Multiple platform build/check report for BioC 3.22 - INSTALL results for ADaCGH2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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*

INSTALL results for ADaCGH2 on nebbiolo2

To the developers/maintainers of the ADaCGH2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADaCGH2.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: ADaCGH2

Version: 2.49.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ADaCGH2

StartedAt: 2025-10-24 16:08:06 -0400 (Fri, 24 Oct 2025)

EndedAt: 2025-10-24 16:08:30 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 24.2 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ADaCGH2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ADaCGH2’ ...
** this is package ‘ADaCGH2’ version ‘2.49.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
   65 |     double totalNorm;
      |            ^~~~~~~~~
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:43: warning: "/*" within comment [-Wcomment]
  152 |                                          }/* for j */
      |                                            
r_haarseg.c:176:43: warning: "/*" within comment [-Wcomment]
  176 |                                          }/* for j */
      |                                            
r_haarseg.c:128:16: warning: unused variable ‘j’ [-Wunused-variable]
  128 |          int k,j;
      |                ^
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized [-Wmaybe-uninitialized]
   98 |             lowWeightSum += weight[k-1] - weight[lowEnd];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:59:12: note: ‘lowWeightSum’ was declared here
   59 |     double lowWeightSum;
      |            ^~~~~~~~~~~~
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized [-Wmaybe-uninitialized]
   96 |             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:63:12: note: ‘lowNonNormed’ was declared here
   63 |     double lowNonNormed;
      |            ^~~~~~~~~~~~
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized [-Wmaybe-uninitialized]
   97 |             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:64:12: note: ‘highNonNormed’ was declared here
   64 |     double highNonNormed;
      |            ^~~~~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-ADaCGH2/00new/ADaCGH2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (ADaCGH2)