Multiple platform build/check report for BioC 3.20 - INSTALL results for VegaMC on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 VegaMC on kunpeng2

To the developers/maintainers of the VegaMC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VegaMC.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: VegaMC

Version: 3.44.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL VegaMC

StartedAt: 2024-11-19 20:56:53 -0000 (Tue, 19 Nov 2024)

EndedAt: 2024-11-19 20:57:16 -0000 (Tue, 19 Nov 2024)

EllapsedTime: 23.0 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL VegaMC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function 'run_vegaMC':
run_vegaMC.c:144:13: warning: too many arguments for format [-Wformat-extra-args]
  144 |     Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c:149:13: warning: too many arguments for format [-Wformat-extra-args]
  149 |     Rprintf("\tStatistical Analysis Successfully Completed\n",
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c: In function 'read_params':
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
  618 |     char *elem, *brkt;
      |                  ^~~~
run_vegaMC.c: In function 'load_data':
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized [-Wmaybe-uninitialized]
  564 |     prev_chr = temp_probe->chromosome;
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c:481:12: note: 'first_probe' was declared here
  481 |     probe *first_probe, *prev_probe, *temp_probe;
      |            ^~~~~~~~~~~
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized [-Wmaybe-uninitialized]
  535 |         temp_probe->position = position;
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:498:20: note: 'position' was declared here
  498 |         int i = 0, position, chr;
      |                    ^~~~~~~~
run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized [-Wmaybe-uninitialized]
  534 |         temp_probe->chromosome = chr;
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:498:30: note: 'chr' was declared here
  498 |         int i = 0, position, chr;
      |                              ^~~
run_vegaMC.c: In function 'call_VegaMC':
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized [-Wmaybe-uninitialized]
  435 |                 prev_seg->next = tmp;
      |                 ~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:373:30: note: 'prev_seg' was declared here
  373 |     seg_element *first_seg, *prev_seg;
      |                              ^~~~~~~~
run_vegaMC.c:461:29: warning: 'first_seg' may be used uninitialized [-Wmaybe-uninitialized]
  461 |         for (i = 0; i < (tmp->num_regions); i++) {
      |                         ~~~~^~~~~~~~~~~~~~
run_vegaMC.c:373:18: note: 'first_seg' was declared here
  373 |     seg_element *first_seg, *prev_seg;
      |                  ^~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c sort_data.c -o sort_data.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c vegaMC.c -o vegaMC.o
vegaMC.c: In function 'heap_delete':
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
  235 |     node deleted;
      |          ^~~~~~~
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
  592 |     int i, j, index;
      |               ^~~~~
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-VegaMC/00new/VegaMC/libs
** R
** 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 (VegaMC)