Hervé Pagès
| Snapshot Date: 2026-03-23 13:40 -0400 (Mon, 23 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: devel |
| git_last_commit: c527085 |
| git_last_commit_date: 2025-10-29 10:14:52 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-24 11:35 -0400 (Tue, 24 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4567 |
| 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 2359/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.51.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
| See other builds for XVector in R Universe. | ||||||||||||||
|
To the developers/maintainers of the XVector package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XVector.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: XVector |
| Version: 0.51.0 |
| Command: rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XVector.buildbin-libdir |
| StartedAt: 2026-03-24 00:15:04 -0400 (Tue, 24 Mar 2026) |
| EndedAt: 2026-03-24 00:15:14 -0400 (Tue, 24 Mar 2026) |
| EllapsedTime: 10.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XVector.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XVector.buildbin-libdir XVector_0.51.0.tar.gz'
>>>>>>>
* installing *source* package ‘XVector’ ...
** this is package ‘XVector’ version ‘0.51.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
793 | SEXPTYPE x_type;
| ^
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
796 | SEXP subscript, ans;
| ^~~
2 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_XVector.c -o R_init_XVector.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SharedDouble_class.c -o SharedDouble_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SharedInteger_class.c -o SharedInteger_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c:396:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
396 | SEXP dest, src_tag;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SharedVector_class.c -o SharedVector_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XDouble_class.c -o XDouble_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XInteger_class.c -o XInteger_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XRawList_comparison.c -o XRawList_comparison.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XRaw_class.c -o XRaw_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVectorList_class.c -o XVectorList_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_class.c -o XVector_class.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io_utils.c -o io_utils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c slice_methods.c -o slice_methods.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vector_copy.c -o vector_copy.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c view_summarization_methods.c -o view_summarization_methods.o
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/XVector.buildbin-libdir/00LOCK-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (XVector)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR XVector.buildbin-libdir/XVector/libs/XVector.so
>>>>>>>
>>>>>>> Paths before fix:
XVector.buildbin-libdir/XVector/libs/XVector.so:
XVector.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!