASS (e594265685cdf3aa) 114300809 checking 'untile' ............................. PASS (5b25f3b7fc0df1b3) 105862114 checking 'abind' .............................. PASS (a413703585d2e713) 9516503 > > ## test: 4D Grayscale 16x33x2x3 > colorMode(x) <- Grayscale > imageData(x) <- aperm(x, c(2L, 1L, 4L, 3L)) > testEBImageFunctions(x) new test (hash=2a321f78219fa026) checking 'show' ............................... PASS (3de182583a8c2cf2) -0.1 checking 'print' .............................. PASS (05d1cebf84274f35) -0.1 checking 'hist' ............................... PASS (885aba01ae2954f5) 229030.4 checking '>' .................................. PASS (c15b137f0122c2ee) 1541186 checking '+' .................................. PASS (2951b29fcfadda51) 4466272 checking '/' .................................. PASS (b0a06579c4ef390d) 1116568 checking '*' .................................. PASS (2951b29fcfadda51) 4466272 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (e6ae9fe3a69fec2c) 2233136 checking 'as.Image' ........................... PASS (2a321f78219fa026) 2233136 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6a221a6a2cec815a) 2233136 checking 'imageData<-' ........................ PASS (2a321f78219fa026) 2233136 checking 'as.raster' .......................... PASS (73a5fd711e0edd14) -0.1 checking 'colorMode<-' ........................ PASS (2a321f78219fa026) 2233136 checking 'numberOfFrames' ..................... PASS (d9914b6bdfe88a1d) 5.9 checking 'getFrames' .......................... PASS (c2a08dc890b333e2) 1229859 checking 'display' ............................ PASS (4ca607589cc2787e) 280.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (d4dbcf7b516a28b0) 2502013 checking '[' .................................. PASS (efc391fc4ded377e) 41200.75 checking 'resize' ............................. PASS (00aef78b69242c90) 72772706 checking 'rotate' ............................. PASS (f42404ca4cc1e57e) 3978266 checking 'flip' ............................... PASS (2578de2eb711ac89) 2296325 checking 'flop' ............................... PASS (c21acaf425029919) 2231772 checking 'translate' .......................... PASS (74e4014bf39793e1) 3827517 checking 'affine' ............................. PASS (9c7b3a7ea964b836) 219714.6 checking 'transpose' .......................... PASS (3b5dcc82ff30daf8) 2284582 checking 'thresh' ............................. PASS (3a92d48cd68a67e8) 1426674 checking 'channel' ............................ PASS (2a321f78219fa026) 2233136 checking 'otsu' ............................... PASS (2cdec937ebdb0543) 9.425391 checking 'bwlabel' ............................ PASS (f698416417dde49c) 2016822 checking 'colorLabels' ........................ PASS (b07a31035fc451d5) 15071536 checking 'stackObjects' ....................... PASS (8e5b00026f507a11) 2575847 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (63b2ef8ac8682f98) 2379341 checking 'rmObjects' .......................... PASS (056669f72385f506) 1934575 checking 'reenumerate' ........................ PASS (056669f72385f506) 1934575 checking 'reenumerate' ........................ PASS (f698416417dde49c) 2016822 checking 'computeFeatures' .................... PASS (6e516e369839bbb1) 734993.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (3a230e30e8d15bee) 118072.8 checking 'localCurvature' ..................... PASS (a1d19191deda947d) 117246.2 checking 'normalize' .......................... PASS (85d2a91256ddfdaa) 2526618 checking 'normalize' .......................... PASS (4accf817a36301dc) 2163958 checking 'gblur' .............................. PASS (c2c22f114f9ac87d) 2237219 checking 'filter2' ............................ PASS (0245e31021e7583c) 56904871 checking 'medianFilter' ....................... PASS (24f248c2c56e7772) 2231438 checking 'equalize' ........................... PASS (97693dcd997265d1) 2447139 checking 'erode' .............................. PASS (5b04187576514eec) 1121204 checking 'dilate' ............................. PASS (4897aaa0d40c4fb8) 2104588 checking 'opening' ............................ PASS (cb86eac9754dbac1) 1451050 checking 'closing' ............................ PASS (13b4d846ef6a77dd) 1569448 checking 'whiteTopHat' ........................ PASS (1c856cc6a52ed865) 12004.54 checking 'blackTopHat' ........................ PASS (f74244f5c4295d35) 20296.87 checking 'selfComplementaryTopHat' ............ PASS (f23286411d6929f7) 4469404 checking 'distmap' ............................ PASS (ff3b2754a2aa8eb3) 7464344 checking 'watershed' .......................... PASS (cd9ef36f457c5d89) 1541186 checking 'floodFill' .......................... PASS (60d288f662756f97) 2234521 checking 'fillHull' ........................... PASS (c15b137f0122c2ee) 1541186 checking 'propagate' .......................... PASS (503cd7ed6238770e) 8948876 checking 'toRGB' .............................. PASS (5a32f2aceec9a146) 20279146 checking 'rgbImage' ........................... PASS (19e0ea95d787d11c) 10796552 checking 'colormap' ........................... PASS (62fb056f168823de) 22585273 checking 'combine' ............................ PASS (67fe5c370ca3a18d) 8992851 checking 'combine' ............................ PASS (41f451bdd6a63a8f) 56431472 checking 'tile' ............................... PASS (0581a6216e8e50e0) 72664167 checking 'untile' ............................. PASS (4e208afef7f298bd) 60048605 checking 'abind' .............................. PASS (e3feb875241cebc2) 9273358 > > ## test: Image subclass > ImageSubclass <- setClass ("ImageSubclass", contains = "Image", slots = c(foo = "character")) > x <- ImageSubclass(x, foo="bar") > testEBImageFunctions(x) new test (hash=9b67f57c77f74d34) checking 'show' ............................... PASS (63597c3473b56977) -0.1 checking 'print' .............................. PASS (1cd88fa9e1ff084e) -0.1 checking 'hist' ............................... PASS (885aba01ae2954f5) 229030.4 checking '>' .................................. PASS (8213f4f8b30b3c46) 1541186 checking '+' .................................. PASS (d9da0200176ead52) 4466272 checking '/' .................................. PASS (c5360d5612508ba0) 1116568 checking '*' .................................. PASS (d9da0200176ead52) 4466272 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (e6ae9fe3a69fec2c) 2233136 checking 'as.Image' ........................... PASS (2a321f78219fa026) 2233136 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6a221a6a2cec815a) 2233136 checking 'imageData<-' ........................ PASS (9b67f57c77f74d34) 2233136 checking 'as.raster' .......................... PASS (73a5fd711e0edd14) -0.1 checking 'colorMode<-' ........................ PASS (9b67f57c77f74d34) 2233136 checking 'numberOfFrames' ..................... PASS (d9914b6bdfe88a1d) 5.9 checking 'getFrames' .......................... PASS (e9438bf3afe19fef) 1229859 checking 'display' ............................ PASS (4ca607589cc2787e) 280.7 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (88969323fe4011cb) 2502013 checking '[' .................................. PASS (856f5f5a7828a96f) 41200.75 checking 'resize' ............................. PASS (e94d70507c46424a) 72772706 checking 'rotate' ............................. PASS (bb28d7a739148c1e) 3978266 checking 'flip' ............................... PASS (753308a7b510662f) 2296325 checking 'flop' ............................... PASS (1ea0c6126c86d976) 2231772 checking 'translate' .......................... PASS (c3111aabac6df5c8) 3827517 checking 'affine' ............................. PASS (00a69976accd24e7) 219714.6 checking 'transpose' .......................... PASS (d9282e9071f27e10) 2284582 checking 'thresh' ............................. PASS (b51eea6755dfd65a) 1426674 checking 'channel' ............................ PASS (9b67f57c77f74d34) 2233136 checking 'otsu' ............................... PASS (2cdec937ebdb0543) 9.425391 checking 'bwlabel' ............................ PASS (edce7604823b90a7) 2016822 checking 'colorLabels' ........................ PASS (05cf97699b52f053) 15969784 checking 'stackObjects' ....................... PASS (bbe84601c71da500) 2575847 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (944b58c80d127777) 2379341 checking 'rmObjects' .......................... PASS (1ed59ae8eb61aef6) 1934575 checking 'reenumerate' ........................ PASS (1ed59ae8eb61aef6) 1934575 checking 'reenumerate' ........................ PASS (edce7604823b90a7) 2016822 checking 'computeFeatures' .................... PASS (6e516e369839bbb1) 734993.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (3a230e30e8d15bee) 118072.8 checking 'localCurvature' ..................... PASS (a1d19191deda947d) 117246.2 checking 'normalize' .......................... PASS (9ace81a69fc88c37) 2526618 checking 'normalize' .......................... PASS (2a78b599de5c2ae9) 2163958 checking 'gblur' .............................. PASS (0d226d91f7036796) 2237219 checking 'filter2' ............................ PASS (7cb701d185d8631b) 56904871 checking 'medianFilter' ....................... PASS (37328d9ce26ed388) 2231438 checking 'equalize' ........................... PASS (05fc2423af12b77a) 2447139 checking 'erode' .............................. PASS (17fcd8b3a8de8535) 1121204 checking 'dilate' ............................. PASS (715c930769bb9119) 2104588 checking 'opening' ............................ PASS (1ef38f55606cdbf4) 1451050 checking 'closing' ............................ PASS (66cb111962e57366) 1569448 checking 'whiteTopHat' ........................ PASS (66e080c20ad98021) 12004.54 checking 'blackTopHat' ........................ PASS (c8b5fb6a0e1d3959) 20296.87 checking 'selfComplementaryTopHat' ............ PASS (d91b85d0f726e766) 4469404 checking 'distmap' ............................ PASS (4ced93e5efc06917) 7464344 checking 'watershed' .......................... PASS (9c1a4d5672652853) 1541186 checking 'floodFill' .......................... PASS (d9a38a5952fe360e) 2234521 checking 'fillHull' ........................... PASS (8213f4f8b30b3c46) 1541186 checking 'propagate' .......................... PASS (0731a1de5ddabcc4) 8948876 checking 'toRGB' .............................. PASS (c62b6c6a269ea1eb) 20279146 checking 'rgbImage' ........................... PASS (27eec26383a0bc15) 10796552 checking 'colormap' ........................... PASS (eef6d0395d7fe0e7) 22585273 checking 'combine' ............................ PASS (5b4994ce3c695b2e) 8992851 checking 'combine' ............................ PASS (03e050af1c7e1af2) 56431472 checking 'tile' ............................... PASS (db685d6eb3480813) 72664167 checking 'untile' ............................. PASS (0e362c45443a3ec0) 60048605 checking 'abind' .............................. PASS (add8d4baab35a5f9) 9273358 > > proc.time() user system elapsed 3.358 0.496 4.241
EBImage.Rcheck/tests/test.Rout.save
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## cat tests/test.R | R --vanilla &>tests/test.Rout.save > library("EBImage") > > set.seed(0) # make random color permutations in 'colorLabels' reproducible > .digits = floor(-log10(.Machine$double.eps^.5) - 1) > > ## returns a hashcode given an object > hash = function (x) .Call(digest:::digest_impl, serialize(x, connection=NULL, ascii=FALSE, xdr=FALSE), 7L, -1L, 14L, 0L, 0L, PACKAGE="digest") > > hash.old <- function(x) { + if (is.list(x) && length(x)>0) { + hash.old(sapply(x, hash.old, USE.NAMES=FALSE)) + } + else { + xd <- suppressWarnings(as.numeric(x)) + xd <- xd[!(is.nan(xd)|is.na(xd))] + sx <- sum(xd*(1:length(xd))) + if (is.matrix(xd)) + sx + 0.7 * hash.old(dim(xd)) + else + sx - 0.1 + } + } > > ## try to evaluate fun(x,...) > check <- function(fun, x, ..., capture.output=FALSE, suppressWarnings=FALSE, suppressMessages=FALSE, expectError=FALSE, round=FALSE, debug=FALSE) { + passed <- TRUE + + cat(sprintf("checking \'%s\' %s ", fun, paste(rep(".", 35L-nchar(fun)), collapse = ""))) + + expr = quote(do.call(fun,c(list(x),list(...)))) + if ( isTRUE(capture.output) ) expr = call("capture.output", expr) + if ( isTRUE(suppressWarnings) ) expr = call("suppressWarnings", expr) + if ( isTRUE(suppressMessages) ) expr = call("suppressMessages", expr) + + y <- try(eval(expr), silent=TRUE) + + if ( (inherits(y, "try-error") && !isTRUE(expectError)) || (is.Image(y) && !validObject(y)) ) { + y <- NULL + passed <- FALSE + } + + if (passed) { + if (isTRUE(round) && !inherits(y, "try-error")) + y = if ( is.list(y) ) lapply(y, round, digits=.digits) else round(y, digits = .digits) + cat("PASS (", hash(y), ") ", hash.old(y), "\n", sep="") + } + else cat("FAIL\n") + + if ( isTRUE(debug) ) { + if (is.Image(y)) show(y) + if (is.array(y)) display(y, all=TRUE, interpolate=FALSE) + else if (is.character(y)) cat(y, sep="\n") + } + + y + } > > checkIO <- function(name) { + cat("checking IO for \'", name, "\' ... ", sep="") + x = get(name) + y = FALSE + if ( !is.null(x) ) { + y <- try({ + xx <- readImage(writeImage(x, tempfile("", fileext = ".tif"))) + dimnames(xx) <- dimnames(x) + identical(x, xx) + }, silent=TRUE) + } + if ( isTRUE(y) ) cat("PASS\n") else cat("FAIL\n") + invisible(y) + } > > testIOFunctions <- function(...) invisible(lapply(list(...), function(y) checkIO(y))) > > testEBImageFunctions <- function(x) { + cat("new test (hash=", hash(x), ")\n", sep="") + + z <- check("show", x, capture.output=TRUE) + z <- check("print", x, short=TRUE, capture.output=TRUE) + if ( typeof(x)=="logical" ) + z <- check("hist", EBImage:::castImage(x), breaks = c(0, .5, 1)) + else + z <- check("hist", x) + + ## pixel arithmetic + z <- check(">", x, 0.5) + z <- check("+", x, x) + z <- check("/", x, 2) + z <- check("*", 2L, x) + z <- check("median", x) + z <- check("quantile", x) + + ## image methods + z <- check("Image", x, colormode="Color") + z <- check("as.Image", x) + z <- check("is.Image", x) + z <- check("imageData", x) + z <- check("imageData<-", x, z) + z <- check("as.raster", x) + z <- check("colorMode<-", x, Grayscale, suppressWarnings=TRUE) + y <- check("numberOfFrames", x, type="render") + z <- if ( y==1L ) check("getFrames", x, 1L, "render") else check("getFrames", x) + z <- check("display", x, method = "browser", tempDir = file.path(dirname(tempdir()), "EBImage_tmp")) + if ( y>2L ) { + z <- check("display", x, method = "raster", all = TRUE) + z <- check("image", x, i = 3L) + } + else { + z <- if (y==1L) check("display", x, method = "raster") else check("display", x, method = "raster", frame = 2L, suppressMessages=TRUE) + z <- check("image", x, suppressMessages=TRUE) + } + + ## drawCircle + d <- dim(x) + c.x <- ceiling(d[1L]/2) + c.y <- ceiling(d[2L]/2) + radius <- max(c.x-1, 1) + nf <- numberOfFrames(x, "render") + fill <- nf > 1 + col <- if ( colorMode(x)==Color ) "yellow" else 1 + z <- check("drawCircle", x, c.x, c.x, radius, col, fill, nf) + + ## subset + sub <- list(x, 1:min(10,d[1L]), 1:min(7,d[2L])) + if (length(d)>2) sub <- c(sub, rep(TRUE, length(d)-2)) + z <- do.call("check", c("[", sub)) + + ## spatial transform + z <- check("resize", x, 137, 22) + z <- check("rotate", x, 20) + z <- check("flip", x) + z <- check("flop", x) + z <- check("translate", x, c(-7, 5), bg.col=1) + z <- check("affine", x, matrix(c(-7, 5, 0.1, -0.2, 0.3, 1), ncol=2L)) + z <- check("transpose", x) + + ## segmentation + fd = pmin(5, (d[1:2]-1)/2) + z <- check("thresh", x, w=fd[1L], h=fd[2L]) + y <- check("channel", x, "luminance") + z <- check("otsu", y) + y <- suppressWarnings(normalize(y, separate=FALSE)) + y <- check("bwlabel", y > 0.5) + z <- check("colorLabels", y, suppressWarnings=TRUE) + z <- check("stackObjects", y, x) + z <- check("stackObjects", Image(dim=dim(y)), x) + cls <- if ( colorMode(x)==Color ) TRUE else FALSE + z <- check("paintObjects", y, x, col=c("#ff00ff", "#ffff00"), opac=c(1.0, 0.5), thick=cls, closed=cls) + z <- check("rmObjects", y, as.list(seq_len(numberOfFrames(y))), cls) + z <- check("reenumerate", z) + z <- check("reenumerate", y) + + ## features + x1 <- getFrame(x, 1) + x2 <- list(x=x1, y=2*x1) + y1 <- getFrame(y, 1) + expandRef <- if ( min(dim(x1)) > 31L ) function(ref, refnames) standardExpandRef(ref, refnames, gblob(n=31L)) else NULL + z <- check("computeFeatures", y1, x2, expandRef = expandRef, round = !is.null(expandRef)) + z <- check("computeFeatures", y1, x2, expandRef = expandRef, properties = TRUE) + + ## curvature + y <- check("ocontour", x>0.5) + if (length(y) > 0L ) z <- check("localCurvature", y[[1L]], round=TRUE) + + ## filtering + z <- check("normalize", x, suppressWarnings=TRUE) + z <- check("normalize", x, inputRange=c(0.1, 0.9), suppressWarnings=TRUE) + z <- check("gblur", x, sigma=1, expectError=min(d)<7, round=TRUE) + y <- if (cls) "replicate" else if (nf>1) 0.5 else "circular" + z <- check("filter2", x, array(1, dim=c(5, 5)), y, round=TRUE) + z <- check("medianFilter", x, 2) + z <- check("equalize", x, suppressWarnings=TRUE) + + ## morphological operations + y <- x > 0.5 + z <- check("erode", y) + z <- check("dilate", y, makeBrush(5, 'disc')) + z <- check("opening", y, makeBrush(7, 'line')) + z <- check("closing", y, makeBrush(4, 'line', angle=0), suppressWarnings=TRUE) + z <- check("whiteTopHat", x, makeBrush(3, 'box')) + z <- check("blackTopHat", x, makeBrush(5, 'disc')) + z <- check("selfComplementaryTopHat", x) + z <- check("distmap", y) + z <- check("watershed", z) + z <- check('floodFill', x, c(5, 5), 0.5) + z <- check('fillHull', y) + + ## propagate + y <- thresh(x, w=fd[1L], h=fd[2L], offset=0.02) + y <- fillHull(y) + y <- bwlabel(y) + z <- check("propagate", x, y, x>0.5) + + ## colorspace + z <- check("toRGB", x) + z <- check("rgbImage", x, x>0.5) + z <- check("colormap", channel(x, "luminance"), heat.colors(16L)) + + ## image stacking, combining, tiling + y <- check("combine", list(NULL, x, x, NULL, NULL)) + z <- check("combine", x, y, y) + y <- check("tile", z, nx=3) + z <- check("untile", y, c(3, 2)) + y <- check("abind", list(x, x), along=length(d)+1L) + cat("\n") + } > > > ## check error handling > try.readImage <- function(...) tryCatch(suppressWarnings(readImage(...)), error = function(e) NULL) > mock <- try.readImage(system.file("images", package="EBImage"), type="png") > mock <- try.readImage("http://www.huber.embl.de/EBImage/missing.file ", type="png") > > ## single greyscale and color images > sample <- try.readImage(system.file("images","sample.png", package="EBImage")) > sample.color <- try.readImage(system.file("images","sample-color.png", package="EBImage")) > ## multi-frame image stack > f = system.file("images","nuclei.tif", package="EBImage") > nuclei = try.readImage(c(f, f)) > ## test reading from URL > logo <- try.readImage("http://www.huber.embl.de/EBImage/logo.png") > > ## test: IO operations > testIOFunctions("sample", "sample.color", "nuclei", "logo") checking IO for 'sample' ... PASS checking IO for 'sample.color' ... PASS checking IO for 'nuclei' ... PASS checking IO for 'logo' ... PASS Warning message: In readTIFF(x, all = all, ...) : TIFFReadDirectory: Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples. > > ## test: black image > testEBImageFunctions(Image(0, c(8, 8))) new test (hash=03724aaea0cf64b4) checking 'show' ............................... PASS (5a93d2a87828912b) -0.1 checking 'print' .............................. PASS (0007ac6dee6a14da) -0.1 checking 'hist' ............................... PASS (8ef6dc298b72d591) Inf checking '>' .................................. PASS (91517a74c2895221) -0.1 checking '+' .................................. PASS (03724aaea0cf64b4) -0.1 checking '/' .................................. PASS (03724aaea0cf64b4) -0.1 checking '*' .................................. PASS (03724aaea0cf64b4) -0.1 checking 'median' ............................. PASS (8396e8397399bb05) -0.1 checking 'quantile' ........................... PASS (5e6b34b7d87730f0) -0.1 checking 'Image' .............................. PASS (e4b04ad17c704314) -0.1 checking 'as.Image' ........................... PASS (03724aaea0cf64b4) -0.1 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1ba6fa2bac2e6157) -0.1 checking 'imageData<-' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'as.raster' .......................... PASS (e8f1c1057deba532) -0.1 checking 'colorMode<-' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (437d348905e7edea) -0.2 checking 'display' ............................ PASS (4c9befc7a9f9f22e) 165.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (76ab1bcd040f633c) 447.9 checking '[' .................................. PASS (3c13b8fa403f3a61) -0.1 checking 'resize' ............................. PASS (59b56ab6bbfb3b98) -0.1 checking 'rotate' ............................. PASS (d9d1aa63f93f02d0) -0.1 checking 'flip' ............................... PASS (03724aaea0cf64b4) -0.1 checking 'flop' ............................... PASS (03724aaea0cf64b4) -0.1 checking 'translate' .......................... PASS (8f2e405bb6973b4a) 1932.9 checking 'affine' ............................. PASS (03724aaea0cf64b4) -0.1 checking 'transpose' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'thresh' ............................. PASS (c13bdaf3a3ddff95) -0.1 checking 'channel' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'otsu' ............................... PASS (e3b39ef666a0ce39) -0.09804688 checking 'bwlabel' ............................ PASS (c13bdaf3a3ddff95) -0.1 checking 'colorLabels' ........................ PASS (73c6f975aa7b9638) -0.1 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (03724aaea0cf64b4) -0.1 checking 'rmObjects' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'reenumerate' ........................ PASS (c13bdaf3a3ddff95) -0.1 checking 'reenumerate' ........................ PASS (c13bdaf3a3ddff95) -0.1 checking 'computeFeatures' .................... PASS (d956c282ac7180e4) -0.1 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (0cbbfbd6c2b5057a) -0.1 checking 'normalize' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'normalize' .......................... PASS (03724aaea0cf64b4) -0.1 checking 'gblur' .............................. PASS (03724aaea0cf64b4) -0.1 checking 'filter2' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'medianFilter' ....................... PASS (03724aaea0cf64b4) -0.1 checking 'equalize' ........................... PASS (03724aaea0cf64b4) -0.1 checking 'erode' .............................. PASS (91517a74c2895221) -0.1 checking 'dilate' ............................. PASS (91517a74c2895221) -0.1 checking 'opening' ............................ PASS (91517a74c2895221) -0.1 checking 'closing' ............................ PASS (91517a74c2895221) -0.1 checking 'whiteTopHat' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'blackTopHat' ........................ PASS (03724aaea0cf64b4) -0.1 checking 'selfComplementaryTopHat' ............ PASS (03724aaea0cf64b4) -0.1 checking 'distmap' ............................ PASS (03724aaea0cf64b4) -0.1 checking 'watershed' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'floodFill' .......................... PASS (b7521415b91cdd6a) 1039.9 checking 'fillHull' ........................... PASS (91517a74c2895221) -0.1 checking 'propagate' .......................... PASS (c13bdaf3a3ddff95) -0.1 checking 'toRGB' .............................. PASS (73c6f975aa7b9638) -0.1 checking 'rgbImage' ........................... PASS (73c6f975aa7b9638) -0.1 checking 'colormap' ........................... PASS (f55f763f0bce6d0e) 2079.9 checking 'combine' ............................ PASS (7d8cabf23a7147bf) -0.1 checking 'combine' ............................ PASS (dfe23dd6a6fd08b8) -0.1 checking 'tile' ............................... PASS (63b8539b976f10f9) 42140.88 checking 'untile' ............................. PASS (fc2ab5092822346e) 16809.31 checking 'abind' .............................. PASS (7d8cabf23a7147bf) -0.1 > > ## test: white image > testEBImageFunctions(Image(1L, c(5, 5))) new test (hash=5e369a5a8c06ea6e) checking 'show' ............................... PASS (d7ff39dcf34291a7) -0.1 checking 'print' .............................. PASS (423045c171032825) -0.1 checking 'hist' ............................... PASS (c32dc2571db86a0f) Inf checking '>' .................................. PASS (ab60d77d8694845c) 324.9 checking '+' .................................. PASS (ccb4c957b356b423) 649.9 checking '/' .................................. PASS (e68dd3c4bf42ae06) 162.4 checking '*' .................................. PASS (ccb4c957b356b423) 649.9 checking 'median' ............................. PASS (7c79dea3bfc1415b) 0.9 checking 'quantile' ........................... PASS (03ab24e6a573bd6b) 14.9 checking 'Image' .............................. PASS (e06d5f65342df035) 324.9 checking 'as.Image' ........................... PASS (5e369a5a8c06ea6e) 324.9 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (a72e950dc2c633c4) 324.9 checking 'imageData<-' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'as.raster' .......................... PASS (76158aebe747f7e1) -0.1 checking 'colorMode<-' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (5be9802bf124fe9c) 324.8 checking 'display' ............................ PASS (174250a6d96dee60) 150.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (a3847050dd15905c) 324.9 checking '[' .................................. PASS (5e369a5a8c06ea6e) 324.9 checking 'resize' ............................. PASS (81601207cc4e4223) 4543605 checking 'rotate' ............................. PASS (3db98677c68c5102) 483.6843 checking 'flip' ............................... PASS (5e369a5a8c06ea6e) 324.9 checking 'flop' ............................... PASS (5e369a5a8c06ea6e) 324.9 checking 'translate' .......................... PASS (a3847050dd15905c) 324.9 checking 'affine' ............................. PASS (92683959c9ed97c3) 39.9 checking 'transpose' .......................... PASS (5e369a5a8c06ea6e) 324.9 checking 'thresh' ............................. PASS (dafc92132d191221) -0.1 checking 'channel' ............................ PASS (5e369a5a8c06ea6e) 324.9 checking 'otsu' ............................... PASS (2abebb5cf42f343e) 0.8980469 checking 'bwlabel' ............................ PASS (5e369a5a8c06ea6e) 324.9 checking 'colorLabels' ........................ PASS (a7e8ce686b7c6eec) 2849.9 checking 'stackObjects' ....................... PASS (995b03d1197fdd56) 324.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (fbe94deb2c7c7e12) 270.7333 checking 'rmObjects' .......................... PASS (dafc92132d191221) -0.1 checking 'reenumerate' ........................ PASS (dafc92132d191221) -0.1 checking 'reenumerate' ........................ PASS (5e369a5a8c06ea6e) 324.9 checking 'computeFeatures' .................... PASS (1e197f38fe3db7df) 950932.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (1ad47b9dc5e279b9) 1087.8 checking 'localCurvature' ..................... PASS (07aef8b9d0c42e30) 1008.955 checking 'normalize' .......................... PASS (a3847050dd15905c) 324.9 checking 'normalize' .......................... PASS (a3847050dd15905c) 324.9 checking 'gblur' .............................. PASS (34be5e3328df689f) -0.1 checking 'filter2' ............................ PASS (046936d9c22a44d3) 8124.9 checking 'medianFilter' ....................... PASS (a3847050dd15905c) 324.9 checking 'equalize' ........................... PASS (5e369a5a8c06ea6e) 324.9 checking 'erode' .............................. PASS (ab60d77d8694845c) 324.9 checking 'dilate' ............................. PASS (ab60d77d8694845c) 324.9 checking 'opening' ............................ PASS (ab60d77d8694845c) 324.9 checking 'closing' ............................ PASS (ab60d77d8694845c) 324.9 checking 'whiteTopHat' ........................ PASS (dafc92132d191221) -0.1 checking 'blackTopHat' ........................ PASS (dafc92132d191221) -0.1 checking 'selfComplementaryTopHat' ............ PASS (ccb4c957b356b423) 649.9 checking 'distmap' ............................ PASS (4620168ff1c2a437) Inf checking 'watershed' .......................... PASS (5e369a5a8c06ea6e) 324.9 checking 'floodFill' .......................... PASS (dafc92132d191221) -0.1 checking 'fillHull' ........................... PASS (ab60d77d8694845c) 324.9 checking 'propagate' .......................... PASS (dafc92132d191221) -0.1 checking 'toRGB' .............................. PASS (f3b87c6a40e54c68) 2849.9 checking 'rgbImage' ........................... PASS (a1c021690e069b07) 1274.9 checking 'colormap' ........................... PASS (948ec87fd2adc7a9) 2652.253 checking 'combine' ............................ PASS (8c39678924e12a09) 1274.9 checking 'combine' ............................ PASS (072d49f53072e43b) 7874.9 checking 'tile' ............................... PASS (16eb65ee8bbcb932) 24420.64 checking 'untile' ............................. PASS (8bcebbd606485233) 10445.49 checking 'abind' .............................. PASS (8c39678924e12a09) 1274.9 > > ## test: 2D Grayscale 64x48 > x <- nuclei[50:113,208:255,2] > testEBImageFunctions(as.array(x)) new test (hash=3e469356855e6210) checking 'show' ............................... PASS (0c6212669ee6288d) -0.1 checking 'print' .............................. PASS (0c6212669ee6288d) -0.1 checking 'hist' ............................... PASS (e7a708b4f96f88dc) 20513.55 checking '>' .................................. PASS (0a927a877b0b85eb) 1217568 checking '+' .................................. PASS (2c51607a58b46974) 2940144 checking '/' .................................. PASS (a872fc97379d58f5) 735035.9 checking '*' .................................. PASS (2c51607a58b46974) 2940144 checking 'median' ............................. PASS (d2a8be6a346c3d28) 0.04509804 checking 'quantile' ........................... PASS (645f4aadbce7bdea) 7.331373 checking 'Image' .............................. PASS (923c3911d773eb6e) 1470072 checking 'as.Image' ........................... PASS (b7ae9a016c5a19ec) 1470072 checking 'is.Image' ........................... PASS (69f0cf1cfd5cd8ed) -0.1 checking 'imageData' .......................... PASS (3e469356855e6210) 1470072 checking 'imageData<-' ........................ PASS (3e469356855e6210) 1470072 checking 'as.raster' .......................... PASS (42efa6b3b04694cf) -0.1 checking 'colorMode<-' ........................ PASS (b8d002268bfac3eb) -0.1 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (d38b8f6c1a1504a8) 1470072 checking 'display' ............................ PASS (dada341199e50c3d) 397.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (872845fa91c628a6) 1607165 checking '[' .................................. PASS (711703fde7cc915e) 48.94314 checking 'resize' ............................. PASS (7882055c8b670bf4) 1419476 checking 'rotate' ............................. PASS (559860bb5c99cb82) 2493977 checking 'flip' ............................... PASS (8834ca70d449207a) 1195977 checking 'flop' ............................... PASS (d73abd773dfc066a) 1462119 checking 'translate' .......................... PASS (5744e19288b9d7f0) 2133961 checking 'affine' ............................. PASS (11616142290451c1) 54171.17 checking 'transpose' .......................... PASS (aa87d51a100b139f) 1522055 checking 'thresh' ............................. PASS (c790c6a6872d73d0) 1262811 checking 'channel' ............................ PASS (3e469356855e6210) 1470072 checking 'otsu' ............................... PASS (3aea1e91f3716bcb) 0.3160156 checking 'bwlabel' ............................ PASS (5055cb94d5293a15) 1199387 checking 'colorLabels' ........................ PASS (464d65c8da42be0d) 10021713 checking 'stackObjects' ....................... PASS (c5669f863a2ba20e) 718602.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (19a9fbb907cee1c4) 1447733 checking 'rmObjects' .......................... PASS (365ace8a4657cb08) -0.1 checking 'reenumerate' ........................ PASS (365ace8a4657cb08) -0.1 checking 'reenumerate' ........................ PASS (5055cb94d5293a15) 1199387 checking 'computeFeatures' .................... PASS (f59aa3f08e782acf) 3634215 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (790a5f5b45092d41) 1050552 checking 'localCurvature' ..................... PASS (fb6d4b13b08dcac4) 1049392 checking 'normalize' .......................... PASS (1f79956b7887dd73) 1431381 checking 'normalize' .......................... PASS (13a2d37d997199f9) 1266798 checking 'gblur' .............................. PASS (203a6d72b1fd5eba) 1466231 checking 'filter2' ............................ PASS (c82a1ece6902714d) 36592176 checking 'medianFilter' ....................... PASS (4140c87b3a1db93d) 1454712 checking 'equalize' ........................... PASS (ba175363e5576ad1) 2642794 checking 'erode' .............................. PASS (bee7898f6d8d547b) 759774.9 checking 'dilate' ............................. PASS (ed04adac54c645fd) 1797576 checking 'opening' ............................ PASS (d1c6ca8aafbd90cb) 1152484 checking 'closing' ............................ PASS (b8cf094b52fe1744) 1232737 checking 'whiteTopHat' ........................ PASS (9b53631dd222dd50) 18730.15 checking 'blackTopHat' ........................ PASS (089cd73847d97de5) 27716.23 checking 'selfComplementaryTopHat' ............ PASS (cc378ce1d0553ecd) 2929436 checking 'distmap' ............................ PASS (f98a44bf21faa222) 3826969 checking 'watershed' .......................... PASS (b39c109238f0c74b) 2762113 checking 'floodFill' .......................... PASS (c59341ffade6129a) 1470197 checking 'fillHull' ........................... PASS (0a927a877b0b85eb) 1217568 checking 'propagate' .......................... PASS (cec466bef7a2a81e) 3464201 checking 'toRGB' .............................. PASS (5051d2b131286d46) 12381911 checking 'rgbImage' ........................... PASS (ccc09b31890cd8df) 4859544 checking 'colormap' ........................... PASS (b7020f3851eb7d7c) 11126039 checking 'combine' ............................ PASS (5bda9f75cbc23401) 5597376 checking 'combine' ............................ PASS (306e27bb3ec346e6) 33922678 checking 'tile' ............................... PASS (870e7501fa1f3338) 78718054 checking 'untile' ............................. PASS (868893e062dea032) 72597772 checking 'abind' .............................. PASS (5bda9f75cbc23401) 5597376 > > ## test: 2D Color 32x48x1 > x <- sample[1:32, 1:48] > testEBImageFunctions(Image(as.vector(x), dim(x), Color)) new test (hash=7718e616f411c340) checking 'show' ............................... PASS (1a2c30323dd5a8ee) -0.1 checking 'print' .............................. PASS (e9fad67b70709e2b) -0.1 checking 'hist' ............................... PASS (596b544e7cd6f458) 130241.3 checking '>' .................................. PASS (e72c38d763e5fabf) 988518.9 checking '+' .................................. PASS (e38cf73f1c0c88a2) 1531522 checking '/' .................................. PASS (df4e8bf818fc26fe) 382880.4 checking '*' .................................. PASS (e38cf73f1c0c88a2) 1531522 checking 'median' ............................. PASS (fc60ee4b14ba4a28) 0.5039216 checking 'quantile' ........................... PASS (436f03b8c9c3ad0e) 10.10392 checking 'Image' .............................. PASS (7718e616f411c340) 765760.9 checking 'as.Image' ........................... PASS (7718e616f411c340) 765760.9 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (19c51d4d9d30d60c) 765760.9 checking 'imageData<-' ........................ PASS (7718e616f411c340) 765760.9 checking 'as.raster' .......................... PASS (05c68b3f51ec838b) -0.1 checking 'colorMode<-' ........................ PASS (733871e596e328df) 765760.9 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (681aab4c8a24c6c5) 765760.8 checking 'display' ............................ PASS (bb2b4586191eb980) 333.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (a6757bb66994b1f7) 782100.7 checking '[' .................................. PASS (25a626878222798c) 1285.273 checking 'resize' ............................. PASS (bb1209a84d6b3709) 2941770 checking 'rotate' ............................. PASS (924fc66d1ec91d44) 1247487 checking 'flip' ............................... PASS (828db3b8ad878bd6) 661525.2 checking 'flop' ............................... PASS (f69b431f36c97abd) 768451.1 checking 'translate' .......................... PASS (3eb2fe0d22e461ed) 820434.5 checking 'affine' ............................. PASS (7a760844869cec92) 22238.15 checking 'transpose' .......................... PASS (d438f72715d302ed) 652051.4 checking 'thresh' ............................. PASS (8b3a72b493ab8540) 382924.9 checking 'channel' ............................ PASS (3982766c7e1077b3) 162800.7 checking 'otsu' ............................... PASS (ebd9ed7a0cf4831d) 0.03085937 checking 'bwlabel' ............................ PASS (498723eb57bcca48) 832970.9 checking 'colorLabels' ........................ PASS (ecbf282c48506ef2) 3692613 checking 'stackObjects' ....................... PASS (e30de50cc1d8e117) 596493.9 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (9b5026b178720a80) 919069.9 checking 'rmObjects' .......................... PASS (e0ab50f8e544290a) 565.9 checking 'reenumerate' ........................ PASS (e0ab50f8e544290a) 565.9 checking 'reenumerate' ........................ PASS (498723eb57bcca48) 832970.9 checking 'computeFeatures' .................... PASS (c1ff2e62e7bb8eee) 3989786 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (ced9c409ca879dc9) 848253.8 checking 'localCurvature' ..................... PASS (25e900bf67a8cdb0) 847428.3 checking 'normalize' .......................... PASS (b8b2cfe4f431fc83) 747801.4 checking 'normalize' .......................... PASS (3ee0aade2890ed53) 809649.2 checking 'gblur' .............................. PASS (0c28ab262af637d1) 761679.3 checking 'filter2' ............................ PASS (bf01322f9e0aed7a) 19130329 checking 'medianFilter' ....................... PASS (189cf2d04b2316f5) 765141.6 checking 'equalize' ........................... PASS (b525d614a289c5a3) 705546.8 checking 'erode' .............................. PASS (84add15c6fa8ac14) 908526.9 checking 'dilate' ............................. PASS (e99e1ecfd4ef49d3) 1072658 checking 'opening' ............................ PASS (80d457c0bcd57e44) 985798.9 checking 'closing' ............................ PASS (cc9339fed43d2c52) 988727.9 checking 'whiteTopHat' ........................ PASS (25444773943cf26b) 3572.998 checking 'blackTopHat' ........................ PASS (10fae7d8c0f86c96) 7139.473 checking 'selfComplementaryTopHat' ............ PASS (2f97211e82aa8221) 1533178 checking 'distmap' ............................ PASS (218b9e66643db8d3) 12740449 checking 'watershed' .......................... PASS (6edd3aa33ad54089) 988518.9 checking 'floodFill' .......................... PASS (228b47626610f8c9) 765755.4 checking 'fillHull' ........................... PASS (e72c38d763e5fabf) 988518.9 checking 'propagate' .......................... PASS (73d53b87d72f0409) 26630579 checking 'toRGB' .............................. PASS (7718e616f411c340) 765760.9 checking 'rgbImage' ........................... PASS (6df3c3d16757cdd6) 3520680 checking 'colormap' ........................... PASS (8e7f90c18580cd50) 1816912 checking 'combine' ............................ PASS (f156de3e1aff037c) 2960568 checking 'combine' ............................ PASS (1bfd38ce66379070) 18119267 checking 'tile' ............................... PASS (3f8e8f9b949597b4) 33061491 checking 'untile' ............................. PASS (9f839c04542fa7e4) 27788327 checking 'abind' .............................. PASS (a65f1e1e2d249be6) 2960568 > > ## test: 3D Color 65x17x3 > x <- sample.color[1:65, 1:17,] > testEBImageFunctions(x) new test (hash=3884fe38962577a7) checking 'show' ............................... PASS (8331bd653405c3be) -0.1 checking 'print' .............................. PASS (de22d3dc188680fd) -0.1 checking 'hist' ............................... PASS (10b008981f19c77a) 348464.1 checking '>' .................................. PASS (e6c8a64e9fff6055) 1058553 checking '+' .................................. PASS (5bb860f09b56b4d9) 4072301 checking '/' .................................. PASS (17b2c344ff60cf34) 1018075 checking '*' .................................. PASS (5bb860f09b56b4d9) 4072301 checking 'median' ............................. PASS (a9ae52973fed588b) 0.2333333 checking 'quantile' ........................... PASS (e51be80ed6288f06) 7.280392 checking 'Image' .............................. PASS (3884fe38962577a7) 2036151 checking 'as.Image' ........................... PASS (3884fe38962577a7) 2036151 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1456dcb0ab2d690b) 2036151 checking 'imageData<-' ........................ PASS (3884fe38962577a7) 2036151 checking 'as.raster' .......................... PASS (abd1d3d0d6329777) -0.1 checking 'colorMode<-' ........................ PASS (0aa63faa9d4e0838) 2036151 checking 'numberOfFrames' ..................... PASS (7c79dea3bfc1415b) 0.9 checking 'getFrames' .......................... PASS (2ed277d7e69a05d2) 2036151 checking 'display' ............................ PASS (3d646d4f07d194ba) 306.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (5175a6622762681a) 2049936 checking '[' .................................. PASS (c60784a663dd1761) 9950.096 checking 'resize' ............................. PASS (fe9aa55b037def9d) 15155777 checking 'rotate' ............................. PASS (2a6f5001ae7d116d) 4525312 checking 'flip' ............................... PASS (192932ac94cae831) 1977928 checking 'flop' ............................... PASS (55c97a05ee9ed805) 2048664 checking 'translate' .......................... PASS (c866b3232cda2c68) 2998417 checking 'affine' ............................. PASS (517c3559acf97cf4) 226067.6 checking 'transpose' .......................... PASS (e6349d8cc35ed017) 1907377 checking 'thresh' ............................. PASS (e98d9e4246c476a4) 954376.9 checking 'channel' ............................ PASS (84d92148a5eda650) 257578.5 checking 'otsu' ............................... PASS (6a2131f538a2a53e) 0.3316406 checking 'bwlabel' ............................ PASS (2fa4cf414bbb7787) 230329.9 checking 'colorLabels' ........................ PASS (b71e0c0d93c0ba5d) 1920855 checking 'stackObjects' ....................... PASS (f30668520190ffed) 712799.6 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (6a1ba970169d82ad) 2090128 checking 'rmObjects' .......................... PASS (3705fc84a07dd0cd) -0.1 checking 'reenumerate' ........................ PASS (3705fc84a07dd0cd) -0.1 checking 'reenumerate' ........................ PASS (2fa4cf414bbb7787) 230329.9 checking 'computeFeatures' .................... PASS (a33c53edd3cf8a46) 746878.2 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (1be2808a87ee437f) 117866.8 checking 'localCurvature' ..................... PASS (ad1fddb421e46506) 116636.2 checking 'normalize' .......................... PASS (edb5f31f14cd540d) 1788995 checking 'normalize' .......................... PASS (6a1005a2ed478c1e) 1858155 checking 'gblur' .............................. PASS (c61849c1f4dc6d25) 2029979 checking 'filter2' ............................ PASS (760ded68d0c55bfa) 50878763 checking 'medianFilter' ....................... PASS (0b06f73d5aecad7d) 2034604 checking 'equalize' ........................... PASS (2d4d0558bb48cbfc) 2942981 checking 'erode' .............................. PASS (94112a39c70cd747) 830816.9 checking 'dilate' ............................. PASS (a9fbe5f3b81787ec) 1339263 checking 'opening' ............................ PASS (957aea2990d2caa1) 1013295 checking 'closing' ............................ PASS (7af64e74f8e80dbb) 1069405 checking 'whiteTopHat' ........................ PASS (d50f6d3e0e26602d) 16585.63 checking 'blackTopHat' ........................ PASS (310953bdffbb07ee) 22039.05 checking 'selfComplementaryTopHat' ............ PASS (dfefa629c102a00d) 4071763 checking 'distmap' ............................ PASS (6c03a6a34b67eec0) 6038778 checking 'watershed' .......................... PASS (61ebc564dd827878) 1058553 checking 'floodFill' .......................... PASS (f537dd1499704563) 2036854 checking 'fillHull' ........................... PASS (e6c8a64e9fff6055) 1058553 checking 'propagate' .......................... PASS (7b81c961226b8218) 7755487 checking 'toRGB' .............................. PASS (3884fe38962577a7) 2036151 checking 'rgbImage' ........................... PASS (43e895266c1b7cae) 7617867 checking 'colormap' ........................... PASS (972e374a8a23c0e1) 1657338 checking 'combine' ............................ PASS (d56bf3140c7cd055) 8350133 checking 'combine' ............................ PASS (b21bd2c702883543) 52959073 checking 'tile' ............................... PASS (4f60a4ae167b4e6e) 107188639 checking 'untile' ............................. PASS (05afb65e638c5769) 97994583 checking 'abind' .............................. PASS (d56bf3140c7cd055) 8350133 > > ## test: 3D Grayscale logical 32x32x2 > x <- sample[32:63, 32:63] > x <- x > otsu(x) > x <- combine(x, x) > testEBImageFunctions(x) new test (hash=db12fa8044d98567) checking 'show' ............................... PASS (75018abdcca926f0) -0.1 checking 'print' .............................. PASS (9bacee8faec96053) -0.1 checking 'hist' ............................... PASS (f0f3640c0aa89c38) 5855.343 checking '>' .................................. PASS (db12fa8044d98567) 1055560 checking '+' .................................. PASS (0b5a21f5cc627e62) 2111120 checking '/' .................................. PASS (bf2545eee0c6aa3e) 527779.9 checking '*' .................................. PASS (0b5a21f5cc627e62) 2111120 checking 'median' ............................. PASS (8396e8397399bb05) -0.1 checking 'quantile' ........................... PASS (130a179fb028f1a7) 8.9 checking 'Image' .............................. PASS (041d3981bcab3129) 1055560 checking 'as.Image' ........................... PASS (db12fa8044d98567) 1055560 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6b02d87cd459ac19) 1055560 checking 'imageData<-' ........................ PASS (db12fa8044d98567) 1055560 checking 'as.raster' .......................... PASS (26cf978328d1a712) -0.1 checking 'colorMode<-' ........................ PASS (db12fa8044d98567) 1055560 checking 'numberOfFrames' ..................... PASS (161e41d6aa749739) 1.9 checking 'getFrames' .......................... PASS (ce29246f73d959c3) 916715.6 checking 'display' ............................ PASS (2fb2fcab54a4ea5a) 285.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (1180c20b46fdaf4e) 1656514 checking '[' .................................. PASS (2a55f6dafc492b42) 1889.9 checking 'resize' ............................. PASS (211e86386b1010af) 9108608 checking 'rotate' ............................. PASS (d67e39e3cb07d275) 1600126 checking 'flip' ............................... PASS (fbb2a6f78f2cc7f1) 714439.9 checking 'flop' ............................... PASS (f6825dda37058381) 1064092 checking 'translate' .......................... PASS (8d027c3127938636) 1105982 checking 'affine' ............................. PASS (a6e552f84324fe21) 133467.8 checking 'transpose' .......................... PASS (eeeb148d04107340) 758083.9 checking 'thresh' ............................. PASS (5b7b2d141f385123) 824497.9 checking 'channel' ............................ PASS (db12fa8044d98567) 1055560 checking 'otsu' ............................... PASS (69c60dc99d5066e3) 1.4 checking 'bwlabel' ............................ PASS (10092f8e4256496b) 1597368 checking 'colorLabels' ........................ PASS (ebf6961f64378f97) 5485361 checking 'stackObjects' ....................... PASS (d1d99850ff4d6d38) 8889538 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (8c5ef6f490aa8762) 834266.6 checking 'rmObjects' .......................... PASS (0a1cd72f8d3c03e8) 1303423 checking 'reenumerate' ........................ PASS (df75276eeec5813d) 1244828 checking 'reenumerate' ........................ PASS (10092f8e4256496b) 1597368 checking 'computeFeatures' .................... PASS (1bf064e6a11f2410) 416164140 checking 'computeFeatures' .................... PASS (4e7e75f941531854) 145634.3 checking 'ocontour' ........................... PASS (9f7d90d6312e32f3) 836958.8 checking 'localCurvature' ..................... PASS (477746e4fee34aeb) 835041.5 checking 'normalize' .......................... PASS (eea76285d45436f7) 1055560 checking 'normalize' .......................... PASS (eea76285d45436f7) 1055560 checking 'gblur' .............................. PASS (9224b720f9d00006) 1037581 checking 'filter2' ............................ PASS (637287a5df76a79d) 26149148 checking 'medianFilter' ....................... PASS (ed8d722e63a36a34) 1030730 checking 'equalize' ........................... PASS (eea76285d45436f7) 1055560 checking 'erode' .............................. PASS (54ccd3aba098da92) 617311.9 checking 'dilate' ............................. PASS (3f0aed5a551e26b5) 1591594 checking 'opening' ............................ PASS (ae3c29b4498904c5) 861145.9 checking 'closing' ............................ PASS (2e26e13058dee387) 1188258 checking 'whiteTopHat' ........................ PASS (28bbffedc1bcb297) 148131.9 checking 'blackTopHat' ........................ PASS (a862285882d4249e) 202411.9 checking 'selfComplementaryTopHat' ............ PASS (92483d40b14844db) 2151192 checking 'distmap' ............................ PASS (766610b2223767b0) 3856630 checking 'watershed' .......................... PASS (eaba5359a5afa00e) 1443978 checking 'floodFill' .......................... PASS (0db2bbd3a6d9a773) 2057384 checking 'fillHull' ........................... PASS (ccded36693237a0e) 1096352 checking 'propagate' .......................... PASS (e3c3ba3dd998f78f) 1613920 checking 'toRGB' .............................. PASS (a594b4f9b88125f1) 8499672 checking 'rgbImage' ........................... PASS (172b07d65c57f496) 4777616 checking 'colormap' ........................... PASS (a6b9bc2f3472cbee) 10283526 checking 'combine' ............................ PASS (f13e4c8ca8445cd0) 3888784 checking 'combine' ............................ PASS (d8a9b6cf082a9146) 23054440 checking 'tile' ............................... PASS (4c3d7086d0c2c786) 48846817 checking 'untile' ............................. PASS (65365043e983ec58) 41221063 checking 'abind' .............................. PASS (af0697002f77c709) 3888784 > > ## test: 4D Color 33x16x3x2 > x <- sample.color[1:33, 1:16,] > x <- combine(x, x) > testEBImageFunctions(x) new test (hash=290d7a45d7468e5f) checking 'show' ............................... PASS (78a7303aa046067b) -0.1 checking 'print' .............................. PASS (9aaf686697ac72be) -0.1 checking 'hist' ............................... PASS (b01a7d139c82f457) 492113.2 checking '>' .................................. PASS (1f65757da86f51b3) 2013322 checking '+' .................................. PASS (86bdea7870f6d0cc) 4709417 checking '/' .................................. PASS (c3533150260f42c4) 1177354 checking '*' .................................. PASS (86bdea7870f6d0cc) 4709417 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (290d7a45d7468e5f) 2354709 checking 'as.Image' ........................... PASS (290d7a45d7468e5f) 2354709 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (1936bbf08b457bab) 2354709 checking 'imageData<-' ........................ PASS (290d7a45d7468e5f) 2354709 checking 'as.raster' .......................... PASS (da1c028f359bf00b) -0.1 checking 'colorMode<-' ........................ PASS (7856ef3bde7528ce) 2354709 checking 'numberOfFrames' ..................... PASS (161e41d6aa749739) 1.9 checking 'getFrames' .......................... PASS (f0d9427233f46fbb) 1440422 checking 'display' ............................ PASS (bc877f5317c575b2) 239.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (ad8f0dc0cad6885c) 2650006 checking '[' .................................. PASS (144b12c39a99e2bc) 40701.82 checking 'resize' ............................. PASS (dd96ecc9ed75e744) 76725662 checking 'rotate' ............................. PASS (19319de30582c1d6) 4140744 checking 'flip' ............................... PASS (91c7918c52fe8718) 2309692 checking 'flop' ............................... PASS (49ae0fb3bef587c5) 2358658 checking 'translate' .......................... PASS (a8fcd75113ffb2d2) 3393923 checking 'affine' ............................. PASS (592877c7d17e1d22) 301692.6 checking 'transpose' .......................... PASS (a42245132dbea662) 2303263 checking 'thresh' ............................. PASS (167470821b508c29) 1549362 checking 'channel' ............................ PASS (d4dd2cc593776db0) 287206.2 checking 'otsu' ............................... PASS (2ff953970aa01423) 1.370703 checking 'bwlabel' ............................ PASS (404699231a09f479) 360413.9 checking 'colorLabels' ........................ PASS (4742967f9e3ced6e) 3039066 checking 'stackObjects' ....................... PASS (71587dec63927412) 2472601 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (0daa597dbe10a6cd) 2558300 checking 'rmObjects' .......................... PASS (ea36bf2e51776461) 261782.9 checking 'reenumerate' ........................ PASS (ea36bf2e51776461) 261782.9 checking 'reenumerate' ........................ PASS (404699231a09f479) 360413.9 checking 'computeFeatures' .................... PASS (151a0d98d309d0b1) 749353.1 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (20fad83d539e2372) 107408.8 checking 'localCurvature' ..................... PASS (469cd750daa03946) 106275.7 checking 'normalize' .......................... PASS (4484b1dbbf34c675) 2693244 checking 'normalize' .......................... PASS (27680837000f1ded) 2315924 checking 'gblur' .............................. PASS (fc2147343f5faed5) 2349701 checking 'filter2' ............................ PASS (958b84b9c0054384) 58841710 checking 'medianFilter' ....................... PASS (8ccc036255fe88d9) 2352447 checking 'equalize' ........................... PASS (e7f99b2a8483f2d3) 2616480 checking 'erode' .............................. PASS (16554ca32b165307) 1547948 checking 'dilate' ............................. PASS (560c069e5292fdc9) 2604996 checking 'opening' ............................ PASS (592d8ab4156490aa) 1919386 checking 'closing' ............................ PASS (c57a6175329f5e45) 2038196 checking 'whiteTopHat' ........................ PASS (6938d64e59a77fe1) 12437.36 checking 'blackTopHat' ........................ PASS (8fbaad8a000d91c5) 19780.97 checking 'selfComplementaryTopHat' ............ PASS (b11bd64d03fe29b9) 4711722 checking 'distmap' ............................ PASS (708df2d4560d23a7) 10836360 checking 'watershed' .......................... PASS (4aa1432f01914277) 2013322 checking 'floodFill' .......................... PASS (02926422d15cf3c2) 2355706 checking 'fillHull' ........................... PASS (1f65757da86f51b3) 2013322 checking 'propagate' .......................... PASS (1656991af484107e) 11618104 checking 'toRGB' .............................. PASS (290d7a45d7468e5f) 2354709 checking 'rgbImage' ........................... PASS (98de7e0def0bab8b) 12071186 checking 'colormap' ........................... PASS (0798dea20c907720) 2273276 checking 'combine' ............................ PASS (579971440faf3f11) 9516503 checking 'combine' ............................ PASS (fb7944257dfefb91) 59844403 checking 'tile' ............................... PASS (e594265685cdf3aa) 114300809 checking 'untile' ............................. PASS (5b25f3b7fc0df1b3) 105862114 checking 'abind' .............................. PASS (a413703585d2e713) 9516503 > > ## test: 4D Grayscale 16x33x2x3 > colorMode(x) <- Grayscale > imageData(x) <- aperm(x, c(2L, 1L, 4L, 3L)) > testEBImageFunctions(x) new test (hash=2a321f78219fa026) checking 'show' ............................... PASS (3de182583a8c2cf2) -0.1 checking 'print' .............................. PASS (05d1cebf84274f35) -0.1 checking 'hist' ............................... PASS (885aba01ae2954f5) 229030.4 checking '>' .................................. PASS (c15b137f0122c2ee) 1541186 checking '+' .................................. PASS (2951b29fcfadda51) 4466272 checking '/' .................................. PASS (b0a06579c4ef390d) 1116568 checking '*' .................................. PASS (2951b29fcfadda51) 4466272 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (e6ae9fe3a69fec2c) 2233136 checking 'as.Image' ........................... PASS (2a321f78219fa026) 2233136 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6a221a6a2cec815a) 2233136 checking 'imageData<-' ........................ PASS (2a321f78219fa026) 2233136 checking 'as.raster' .......................... PASS (73a5fd711e0edd14) -0.1 checking 'colorMode<-' ........................ PASS (2a321f78219fa026) 2233136 checking 'numberOfFrames' ..................... PASS (d9914b6bdfe88a1d) 5.9 checking 'getFrames' .......................... PASS (c2a08dc890b333e2) 1229859 checking 'display' ............................ PASS (d28e3e75eed04056) 256.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (d4dbcf7b516a28b0) 2502013 checking '[' .................................. PASS (efc391fc4ded377e) 41200.75 checking 'resize' ............................. PASS (5ab5e219e21b7d77) 72772706 checking 'rotate' ............................. PASS (5ea8cc41d39fe2c4) 3978266 checking 'flip' ............................... PASS (2578de2eb711ac89) 2296325 checking 'flop' ............................... PASS (c21acaf425029919) 2231772 checking 'translate' .......................... PASS (74e4014bf39793e1) 3827517 checking 'affine' ............................. PASS (76f6b18d2cb7c9c2) 219714.6 checking 'transpose' .......................... PASS (3b5dcc82ff30daf8) 2284582 checking 'thresh' ............................. PASS (3a92d48cd68a67e8) 1426674 checking 'channel' ............................ PASS (2a321f78219fa026) 2233136 checking 'otsu' ............................... PASS (2cdec937ebdb0543) 9.425391 checking 'bwlabel' ............................ PASS (f698416417dde49c) 2016822 checking 'colorLabels' ........................ PASS (b07a31035fc451d5) 15071536 checking 'stackObjects' ....................... PASS (8e5b00026f507a11) 2575847 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (63b2ef8ac8682f98) 2379341 checking 'rmObjects' .......................... PASS (056669f72385f506) 1934575 checking 'reenumerate' ........................ PASS (056669f72385f506) 1934575 checking 'reenumerate' ........................ PASS (f698416417dde49c) 2016822 checking 'computeFeatures' .................... PASS (53798e843cdbfa9f) 734993.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (3a230e30e8d15bee) 118072.8 checking 'localCurvature' ..................... PASS (a1d19191deda947d) 117246.2 checking 'normalize' .......................... PASS (85d2a91256ddfdaa) 2526618 checking 'normalize' .......................... PASS (4accf817a36301dc) 2163958 checking 'gblur' .............................. PASS (c2c22f114f9ac87d) 2237219 checking 'filter2' ............................ PASS (0245e31021e7583c) 56904871 checking 'medianFilter' ....................... PASS (24f248c2c56e7772) 2231438 checking 'equalize' ........................... PASS (97693dcd997265d1) 2447139 checking 'erode' .............................. PASS (5b04187576514eec) 1121204 checking 'dilate' ............................. PASS (4897aaa0d40c4fb8) 2104588 checking 'opening' ............................ PASS (cb86eac9754dbac1) 1451050 checking 'closing' ............................ PASS (13b4d846ef6a77dd) 1569448 checking 'whiteTopHat' ........................ PASS (1c856cc6a52ed865) 12004.54 checking 'blackTopHat' ........................ PASS (f74244f5c4295d35) 20296.87 checking 'selfComplementaryTopHat' ............ PASS (f23286411d6929f7) 4469404 checking 'distmap' ............................ PASS (ff3b2754a2aa8eb3) 7464344 checking 'watershed' .......................... PASS (cd9ef36f457c5d89) 1541186 checking 'floodFill' .......................... PASS (60d288f662756f97) 2234521 checking 'fillHull' ........................... PASS (c15b137f0122c2ee) 1541186 checking 'propagate' .......................... PASS (503cd7ed6238770e) 8948876 checking 'toRGB' .............................. PASS (5a32f2aceec9a146) 20279146 checking 'rgbImage' ........................... PASS (19e0ea95d787d11c) 10796552 checking 'colormap' ........................... PASS (62fb056f168823de) 22585273 checking 'combine' ............................ PASS (67fe5c370ca3a18d) 8992851 checking 'combine' ............................ PASS (41f451bdd6a63a8f) 56431472 checking 'tile' ............................... PASS (0581a6216e8e50e0) 72664167 checking 'untile' ............................. PASS (4e208afef7f298bd) 60048605 checking 'abind' .............................. PASS (e3feb875241cebc2) 9273358 > > ## test: Image subclass > ImageSubclass <- setClass ("ImageSubclass", contains = "Image", slots = c(foo = "character")) > x <- ImageSubclass(x, foo="bar") > testEBImageFunctions(x) new test (hash=9b67f57c77f74d34) checking 'show' ............................... PASS (63597c3473b56977) -0.1 checking 'print' .............................. PASS (1cd88fa9e1ff084e) -0.1 checking 'hist' ............................... PASS (885aba01ae2954f5) 229030.4 checking '>' .................................. PASS (8213f4f8b30b3c46) 1541186 checking '+' .................................. PASS (d9da0200176ead52) 4466272 checking '/' .................................. PASS (c5360d5612508ba0) 1116568 checking '*' .................................. PASS (d9da0200176ead52) 4466272 checking 'median' ............................. PASS (06af3e4c86ccda6d) 0.3823529 checking 'quantile' ........................... PASS (11ef7960975f6975) 8.139216 checking 'Image' .............................. PASS (e6ae9fe3a69fec2c) 2233136 checking 'as.Image' ........................... PASS (2a321f78219fa026) 2233136 checking 'is.Image' ........................... PASS (e3aef3409e870c0e) 0.9 checking 'imageData' .......................... PASS (6a221a6a2cec815a) 2233136 checking 'imageData<-' ........................ PASS (9b67f57c77f74d34) 2233136 checking 'as.raster' .......................... PASS (73a5fd711e0edd14) -0.1 checking 'colorMode<-' ........................ PASS (9b67f57c77f74d34) 2233136 checking 'numberOfFrames' ..................... PASS (d9914b6bdfe88a1d) 5.9 checking 'getFrames' .......................... PASS (e9438bf3afe19fef) 1229859 checking 'display' ............................ PASS (d28e3e75eed04056) 256.3 checking 'display' ............................ PASS (d956c282ac7180e4) -0.1 checking 'image' .............................. PASS (d956c282ac7180e4) -0.1 checking 'drawCircle' ......................... PASS (88969323fe4011cb) 2502013 checking '[' .................................. PASS (856f5f5a7828a96f) 41200.75 checking 'resize' ............................. PASS (22d4ff5205c02f14) 72772706 checking 'rotate' ............................. PASS (3e6dee126668bb5a) 3978266 checking 'flip' ............................... PASS (753308a7b510662f) 2296325 checking 'flop' ............................... PASS (1ea0c6126c86d976) 2231772 checking 'translate' .......................... PASS (c3111aabac6df5c8) 3827517 checking 'affine' ............................. PASS (559df6f741145f7f) 219714.6 checking 'transpose' .......................... PASS (d9282e9071f27e10) 2284582 checking 'thresh' ............................. PASS (b51eea6755dfd65a) 1426674 checking 'channel' ............................ PASS (9b67f57c77f74d34) 2233136 checking 'otsu' ............................... PASS (2cdec937ebdb0543) 9.425391 checking 'bwlabel' ............................ PASS (edce7604823b90a7) 2016822 checking 'colorLabels' ........................ PASS (05cf97699b52f053) 15969784 checking 'stackObjects' ....................... PASS (bbe84601c71da500) 2575847 checking 'stackObjects' ....................... PASS (d956c282ac7180e4) -0.1 checking 'paintObjects' ....................... PASS (944b58c80d127777) 2379341 checking 'rmObjects' .......................... PASS (1ed59ae8eb61aef6) 1934575 checking 'reenumerate' ........................ PASS (1ed59ae8eb61aef6) 1934575 checking 'reenumerate' ........................ PASS (edce7604823b90a7) 2016822 checking 'computeFeatures' .................... PASS (53798e843cdbfa9f) 734993.9 checking 'computeFeatures' .................... PASS (8cd691a663f460c1) 19422.3 checking 'ocontour' ........................... PASS (3a230e30e8d15bee) 118072.8 checking 'localCurvature' ..................... PASS (a1d19191deda947d) 117246.2 checking 'normalize' .......................... PASS (9ace81a69fc88c37) 2526618 checking 'normalize' .......................... PASS (2a78b599de5c2ae9) 2163958 checking 'gblur' .............................. PASS (0d226d91f7036796) 2237219 checking 'filter2' ............................ PASS (7cb701d185d8631b) 56904871 checking 'medianFilter' ....................... PASS (37328d9ce26ed388) 2231438 checking 'equalize' ........................... PASS (05fc2423af12b77a) 2447139 checking 'erode' .............................. PASS (17fcd8b3a8de8535) 1121204 checking 'dilate' ............................. PASS (715c930769bb9119) 2104588 checking 'opening' ............................ PASS (1ef38f55606cdbf4) 1451050 checking 'closing' ............................ PASS (66cb111962e57366) 1569448 checking 'whiteTopHat' ........................ PASS (66e080c20ad98021) 12004.54 checking 'blackTopHat' ........................ PASS (c8b5fb6a0e1d3959) 20296.87 checking 'selfComplementaryTopHat' ............ PASS (d91b85d0f726e766) 4469404 checking 'distmap' ............................ PASS (4ced93e5efc06917) 7464344 checking 'watershed' .......................... PASS (9c1a4d5672652853) 1541186 checking 'floodFill' .......................... PASS (d9a38a5952fe360e) 2234521 checking 'fillHull' ........................... PASS (8213f4f8b30b3c46) 1541186 checking 'propagate' .......................... PASS (0731a1de5ddabcc4) 8948876 checking 'toRGB' .............................. PASS (c62b6c6a269ea1eb) 20279146 checking 'rgbImage' ........................... PASS (27eec26383a0bc15) 10796552 checking 'colormap' ........................... PASS (eef6d0395d7fe0e7) 22585273 checking 'combine' ............................ PASS (5b4994ce3c695b2e) 8992851 checking 'combine' ............................ PASS (03e050af1c7e1af2) 56431472 checking 'tile' ............................... PASS (db685d6eb3480813) 72664167 checking 'untile' ............................. PASS (0e362c45443a3ec0) 60048605 checking 'abind' .............................. PASS (add8d4baab35a5f9) 9273358 >
EBImage.Rcheck/EBImage-Ex.timings
name | user | system | elapsed | |
EBImage | 4.709 | 0.312 | 5.292 | |
Image | 0.409 | 0.034 | 0.445 | |
abind | 0.669 | 0.069 | 0.739 | |
bwlabel | 1.533 | 0.142 | 1.677 | |
channel | 0.590 | 0.121 | 0.713 | |
clahe | 0.162 | 0.013 | 0.176 | |
colorLabels | 0.097 | 0.008 | 0.105 | |
colormap | 0.307 | 0.084 | 0.391 | |
combine | 0.811 | 0.184 | 0.996 | |
computeFeatures | 0.547 | 0.143 | 0.691 | |
display-shiny | 0.003 | 0.000 | 0.004 | |
display | 1.075 | 0.141 | 1.218 | |
distmap | 0.281 | 0.017 | 0.298 | |
drawCircle | 0.027 | 0.024 | 0.052 | |
equalize | 1.289 | 0.226 | 1.516 | |
fillHull | 0.295 | 0.035 | 0.331 | |
filter2 | 2.129 | 0.528 | 2.658 | |
floodFill | 0.694 | 0.072 | 0.766 | |
gblur | 0.274 | 0.033 | 0.307 | |
io | 0.307 | 0.034 | 0.343 | |
localCurvature | 0.527 | 0.151 | 0.679 | |
medianFilter | 0.832 | 0.185 | 1.022 | |
morphology | 0.126 | 0.045 | 0.172 | |
normalize | 0.014 | 0.017 | 0.031 | |
ocontour | 0.012 | 0.015 | 0.027 | |
otsu | 0.266 | 0.031 | 0.297 | |
paintObjects | 1.691 | 0.156 | 1.849 | |
propagate | 1.628 | 0.047 | 1.676 | |
rmObjects | 0.097 | 0.017 | 0.114 | |
spatial | 0.958 | 0.032 | 0.991 | |
stackObjects | 2.932 | 0.581 | 3.513 | |
thresh | 0.153 | 0.013 | 0.167 | |
tile | 0.276 | 0.058 | 0.334 | |
transpose | 0.167 | 0.030 | 0.197 | |
watershed | 0.128 | 0.019 | 0.148 | |