Wenjie Sun
| Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/CellBarcode |
| git_branch: devel |
| git_last_commit: 9c54c56 |
| git_last_commit_date: 2025-03-04 15:05:23 -0400 (Tue, 04 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-20 11:43 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 296/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellBarcode 1.13.2 (landing page) Wenjie Sun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CellBarcode package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellBarcode.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: CellBarcode |
| Version: 1.13.2 |
| Command: rm -rf CellBarcode.buildbin-libdir && mkdir CellBarcode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CellBarcode_1.13.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CellBarcode.buildbin-libdir |
| StartedAt: 2025-03-20 01:11:54 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 01:13:45 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 111.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CellBarcode_1.13.2.tgz |
| PackageFileSize: 4.372 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CellBarcode.buildbin-libdir && mkdir CellBarcode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CellBarcode_1.13.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CellBarcode.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CellBarcode.buildbin-libdir CellBarcode_1.13.2.tar.gz'
>>>>>>>
* installing *source* package ‘CellBarcode’ ...
** this is package ‘CellBarcode’ version ‘1.13.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
rm -Rf CellBarcode.so ./rust/target/release/libCellBarcode.a entrypoint.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c entrypoint.c -o entrypoint.o
# In some environments, ~/.cargo/bin might not be included in PATH, so we need
# to set it here to ensure cargo can be invoked. It is appended to PATH and
# therefore is only used if cargo is absent from the user's PATH.
if [ "" != "true" ]; then \
export CARGO_HOME=/private/tmp/Rtmp4Jjq2e/R.INSTALL11977718ed8c2/CellBarcode/src/.cargo; \
fi && \
export PATH="/Users/biocbuild/.cargo/bin:/Applications/CMake.app/Contents/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/share/dotnet:/opt/salt:/opt/X11/bin:/opt/gfortran/bin:/opt/R/x86_64/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/Users/biocbuild/.cargo/bin" && \
cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target
Updating crates.io index
Downloading crates ...
Downloaded leven-distance v1.0.0
Downloaded adler2 v2.0.0
Downloaded paste v1.0.15
Downloaded unicode-ident v1.0.17
Downloaded proc-macro2 v1.0.93
Downloaded miniz_oxide v0.8.5
Downloaded quote v1.0.38
Downloaded memchr v2.7.4
Downloaded flate2 v1.1.0
Downloaded itertools v0.10.5
Downloaded extendr-api v0.7.1
Downloaded once_cell v1.20.3
Downloaded aho-corasick v1.1.3
Downloaded extendr-macros v0.7.1
Downloaded either v1.14.0
Downloaded regex-syntax v0.8.5
Downloaded syn v2.0.98
Downloaded regex v1.11.1
Downloaded crc32fast v1.4.2
Downloaded cfg-if v1.0.0
Downloaded lazy_static v1.5.0
Downloaded regex-automata v0.4.9
Downloaded libR-sys v0.7.1
Compiling proc-macro2 v1.0.93
Compiling unicode-ident v1.0.17
Compiling libR-sys v0.7.1
Compiling paste v1.0.15
Compiling memchr v2.7.4
Compiling adler2 v2.0.0
Compiling extendr-api v0.7.1
Compiling cfg-if v1.0.0
Compiling regex-syntax v0.8.5
Compiling once_cell v1.20.3
Compiling either v1.14.0
Compiling leven-distance v1.0.0
Compiling lazy_static v1.5.0
Compiling crc32fast v1.4.2
Compiling miniz_oxide v0.8.5
Compiling itertools v0.10.5
Compiling aho-corasick v1.1.3
Compiling flate2 v1.1.0
Compiling quote v1.0.38
Compiling syn v2.0.98
Compiling regex-automata v0.4.9
Compiling regex v1.11.1
Compiling extendr-macros v0.7.1
Compiling CellBarcode v0.1.0 (/private/tmp/Rtmp4Jjq2e/R.INSTALL11977718ed8c2/CellBarcode/src/rust)
warning: crate `CellBarcode` should have a snake case name
|
= help: convert the identifier to snake case: `cell_barcode`
= note: `#[warn(non_snake_case)]` on by default
warning: `CellBarcode` (lib) generated 1 warning
Finished `release` profile [optimized] target(s) in 56.04s
if [ "" != "true" ]; then \
rm -Rf /private/tmp/Rtmp4Jjq2e/R.INSTALL11977718ed8c2/CellBarcode/src/.cargo && \
rm -Rf ./rust/target/release/build; \
fi
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CellBarcode.so entrypoint.o -L./rust/target/release -lCellBarcode -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/CellBarcode.buildbin-libdir/00LOCK-CellBarcode/00new/CellBarcode/libs
** R
** data
** 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 (CellBarcode)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so
>>>>>>>
>>>>>>> Paths before fix:
CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so:
CellBarcode.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so"
>>>>>>> Paths after fix:
CellBarcode.buildbin-libdir/CellBarcode/libs/CellBarcode.so:
CellBarcode.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)