Davide Risso
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/mbkmeans |
| git_branch: RELEASE_3_17 |
| git_last_commit: 1f8f519 |
| git_last_commit_date: 2023-04-25 11:09:13 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1137/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mbkmeans 1.16.0 (landing page) Davide Risso
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the mbkmeans package: - 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: mbkmeans |
| Version: 1.16.0 |
| Command: rm -rf mbkmeans.buildbin-libdir && mkdir mbkmeans.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mbkmeans_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mbkmeans.buildbin-libdir |
| StartedAt: 2023-10-19 14:36:42 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 14:38:44 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 122.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: mbkmeans_1.16.0.tgz |
| PackageFileSize: 429.5 KiB |
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### Running command:
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### rm -rf mbkmeans.buildbin-libdir && mkdir mbkmeans.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mbkmeans_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mbkmeans.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mbkmeans.buildbin-libdir mbkmeans_1.16.0.tar.gz'
>>>>>>>
* installing *source* package ‘mbkmeans’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ClusterR/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ClusterR/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mini_batch.cpp -o mini_batch.o
In file included from mini_batch.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo:26:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
#pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
#pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
In file included from mini_batch.cpp:3:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
bool status;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
bool status;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mbkmeans.so RcppExports.o mini_batch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mbkmeans.buildbin-libdir/00LOCK-mbkmeans/00new/mbkmeans/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 (mbkmeans)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so
>>>>>>>
>>>>>>> Paths before fix:
mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so:
mbkmeans.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so"
>>>>>>> Paths after fix:
mbkmeans.buildbin-libdir/mbkmeans/libs/mbkmeans.so:
mbkmeans.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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)