Benjamin Story
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/mitoClone2 |
| git_branch: RELEASE_3_21 |
| git_last_commit: 9f9dee6 |
| git_last_commit_date: 2025-04-15 12:35:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1314/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mitoClone2 1.14.0 (landing page) Benjamin Story
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the mitoClone2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.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: mitoClone2 |
| Version: 1.14.0 |
| Command: rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mitoClone2_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mitoClone2.buildbin-libdir |
| StartedAt: 2025-10-15 19:22:29 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 19:23:39 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 69.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: mitoClone2_1.14.0.tgz |
| PackageFileSize: 2.053 MiB |
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### Running command:
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### rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mitoClone2_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mitoClone2.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mitoClone2.buildbin-libdir mitoClone2_1.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘mitoClone2’ ...
** this is package ‘mitoClone2’ version ‘1.14.0’
** 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 -std=gnu++17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
mkdir -p "/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "/Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:144:11: warning: variable 'missingBC' set but not used [-Wunused-but-set-variable]
int missingBC = 0;
^
1 warning generated.
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 mitoClone2.so bam2R_10x.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (mitoClone2)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so
>>>>>>>
>>>>>>> Paths before fix:
mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so:
mitoClone2.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/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" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so"
>>>>>>> Paths after fix:
mitoClone2.buildbin-libdir/mitoClone2/libs/mitoClone2.so:
mitoClone2.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/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)