Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:43 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 |
Package 2291/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VegaMC 3.46.0 (landing page) Sandro Morganella
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: VegaMC |
Version: 3.46.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL VegaMC |
StartedAt: 2025-08-18 20:39:16 -0000 (Mon, 18 Aug 2025) |
EndedAt: 2025-08-18 20:39:38 -0000 (Mon, 18 Aug 2025) |
EllapsedTime: 21.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL VegaMC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘VegaMC’ ... ** this is package ‘VegaMC’ version ‘3.46.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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; | ^~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sort_data.c -o sort_data.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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; | ^~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/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)