Aaron Lun
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/beachmat.tiledb |
| git_branch: devel |
| git_last_commit: c0c20e1 |
| git_last_commit_date: 2025-07-14 01:24:42 -0400 (Mon, 14 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 154/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beachmat.tiledb 1.1.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the beachmat.tiledb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beachmat.tiledb.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: beachmat.tiledb |
| Version: 1.1.1 |
| Command: rm -rf beachmat.tiledb.buildbin-libdir && mkdir beachmat.tiledb.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat.tiledb_1.1.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R beachmat.tiledb.buildbin-libdir |
| StartedAt: 2025-08-08 22:23:56 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 22:24:20 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 23.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: beachmat.tiledb_1.1.1.tgz |
| PackageFileSize: 481 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf beachmat.tiledb.buildbin-libdir && mkdir beachmat.tiledb.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat.tiledb_1.1.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R beachmat.tiledb.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beachmat.tiledb.buildbin-libdir beachmat.tiledb_1.1.1.tar.gz' >>>>>>> * installing *source* package ‘beachmat.tiledb’ ... ** this is package ‘beachmat.tiledb’ version ‘1.1.1’ ** using staged installation checking if tiledb-R downloaded its own TileDB... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c initialize.cpp -o initialize.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_dense.cpp -o load_dense.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_sparse.cpp -o load_sparse.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o beachmat.tiledb.so RcppExports.o initialize.o load_dense.o load_sparse.o -ltiledb -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/lib -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/tiledb/tiledb/lib -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.22-bioc/meat/beachmat.tiledb.buildbin-libdir/00LOCK-beachmat.tiledb/00new/beachmat.tiledb/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 (beachmat.tiledb) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so >>>>>>> >>>>>>> Paths before fix: beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so: beachmat.tiledb.so (compatibility version 0.0.0, current version 0.0.0) @rpath/libtiledb.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so" >>>>>>> Paths after fix: beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so: beachmat.tiledb.so (compatibility version 0.0.0, current version 0.0.0) @rpath/libtiledb.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)