Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1897/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scran 1.34.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the scran package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.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: scran |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scran_1.34.0.tar.gz |
StartedAt: 2024-12-21 08:40:27 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 08:53:32 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 785.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scran.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scran_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scran.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scran/DESCRIPTION’ ... OK * this is package ‘scran’ version ‘1.34.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scran’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning in combinePValues(p1, p2, p3) : 'combinePValues' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed cyclone 9.855 1.289 11.205 buildSNNGraph 7.871 0.092 7.997 pseudoBulkSpecific 4.972 0.080 5.064 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scran.Rcheck/00check.log’ for details.
scran.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘scran’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c choose_effect_size.cpp -o choose_effect_size.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c combine_rho.cpp -o combine_rho.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o In file included from compute_blocked_stats.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_residual_stats.cpp -o compute_residual_stats.o In file included from compute_residual_stats.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_rho_null.cpp -o compute_rho_null.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cyclone_scores.cpp -o cyclone_scores.o In file included from cyclone_scores.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c overlap_exprs.cpp -o overlap_exprs.o In file included from overlap_exprs.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [-Wunused-variable] const size_t ngroups=groups.size(); ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/scuttle/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rand_custom.cpp -o rand_custom.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-scran/00new/scran/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 (scran)
scran.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(scran) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: scuttle > test_check("scran") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep [ FAIL 0 | WARN 192 | SKIP 2 | PASS 4452 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On Mac (1): 'test-cyclone.R:10:1' • monocle is a little broken because of clusterApply (1): 'test-convert.R:71:5' [ FAIL 0 | WARN 192 | SKIP 2 | PASS 4452 ] > > proc.time() user system elapsed 364.640 10.426 486.931
scran.Rcheck/scran-Ex.timings
name | user | system | elapsed | |
DM | 0.055 | 0.001 | 0.057 | |
buildSNNGraph | 7.871 | 0.092 | 7.997 | |
clusterCells | 2.191 | 0.030 | 2.247 | |
combineBlocks | 0.897 | 0.050 | 0.961 | |
combineMarkers | 1.518 | 0.031 | 1.565 | |
combinePValues | 0.037 | 0.006 | 0.043 | |
combineVar | 0.883 | 0.031 | 0.927 | |
computeMinRank | 0.001 | 0.000 | 0.003 | |
convertTo | 1.144 | 0.027 | 1.192 | |
correlateGenes | 1.633 | 0.049 | 1.702 | |
correlateNull | 0.379 | 0.007 | 0.394 | |
correlatePairs | 1.589 | 0.050 | 1.660 | |
cyclone | 9.855 | 1.289 | 11.205 | |
decideTestsPerLabel | 3.448 | 0.077 | 3.551 | |
defunct | 0.001 | 0.000 | 0.001 | |
denoisePCA | 1.594 | 0.017 | 1.618 | |
findMarkers | 2.073 | 0.030 | 2.123 | |
fitTrendCV2 | 0.520 | 0.026 | 0.587 | |
fitTrendPoisson | 0.129 | 0.012 | 0.164 | |
fitTrendVar | 0.559 | 0.019 | 0.591 | |
fixedPCA | 1.023 | 0.015 | 1.055 | |
getClusteredPCs | 3.228 | 0.081 | 3.316 | |
getMarkerEffects | 0.885 | 0.016 | 0.911 | |
getTopHVGs | 0.738 | 0.030 | 0.769 | |
getTopMarkers | 0.819 | 0.015 | 0.836 | |
logBH | 0.001 | 0.000 | 0.002 | |
modelGeneCV2 | 0.904 | 0.035 | 0.942 | |
modelGeneCV2WithSpikes | 0.920 | 0.025 | 0.949 | |
modelGeneVar | 1.190 | 0.030 | 1.227 | |
modelGeneVarByPoisson | 0.993 | 0.024 | 1.021 | |
modelGeneVarWithSpikes | 1.070 | 0.030 | 1.106 | |
multiMarkerStats | 1.478 | 0.030 | 1.514 | |
pairwiseBinom | 0.677 | 0.020 | 0.699 | |
pairwiseTTests | 0.768 | 0.015 | 0.785 | |
pairwiseWilcox | 0.675 | 0.019 | 0.698 | |
pseudoBulkDGE | 4.220 | 0.098 | 4.398 | |
pseudoBulkSpecific | 4.972 | 0.080 | 5.064 | |
quickCluster | 2.149 | 0.035 | 2.194 | |
quickSubCluster | 3.489 | 0.063 | 3.561 | |
rhoToPValue | 0.000 | 0.000 | 0.001 | |
sandbag | 0.484 | 0.013 | 0.500 | |
scaledColRanks | 1.447 | 0.016 | 1.474 | |
scoreMarkers | 1.018 | 0.024 | 1.044 | |
summaryMarkerStats | 1.591 | 0.039 | 1.635 | |
testLinearModel | 0.064 | 0.003 | 0.068 | |