Aaron Lun
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 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 -0400 (Fri, 05 Jan 2024) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:19 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the SingleR 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: SingleR |
| Version: 2.4.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR |
| StartedAt: 2024-04-16 12:26:15 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 12:27:32 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 77.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/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/BiocNeighbors/include' -I/opt/R/arm64/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 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 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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)