Multiple platform build/check report for BioC 3.21 - INSTALL results for EBImage on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4456
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INSTALL results for EBImage on nebbiolo1

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.

raw results

Summary

Package: EBImage

Version: 4.49.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EBImage

StartedAt: 2024-11-20 15:27:12 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 15:27:26 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 13.2 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EBImage
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘EBImage’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c EBImage.c -o EBImage.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c clahe.c -o clahe.o
clahe.c: In function ‘CLAHE’:
clahe.c:223:33: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
  223 |                 uiSubY = uiYSize+1 >> 1;        uiYU = uiNrY-1;  uiYB = uiYU;
      |                          ~~~~~~~^~
clahe.c:235:37: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
  235 |                     uiSubX = uiXSize+1 >> 1;  uiXL = uiNrX - 1; uiXR = uiXL;
      |                              ~~~~~~~^~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c distmap.cpp -o distmap.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c drawCircle.c -o drawCircle.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c floodFill.cpp -o floodFill.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c getFrames.c -o getFrames.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c haralick.c -o haralick.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c medianFilter.c -o medianFilter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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:253:41:   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:374:25:   required from here
morphology.cpp:196:14: warning: statement has no effect [-Wunused-value]
  196 |         for (i; i < 0; ++i) {
      |              ^
morphology.cpp:199:14: warning: statement has no effect [-Wunused-value]
  199 |         for (i; i < maxX; ++i) {
      |              ^
morphology.cpp:203:14: warning: statement has no effect [-Wunused-value]
  203 |         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:257:41:   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:374:25:   required from here
morphology.cpp:163:14: warning: statement has no effect [-Wunused-value]
  163 |         for (i; i < 0; ++i) {
      |              ^
morphology.cpp:166:14: warning: statement has no effect [-Wunused-value]
  166 |         for (i; i < maxX; ++i) {
      |              ^
morphology.cpp:170:14: warning: statement has no effect [-Wunused-value]
  170 |         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:253:41:   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:377:28:   required from here
morphology.cpp:196:14: warning: statement has no effect [-Wunused-value]
  196 |         for (i; i < 0; ++i) {
      |              ^
morphology.cpp:199:14: warning: statement has no effect [-Wunused-value]
  199 |         for (i; i < maxX; ++i) {
      |              ^
morphology.cpp:203:14: warning: statement has no effect [-Wunused-value]
  203 |         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:257:41:   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:377:28:   required from here
morphology.cpp:163:14: warning: statement has no effect [-Wunused-value]
  163 |         for (i; i < 0; ++i) {
      |              ^
morphology.cpp:166:14: warning: statement has no effect [-Wunused-value]
  166 |         for (i; i < maxX; ++i) {
      |              ^
morphology.cpp:170:14: warning: statement has no effect [-Wunused-value]
  170 |         for (i; i < size.x + set->maxXoffset; ++i) {
      |              ^
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c nativeRaster.c -o nativeRaster.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c normalize.c -o normalize.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -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]
   21 |     double *obj, *src, *tgt, dp, val;
      |                              ^~
objects.c: In function ‘stackObjects’:
objects.c:291:10: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized]
  291 |     else SET_VECTOR_ELT(res, im, img);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
objects.c:192:8: note: ‘res’ was declared here
  192 |   SEXP res, dim, xys, img;
      |        ^~~
In file included from objects.h:5,
                 from objects.c:1:
/home/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:143:33: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized]
  143 | #define SET_DIM(x, n)           Rf_setAttrib(x, R_DimSymbol, n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
objects.c:257:7: note: in expansion of macro ‘SET_DIM’
  257 |       SET_DIM (img, dim);
      |       ^~~~~~~
objects.c:192:13: note: ‘dim’ was declared here
  192 |   SEXP res, dim, xys, img;
      |             ^~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c ocontour.c -o ocontour.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c propagate.cpp -o propagate.o
In function ‘void _propagate(int*, double*, int*, int*, double*, unsigned int, unsigned int, double)’,
    inlined from ‘SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)’ at propagate.cpp:209:15:
propagate.cpp:164:42: warning: ‘mask’ may be used uninitialized [-Wmaybe-uninitialized]
  164 |       if ((label > 0) && (mask_in[IJ(i,j)])) {
      |                                          ^
propagate.cpp: In function ‘SEXPREC* propagate(SEXP, SEXP, SEXP, SEXP)’:
propagate.cpp:197:8: note: ‘mask’ was declared here
  197 |   int *mask;
      |        ^~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c spatial.c -o spatial.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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:50:25:   required from here
thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable]
   64 |     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:53:28:   required from here
thresh.cpp:64:42: warning: unused variable ‘i’ [-Wunused-variable]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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]
   24 |   SEXP res, dm, ims;
      |                 ^~~
tile.cpp: In function ‘SEXPREC* untile(SEXP, SEXP, SEXP)’:
tile.cpp:161:29: warning: unused variable ‘y’ [-Wunused-variable]
  161 |   int nprotect=0, i, j, im, y, iim;
      |                             ^
tile.cpp:162:18: warning: unused variable ‘dat’ [-Wunused-variable]
  162 |   SEXP res, dim, dat;
      |                  ^~~
tile.cpp:163:11: warning: unused variable ‘src’ [-Wunused-variable]
  163 |   double *src, *tgt;
      |           ^~~
tile.cpp:163:17: warning: unused variable ‘tgt’ [-Wunused-variable]
  163 |   double *src, *tgt;
      |                 ^~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c tools.c -o tools.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c transpose.cpp -o transpose.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c watershed.cpp -o watershed.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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)