Hervé Pagès
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/IRanges |
| git_branch: devel |
| git_last_commit: cba0bb6 |
| git_last_commit_date: 2025-10-24 12:19:47 -0400 (Fri, 24 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:07 -0400 (Sat, 25 Oct 2025).
| 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 | ||||
| Package 1080/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRanges 2.43.6 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the IRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRanges.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: IRanges |
| Version: 2.43.5 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL IRanges |
| StartedAt: 2025-10-23 20:31:52 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:33:09 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 77.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL IRanges
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘IRanges’ ...
** this is package ‘IRanges’ version ‘2.43.5’
** 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-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CompressedList_class.c -o CompressedList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c Grouping_class.c -o Grouping_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c IPosRanges_comparison.c -o IPosRanges_comparison.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_class.c -o IRanges_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_constructor.c -o IRanges_constructor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c NCList.c -o NCList.o
NCList.c:1303:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
1303 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:203:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
203 | static const NCList *next_top_down(NCListWalkingStack *stack,
| ^~~~~~~~~~~~~
NCList.c: In function ‘C_find_overlaps_in_groups_NCList’:
NCList.c:1782:24: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
1782 | return ans;
| ^~~
NCList.c:1751:14: note: ‘ans’ was declared here
1751 | SEXP ans;
| ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c R_init_IRanges.c -o R_init_IRanges.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c Ranges_class.c -o Ranges_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RleViews_utils.c -o RleViews_utils.o
In function ‘viewWhichMaxs_int_RleViews’,
inlined from ‘viewWhichMaxs_RleViews’ at RleViews_utils.c:579:3,
inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:694:9:
RleViews_utils.c:325:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
325 | if (!max_is_initialized || v > max) {
| ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:316:21: note: ‘max’ was declared here
316 | int max; /* uninitialized */
| ^~~
In function ‘viewWhichMins_int_RleViews’,
inlined from ‘viewWhichMins_RleViews’ at RleViews_utils.c:546:3,
inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:686:9:
RleViews_utils.c:293:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
293 | if (!min_is_initialized || v < min) {
| ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:284:21: note: ‘min’ was declared here
284 | int min; /* uninitialized */
| ^~~
In function ‘viewMaxs_int_RleViews’,
inlined from ‘viewMaxs_RleViews’ at RleViews_utils.c:443:3,
inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:665:9:
RleViews_utils.c:67:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
67 | if (!max_is_initialized || v > max) {
| ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:54:21: note: ‘max’ was declared here
54 | int max; /* uninitialized */
| ^~~
In function ‘viewMins_int_RleViews’,
inlined from ‘viewMins_RleViews’ at RleViews_utils.c:413:3,
inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:660:9:
RleViews_utils.c:36:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
36 | if (!min_is_initialized || v < min) {
| ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:23:21: note: ‘min’ was declared here
23 | int min; /* uninitialized */
| ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c coverage_methods.c -o coverage_methods.o
In function ‘shift_and_clip_ranges’,
inlined from ‘compute_coverage_from_IRanges_holder’ at coverage_methods.c:609:12:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized [-Wmaybe-uninitialized]
579 | if (*out_ranges_are_tiles && x_end != cvg_len)
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:495:28: note: ‘x_end’ was declared here
495 | i, j, x_start, x_end, shift_elt, tmp;
| ^~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:85:25: warning: ‘split_partitions_buf’ may be used uninitialized [-Wmaybe-uninitialized]
85 | IntAE_insert_at(split_partitions_buf,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
86 | IntAE_get_nelt(split_partitions_buf),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
87 | q_prev_end);
| ~~~~~~~~~~~
extractListFragments.c:35:16: note: ‘split_partitions_buf’ was declared here
35 | IntAE *split_partitions_buf;
| ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges.isra’:
inter_range_methods.c:154:39: warning: ‘gapwidth’ may be used uninitialized [-Wmaybe-uninitialized]
154 | delta += gapwidth;
| ~~~~~~^~~~~~~~~~~
inter_range_methods.c:102:38: note: ‘gapwidth’ was declared here
102 | append_or_drop, max_end, gapwidth, delta, width_inc;
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c thread_control.c -o thread_control.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o thread_control.o -fopenmp -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** 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 (IRanges)