Andrzej Oleś
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) |
| URL: https://git.bioconductor.org/packages/EBImage |
| Branch: RELEASE_3_5 |
| Last Commit: 57f6a1e |
| Last Changed Date: 2017-10-05 07:53:10 -0400 (Thu, 05 Oct 2017) |
| Back to the "Multiple platform build/check report" | A B C D [E] F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:12:45 -0400 (Wed, 18 Oct 2017).
| Package 381/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EBImage 4.18.3 Andrzej Oleś
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: EBImage |
| Version: 4.18.3 |
| Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.18.3.tar.gz |
| StartedAt: 2017-10-17 22:51:56 -0400 (Tue, 17 Oct 2017) |
| EndedAt: 2017-10-17 22:53:09 -0400 (Tue, 17 Oct 2017) |
| EllapsedTime: 72.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBImage.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.18.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.18.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EBImage’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
doc 5.0Mb
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
stackObjects 2.548 3.304 5.870
EBImage 4.328 0.244 6.516
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
Comparing ‘test.Rout’ to ‘test.Rout.save’ ...256,259c256
< checking 'flip' ............................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (bb3d006dd4423285) -0.1
---
> checking 'flip' ............................... PASS (bb3d006dd4423285) -0.1
331,334c328
< checking 'display' ............................ Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (57f54e3531a18f4e) -0.1
---
> checking 'display' ............................ PASS (57f54e3531a18f4e) -0.1
361d354
< checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
362a356
> checking 'normalize' .......................... PASS (545d29ae11f62e79) 324.9
440,443c434
< Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< checking 'localCurvature' ..................... Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (48edb77f99eb5e0a) a351f1682141f4de
---
> checking 'localCurvature' ..................... PASS (48edb77f99eb5e0a) a351f1682141f4de
524,527c515
< checking 'localCurvature' ..................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (744209c192ca349a) 97da7b3a7c2ec717
---
> checking 'localCurvature' ..................... PASS (744209c192ca349a) 97da7b3a7c2ec717
607,610c595
< checking 'localCurvature' ..................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (9ddeedd40b4e5c7b) a2c60afaa6d43988
---
> checking 'localCurvature' ..................... PASS (9ddeedd40b4e5c7b) a2c60afaa6d43988
689,692c674
< checking 'computeFeatures' .................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (1d847743be56e5a7) 416164140
---
> checking 'computeFeatures' .................... PASS (1d847743be56e5a7) 416164140
776,779c758
< checking 'localCurvature' ..................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (91ac6bafe7f8c008) feedc85342708fe9
---
> checking 'localCurvature' ..................... PASS (91ac6bafe7f8c008) feedc85342708fe9
860,863c839
< checking 'localCurvature' ..................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (14e7e43044a6edce) dbbde661d27cf4d5
---
> checking 'localCurvature' ..................... PASS (14e7e43044a6edce) dbbde661d27cf4d5
941,944c917
< checking 'computeFeatures' .................... Failed to connect to Mir: Failed to connect to server socket: No such file or directory
< Unable to init server: Could not connect: Connection refused
< Error: cannot open display: :1.0
< PASS (5f168ac8bf99f53d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck/00check.log’
for details.
EBImage.Rcheck/00install.out:
* installing *source* package ‘EBImage’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c EBImage.c -o EBImage.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c clahe.c -o clahe.o
clahe.c: In function ‘CLAHE’:
clahe.c:219:19: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU;
^
clahe.c:231:23: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c distmap.cpp -o distmap.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c drawCircle.c -o drawCircle.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c floodFill.cpp -o floodFill.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c getFrames.c -o getFrames.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c haralick.c -o haralick.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c medianFilter.c -o medianFilter.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c morphology.cpp -o morphology.o
morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = int]’:
morphology.cpp:253:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]’
morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]’
morphology.cpp:374:79: required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = int]’:
morphology.cpp:257:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = int]’
morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = int; SEXP = SEXPREC*]’
morphology.cpp:374:79: required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_erode(type***, type*, int, int, chordSet*, PointXY) [with type = double]’:
morphology.cpp:253:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]’
morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]’
morphology.cpp:377:76: required from here
morphology.cpp:196:15: warning: statement has no effect [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:199:15: warning: statement has no effect [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:203:15: warning: statement has no effect [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
morphology.cpp: In instantiation of ‘void compute_lookup_table_for_line_dilate(type***, type*, int, int, chordSet*, PointXY) [with type = double]’:
morphology.cpp:257:39: required from ‘void erode_dilate(type*, type*, PointXY, int, int, chordSet*, type***) [with type = double]’
morphology.cpp:340:27: required from ‘void _morphology(type*, type*, PointXY, int, SEXP, int) [with type = double; SEXP = SEXPREC*]’
morphology.cpp:377:76: required from here
morphology.cpp:163:15: warning: statement has no effect [-Wunused-value]
for (i; i < 0; ++i) {
^
morphology.cpp:166:15: warning: statement has no effect [-Wunused-value]
for (i; i < maxX; ++i) {
^
morphology.cpp:170:15: warning: statement has no effect [-Wunused-value]
for (i; i < size.x + set->maxXoffset; ++i) {
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function ‘nativeRaster’:
nativeRaster.c:38:7: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
out = INTEGER(res);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c normalize.c -o normalize.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objects.c -o objects.o
objects.c: In function ‘paintObjects’:
objects.c:21:30: warning: unused variable ‘dp’ [-Wunused-variable]
double *obj, *src, *tgt, dp, val;
^
objects.c: In function ‘stackObjects’:
objects.c:295:10: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return res;
^
In file included from objects.h:5:0,
from objects.c:1:
/home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:152:28: warning: ‘dim’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SET_DIM(x, n) Rf_setAttrib(x, R_DimSymbol, n)
^
objects.c:192:13: note: ‘dim’ was declared here
SEXP res, dim, xys, img;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ocontour.c -o ocontour.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c propagate.cpp -o propagate.o
propagate.cpp: In function ‘SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)’:
propagate.cpp:174:31: warning: ‘mask’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (! mask_in[IJ(p.i, p.j)]) continue;
^
propagate.cpp:197:8: note: ‘mask’ was declared here
int *mask;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spatial.c -o spatial.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c thresh.cpp -o thresh.o
thresh.cpp: In instantiation of ‘void _thresh(T*, int*, int, int, int, int, double) [with T = int]’:
thresh.cpp:50:76: required from here
thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable]
int xi, yi, u, k, l, ou, nu, ov, nv, i;
^
thresh.cpp: In instantiation of ‘void _thresh(T*, int*, int, int, int, int, double) [with T = double]’:
thresh.cpp:53:76: required from here
thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tile.cpp -o tile.o
tile.cpp: In function ‘SEXPREC* tile(SEXP, SEXP, SEXP)’:
tile.cpp:24:17: warning: unused variable ‘ims’ [-Wunused-variable]
SEXP res, dm, ims;
^
tile.cpp: In function ‘SEXPREC* untile(SEXP, SEXP, SEXP)’:
tile.cpp:161:29: warning: unused variable ‘y’ [-Wunused-variable]
int nprotect=0, i, j, im, y, iim;
^
tile.cpp:162:18: warning: unused variable ‘dat’ [-Wunused-variable]
SEXP res, dim, dat;
^
tile.cpp:163:11: warning: unused variable ‘src’ [-Wunused-variable]
double *src, *tgt;
^
tile.cpp:163:17: warning: unused variable ‘tgt’ [-Wunused-variable]
double *src, *tgt;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tools.c -o tools.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c transpose.cpp -o transpose.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c watershed.cpp -o watershed.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o EBImage.so EBImage.o clahe.o distmap.o drawCircle.o floodFill.o getFrames.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o transpose.o watershed.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/EBImage.Rcheck/EBImage/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBImage)
EBImage.Rcheck/EBImage-Ex.timings:
| name | user | system | elapsed | |
| EBImage | 4.328 | 0.244 | 6.516 | |
| Image | 0.344 | 0.004 | 0.349 | |
| bwlabel | 0.636 | 0.028 | 0.666 | |
| channel | 0.672 | 0.132 | 0.804 | |
| clahe | 0.128 | 0.004 | 0.133 | |
| colorLabels | 0.092 | 0.000 | 0.092 | |
| colormap | 0.320 | 0.064 | 0.383 | |
| combine | 0.644 | 0.060 | 0.704 | |
| computeFeatures | 0.556 | 0.004 | 0.561 | |
| display | 0.776 | 0.000 | 0.780 | |
| distmap | 0.172 | 0.004 | 0.178 | |
| drawCircle | 0.06 | 0.00 | 0.06 | |
| equalize | 0.968 | 0.000 | 0.965 | |
| fillHull | 0.188 | 0.000 | 0.189 | |
| filter2 | 1.788 | 0.012 | 1.801 | |
| floodFill | 0.176 | 0.004 | 0.181 | |
| gblur | 0.324 | 0.008 | 0.332 | |
| io | 0.440 | 0.020 | 2.288 | |
| localCurvature | 0.708 | 0.000 | 0.709 | |
| medianFilter | 0.696 | 0.308 | 1.009 | |
| morphology | 0.084 | 0.000 | 0.084 | |
| normalize | 0.012 | 0.000 | 0.014 | |
| ocontour | 0.012 | 0.000 | 0.011 | |
| otsu | 0.164 | 0.000 | 0.163 | |
| paintObjects | 1.244 | 0.044 | 1.288 | |
| propagate | 1.396 | 0.040 | 1.436 | |
| rmObjects | 0.080 | 0.000 | 0.079 | |
| spatial | 0.652 | 0.000 | 0.656 | |
| stackObjects | 2.548 | 3.304 | 5.870 | |
| thresh | 0.128 | 0.012 | 0.143 | |
| tile | 0.320 | 0.176 | 0.500 | |
| transpose | 0.116 | 0.004 | 0.122 | |
| watershed | 0.084 | 0.000 | 0.082 | |