Hervé Pagès
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/IRanges |
| git_branch: RELEASE_3_17 |
| git_last_commit: ce72113 |
| git_last_commit_date: 2023-06-21 22:44:53 -0400 (Wed, 21 Jun 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:15 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1019/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRanges 2.34.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: IRanges |
| Version: 2.34.1 |
| Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir IRanges_2.34.1.tar.gz |
| StartedAt: 2023-10-16 08:58:36 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 09:00:18 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 101.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: IRanges_2.34.1.zip |
| PackageFileSize: 2.191 MiB |
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### Running command:
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### rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir IRanges_2.34.1.tar.gz
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* installing *source* package 'IRanges' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
202 | static const NCList *next_top_down(const NCList *nclist)
| ^~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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;
| ^~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'C_find_partition_overlaps':
extractListFragments.c:66:33: warning: 'split_partitions_buf' may be used uninitialized [-Wmaybe-uninitialized]
66 | IntAE_insert_at(split_partitions_buf,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
67 | IntAE_get_nelt(split_partitions_buf),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | q_prev_end);
| ~~~~~~~~~~~
extractListFragments.c:35:16: note: 'split_partitions_buf' was declared here
35 | IntAE *split_partitions_buf;
| ^~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -s -static-libgcc -o IRanges.dll tmp.def 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 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs/x64
** 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'
Creating a new generic function for 'windows' in package 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.34.1.zip
* DONE (IRanges)