EBImage 4.17.16
Andrzej Oleś
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage | | Last Changed Rev: 127136 / Revision: 127142 | | Last Changed Date: 2017-03-03 10:24:40 -0500 (Fri, 03 Mar 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.17.16.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.17.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EBImage’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
doc 5.1Mb
images 1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EBImage 5.286 0.653 8.18
stackObjects 4.160 1.316 5.48
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
Comparing ‘test.Rout’ to ‘test.Rout.save’ ...251,252c251
< checking 'rotate' ............................. LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd320e38ed/display.html.
< PASS (6ace606563c0af26) -0.1
---
> checking 'rotate' ............................. PASS (6ace606563c0af26) -0.1
270c269
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
321,322c320
< checking 'display' ............................ LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd9f252cd/display.html.
< PASS (57f54e3531a18f4e) -0.1
---
> checking 'display' ............................ PASS (57f54e3531a18f4e) -0.1
345c343
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
422,423c420
< checking 'computeFeatures' .................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd18c8301d/display.html.
< PASS (3a766122214a21a8) cf1b0ac94ace207a
---
> checking 'computeFeatures' .................... PASS (12407c053a81599e) 5aee329f7b8a0af0
499,501c496,497
< checking 'computeFeatures' .................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd26ce2373/display.html.
< PASS (2f1272bf9a3428b3) 3989786
< checking 'computeFeatures' .................... PASS (3a766122214a21a8) cf1b0ac94ace207a
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
> checking 'computeFeatures' .................... PASS (12407c053a81599e) 5aee329f7b8a0af0
572,573c568
< checking 'paintObjects' ....................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd79b4cac6/display.html.
< PASS (1812b3a1be6f2a21) 2090128
---
> checking 'paintObjects' ....................... PASS (1812b3a1be6f2a21) 2090128
577,578c572,573
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
655,657c650,651
< checking 'computeFeatures' .................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd337fd3f7/display.html.
< PASS (1d847743be56e5a7) 416164140
< checking 'computeFeatures' .................... PASS (3a766122214a21a8) cf1b0ac94ace207a
---
> checking 'computeFeatures' .................... PASS (1d847743be56e5a7) 416164140
> checking 'computeFeatures' .................... PASS (12407c053a81599e) 5aee329f7b8a0af0
662c656
< checking 'filter2' ............................ PASS (f63788502234dbd7) 26149148
---
> checking 'filter2' ............................ PASS (e5a3d2e924e050fe) 26149148
733,735c727,728
< checking 'computeFeatures' .................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd51261dcd/display.html.
< PASS (5eaf503a54600569) 749353.1
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
811,813c804,805
< LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd482171dd/display.html.
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
883,884c875
< checking 'stackObjects' ....................... LSOpenURLsWithRole() failed with error -10810 for the file /private/tmp/RtmpRXnhQ4/105fd2f1b95ee/display.html.
< PASS (3dfb061836ca6d36) 2575847
---
> checking 'stackObjects' ....................... PASS (3dfb061836ca6d36) 2575847
890,891c881,882
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
< checking 'computeFeatures' .................... PASS (6dc4c63dde7e7828) 32d95b1456f80f68
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
> checking 'computeFeatures' .................... PASS (5b0f17d23f0847ff) 9cbf0d301c547318
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck/00check.log’
for details.
* installing *source* package ‘EBImage’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c EBImage.c -o EBImage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c distmap.c -o distmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c drawCircle.c -o drawCircle.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c floodFill.cpp -o floodFill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c getFrames.c -o getFrames.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c haralick.c -o haralick.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c medianFilter.c -o medianFilter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c morphology.c -o morphology.o
morphology.c:59:12: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.c:62:12: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.c:66:12: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.c:90:10: warning: expression result unused [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.c:93:10: warning: expression result unused [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.c:97:10: warning: expression result unused [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c:38:7: warning: assigning to 'uint32_t *' (aka 'unsigned int *') from 'int *' converts between pointers to integer types with different sign [-Wpointer-sign]
out = INTEGER(res);
^ ˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c normalize.c -o normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c objects.c -o objects.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ocontour.c -o ocontour.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c propagate.cpp -o propagate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c spatial.c -o spatial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c thresh.c -o thresh.o
thresh.c:23:21: warning: unused variable 'ey' [-Wunused-variable]
int sx, ex, sy, ey;
^
thresh.c:23:17: warning: unused variable 'sy' [-Wunused-variable]
int sx, ex, sy, ey;
^
thresh.c:23:13: warning: unused variable 'ex' [-Wunused-variable]
int sx, ex, sy, ey;
^
thresh.c:23:9: warning: unused variable 'sx' [-Wunused-variable]
int sx, ex, sy, ey;
^
thresh.c:22:57: warning: unused variable 'v' [-Wunused-variable]
int dx, dy, nx, ny, nz, nprotect, * dim, xi, yi, u, v, k, l, ou, nu, ov, nv, i;
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tile.c -o tile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tools.c -o tools.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c watershed.cpp -o watershed.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o EBImage.so EBImage.o 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 watershed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck/EBImage/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBImage)