Hervé Pagès
| Snapshot Date: 2026-03-24 13:40 -0400 (Tue, 24 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/cigarillo |
| git_branch: devel |
| git_last_commit: f89db3d |
| git_last_commit_date: 2025-10-29 11:39:18 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-25 11:34 -0400 (Wed, 25 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" | 4876 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4573 |
| 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 367/2372 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cigarillo 1.1.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for cigarillo in R Universe. | ||||||||||||||
|
To the developers/maintainers of the cigarillo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cigarillo.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: cigarillo |
| Version: 1.1.0 |
| Command: rm -rf cigarillo.buildbin-libdir && mkdir cigarillo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cigarillo_1.1.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cigarillo.buildbin-libdir |
| StartedAt: 2026-03-24 23:08:37 -0400 (Tue, 24 Mar 2026) |
| EndedAt: 2026-03-24 23:08:43 -0400 (Tue, 24 Mar 2026) |
| EllapsedTime: 6.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf cigarillo.buildbin-libdir && mkdir cigarillo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cigarillo_1.1.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cigarillo.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cigarillo.buildbin-libdir cigarillo_1.1.0.tar.gz' >>>>>>> * installing *source* package ‘cigarillo’ ... ** this is package ‘cigarillo’ version ‘1.1.0’ ** 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 R_init_cigarillo.c -o R_init_cigarillo.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 cigar_extent.c -o cigar_extent.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 cigar_ops_visibility.c -o cigar_ops_visibility.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 cigars_as_ranges.c -o cigars_as_ranges.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 explode_cigars.c -o explode_cigars.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 map_ref_ranges_to_query.c -o map_ref_ranges_to_query.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 project_positions.c -o project_positions.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 tabulate_cigar_ops.c -o tabulate_cigar_ops.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 trim_cigars.c -o trim_cigars.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 cigarillo.so IRanges_stubs.o R_init_cigarillo.o S4Vectors_stubs.o cigar_extent.o cigar_ops_visibility.o cigars_as_ranges.o explode_cigars.o map_ref_ranges_to_query.o project_positions.o tabulate_cigar_ops.o trim_cigars.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.23-bioc/meat/cigarillo.buildbin-libdir/00LOCK-cigarillo/00new/cigarillo/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 (cigarillo) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR cigarillo.buildbin-libdir/cigarillo/libs/cigarillo.so >>>>>>> >>>>>>> Paths before fix: cigarillo.buildbin-libdir/cigarillo/libs/cigarillo.so: cigarillo.so (compatibility version 0.0.0, current version 0.0.0) /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!