Aaron Lun
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SingleR |
| git_branch: RELEASE_3_18 |
| git_last_commit: fab56fd |
| git_last_commit_date: 2024-01-05 19:00:37 -0500 (Fri, 05 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:52 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 1973/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.4.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SingleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.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: SingleR |
| Version: 2.4.1 |
| Command: rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.4.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir |
| StartedAt: 2024-03-04 01:05:26 -0500 (Mon, 04 Mar 2024) |
| EndedAt: 2024-03-04 01:07:05 -0500 (Mon, 04 Mar 2024) |
| EllapsedTime: 99.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SingleR_2.4.1.tgz |
| PackageFileSize: 996.7 KiB |
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### Running command:
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### rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.4.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SingleR.buildbin-libdir SingleR_2.4.1.tar.gz'
>>>>>>>
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o
In file included from find_classic_markers.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from find_classic_markers.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_medians.cpp -o grouped_medians.o
In file included from grouped_medians.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from grouped_medians.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_build.cpp -o integrate_build.o
In file included from integrate_build.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_build.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_run.cpp -o integrate_run.o
In file included from integrate_run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c prebuild.cpp -o prebuild.o
In file included from prebuild.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from prebuild.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run.cpp -o run.o
In file included from run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:9:
In file included from ../inst/include/singlepp/BasicScorer.hpp:8:
In file included from ../inst/include/singlepp/annotate_cells.hpp:11:
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from run.cpp:1:
In file included from ./utils.h:11:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:41:10: warning: unused variable 'remaining' [-Wunused-variable]
bool remaining = true;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc/meat/SingleR.buildbin-libdir/00LOCK-SingleR/00new/SingleR/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 (SingleR)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SingleR.buildbin-libdir/SingleR/libs/SingleR.so
>>>>>>>
>>>>>>> Paths before fix:
SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
SingleR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
>>>>>>> Paths after fix:
SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
SingleR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
/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)