Hervé Pagès
| Snapshot Date: 2025-04-24 15:01 -0400 (Thu, 24 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/DelayedArray |
| git_branch: RELEASE_3_21 |
| git_last_commit: 93033ab |
| git_last_commit_date: 2025-04-17 13:33:44 -0400 (Thu, 17 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-28 13:01 -0400 (Mon, 28 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4558 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 544/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DelayedArray 0.34.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | ERROR | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
|
To the developers/maintainers of the DelayedArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedArray.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: DelayedArray |
| Version: 0.34.1 |
| Command: rm -rf DelayedArray.buildbin-libdir && mkdir DelayedArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DelayedArray_0.34.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DelayedArray.buildbin-libdir |
| StartedAt: 2025-04-26 16:57:02 -0400 (Sat, 26 Apr 2025) |
| EndedAt: 2025-04-26 16:57:39 -0400 (Sat, 26 Apr 2025) |
| EllapsedTime: 37.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DelayedArray.buildbin-libdir && mkdir DelayedArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DelayedArray_0.34.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DelayedArray.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DelayedArray.buildbin-libdir DelayedArray_0.34.1.tar.gz' >>>>>>> * installing *source* package ‘DelayedArray’ ... ** this is package ‘DelayedArray’ version ‘0.34.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_DelayedArray.c -o R_init_DelayedArray.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compress_atomic_vector.c -o compress_atomic_vector.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.21-bioc/meat/DelayedArray.buildbin-libdir/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** 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 (DelayedArray) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so >>>>>>> >>>>>>> Paths before fix: DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so: DelayedArray.so (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 4.5.0) /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" "DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so" >>>>>>> Paths after fix: DelayedArray.buildbin-libdir/DelayedArray/libs/DelayedArray.so: DelayedArray.so (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 4.5.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) chown: DelayedArray.buildbin-libdir/DelayedArray/R/DelayedArray: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/R/DelayedArray.rdx: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/R/DelayedArray.rdb: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedAperm-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedArray-utils.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_makeCappedVolumeBox.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedNaryIsoOp-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_ConstantArray-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedMatrix-rowsum.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedMatrix-mult.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedArray-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedSubset-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_cbind-methods.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedUnaryIsoOpWithArgs-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedSetDimnames-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_RleArray-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedMatrix-stats.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests/test_DelayedUnaryIsoOpStack-class.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/unitTests: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/Meta/vignette.rds: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/Meta/links.rds: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/Meta/features.rds: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/Meta/nsInfo.rds: 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DelayedArray.buildbin-libdir/DelayedArray/NEWS: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/scripts/benchmark_DelayedMatrix-mult.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/scripts: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/INDEX: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/C-DelayedArray_HDF5Array_update.Rnw: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/C-DelayedArray_HDF5Array_update.pdf: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/index.html: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/A-Working_with_large_arrays.pdf: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/A-Working_with_large_arrays.Rnw: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/A-Working_with_large_arrays.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/C-DelayedArray_HDF5Array_update.R: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/B-Implementing_a_backend.Rmd: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc/B-Implementing_a_backend.html: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/doc: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help/AnIndex: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help/aliases.rds: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help/DelayedArray.rdx: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help/DelayedArray.rdb: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help/paths.rds: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray/help: Operation not permitted chown: DelayedArray.buildbin-libdir/DelayedArray: Operation not 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