Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:40 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 859/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
glmGamPoi 1.17.3 (landing page) Constantin Ahlmann-Eltze
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the glmGamPoi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmGamPoi.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: glmGamPoi |
Version: 1.17.3 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings glmGamPoi_1.17.3.tar.gz |
StartedAt: 2024-08-26 23:23:59 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 23:33:52 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 593.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: glmGamPoi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings glmGamPoi_1.17.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/glmGamPoi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘glmGamPoi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘glmGamPoi’ version ‘1.17.3’ * package encoding: UTF-8 * 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 ‘glmGamPoi’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 10.7Mb sub-directories of 1Mb or more: libs 10.2Mb * 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 loading without being on the library search path ... 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 20. ├─methods::as(extract_sparse_array(x@seed, index), "COO_SparseArray") 21. │ └─methods:::.class1(object) 22. ├─SparseArray::extract_sparse_array(x@seed, index) 23. └─DelayedArray::extract_sparse_array(x@seed, index) 24. ├─SparseArray::extract_sparse_array(x@seed, index) 25. └─DelayedArray::extract_sparse_array(x@seed, index) 26. ├─SparseArray::extract_sparse_array(x@seed, seed_index) 27. └─SparseArray::extract_sparse_array(x@seed, seed_index) 28. └─S4Arrays:::subset_by_Nindex(x, index) 29. ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop))) 30. └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop))) [ FAIL 1 | WARN 420 | SKIP 5 | PASS 444 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/glmGamPoi.Rcheck/00check.log’ for details.
glmGamPoi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL glmGamPoi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘glmGamPoi’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -c beta_estimation.cpp -o beta_estimation.o beta_estimation.cpp: In function ‘bool lte_n_equal_rows(const NumericMatrix&, int, double)’: beta_estimation.cpp:32:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 32 | for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){ | ~~~~~~~~^~~~~~~~~~~~~~~ beta_estimation.cpp:44:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 44 | if(n_matches > n){ | ~~~~~~~~~~^~~ beta_estimation.cpp: In function ‘Rcpp::IntegerVector get_row_groups(const NumericMatrix&, int, double)’: beta_estimation.cpp:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){ | ~~~~~~~~^~~~~~~~~~~~~~~ In file included from beta_estimation.cpp:6: ../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’: ../inst/include/deviance.h:88:58: required from here ../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] 76 | for(int i = 0; i < Y.n_elem; i++){ | ~~^~~~~~~~~~ ../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’: ../inst/include/deviance.h:91:61: required from here ../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] beta_estimation.cpp: In instantiation of ‘void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]’: beta_estimation.cpp:81:16: required from here beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] 15 | for(int i = 0; i < v.n_elem; i++){ | ~~^~~~~~~~~~ In file included from beta_estimation.cpp:6: ../inst/include/deviance.h: In instantiation of ‘double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = int]’: beta_estimation.cpp:246:40: required from ‘Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = int; BMNumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]’ beta_estimation.cpp:301:70: required from here ../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] 53 | for (int i = 0; i < Y.n_elem; i++) { | ~~^~~~~~~~~~ ../inst/include/deviance.h: In instantiation of ‘double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]’: beta_estimation.cpp:246:40: required from ‘Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = double; BMNumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]’ beta_estimation.cpp:307:73: required from here ../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -c deviance.cpp -o deviance.o In file included from deviance.cpp:3: ../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’: ../inst/include/deviance.h:88:58: required from here ../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] 76 | for(int i = 0; i < Y.n_elem; i++){ | ~~^~~~~~~~~~ ../inst/include/deviance.h: In instantiation of ‘arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’: ../inst/include/deviance.h:91:61: required from here ../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare] g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -c overdispersion.cpp -o overdispersion.o overdispersion.cpp: In function ‘Rcpp::List make_table_if_small(const NumericVector&, int)’: overdispersion.cpp:26:22: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<long int, long unsigned int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 26 | if(counts.size() > stop_if_larger){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ overdispersion.cpp: In function ‘double conventional_loglikelihood_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’: overdispersion.cpp:93:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 93 | for(size_t iter = 0; iter < count_frequencies.size(); ++iter){ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp:101:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 101 | for(size_t i = 0; i < y.size(); ++i){ | ~~^~~~~~~~~~ overdispersion.cpp: In function ‘double conventional_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’: overdispersion.cpp:137:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 137 | for(size_t iter = 0; iter < count_frequencies.size(); ++iter){ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp:160:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 160 | for(size_t iter = 0; iter < y.size(); ++iter){ | ~~~~~^~~~~~~~~~ overdispersion.cpp:178:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 178 | for(size_t i = 0; i < y.size(); ++i){ | ~~^~~~~~~~~~ overdispersion.cpp: In function ‘double conventional_deriv_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’: overdispersion.cpp:234:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 234 | for(size_t iter = 0; iter < count_frequencies.size(); ++iter){ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp:252:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 252 | for(size_t i = 0; i < y.size(); ++i){ | ~~^~~~~~~~~~ overdispersion.cpp: In instantiation of ‘Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]’: overdispersion.cpp:313:76: required from here overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){ | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp: In instantiation of ‘Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]’: overdispersion.cpp:315:76: required from here overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){ | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-glmGamPoi/00new/glmGamPoi/libs ** R ** 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 (glmGamPoi)
glmGamPoi.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(glmGamPoi) > > test_check("glmGamPoi") [ FAIL 1 | WARN 420 | SKIP 5 | PASS 444 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • Beta estimation is unprecise on Non-MacOS architectures (1): 'test-estimate_betas.R:228:3' • Printing tests should be run interactively (1): 'test-printing.R:1:1' • empty test (2): 'test-test_de.R:60:1', 'test-test_de.R:93:1' • isNamespaceLoaded("devtools") is not TRUE (1): 'test-glm_gp.R:413:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-residuals.R:48:3'): residual calculation works with Delayed Matrix ── <notSubsettableError/error/condition> Error in `.Primitive("[")(new("SparseArraySeed", dim = c(2L, 4L), nzindex = structure(integer(0), dim = c(0L, 2L)), nzdata = logical(0), dimnames = list(NULL, NULL)), , , drop = FALSE)`: object of type 'S4' is not subsettable Backtrace: ▆ 1. └─glmGamPoi::glm_gp(Y_hdf5, X, size_factors = FALSE, overdispersion = 1/0.7) at test-residuals.R:48:3 2. └─glmGamPoi:::glm_gp_impl(...) 3. └─glmGamPoi:::combine_size_factors_and_offset(...) 4. └─HDF5Array::writeHDF5Array(offset_matrix) 5. └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose) 6. └─DelayedArray::sinkApply(...) 7. └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose) 8. └─DelayedArray (local) FUN(viewport, init, ...) 9. └─DelayedArray (local) FUN(init, viewport, ...) 10. └─S4Arrays::read_block(x, viewport, as.sparse = NA) 11. └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse) 12. ├─SparseArray::read_block_as_sparse(x, viewport) 13. └─SparseArray::read_block_as_sparse(x, viewport) 14. ├─SparseArray::extract_sparse_array(x, Nindex) 15. └─DelayedArray::extract_sparse_array(x, Nindex) 16. ├─SparseArray::extract_sparse_array(x@seed, index) 17. └─DelayedArray::extract_sparse_array(x@seed, index) 18. ├─SparseArray::extract_sparse_array(x@seed, seed_index) 19. └─DelayedArray::extract_sparse_array(x@seed, seed_index) 20. ├─methods::as(extract_sparse_array(x@seed, index), "COO_SparseArray") 21. │ └─methods:::.class1(object) 22. ├─SparseArray::extract_sparse_array(x@seed, index) 23. └─DelayedArray::extract_sparse_array(x@seed, index) 24. ├─SparseArray::extract_sparse_array(x@seed, index) 25. └─DelayedArray::extract_sparse_array(x@seed, index) 26. ├─SparseArray::extract_sparse_array(x@seed, seed_index) 27. └─SparseArray::extract_sparse_array(x@seed, seed_index) 28. └─S4Arrays:::subset_by_Nindex(x, index) 29. ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop))) 30. └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop))) [ FAIL 1 | WARN 420 | SKIP 5 | PASS 444 ] Error: Test failures Execution halted
glmGamPoi.Rcheck/glmGamPoi-Ex.timings
name | user | system | elapsed | |
glm_gp | 1.174 | 0.040 | 1.214 | |
loc_median_fit | 0.071 | 0.005 | 0.076 | |
overdispersion_mle | 0.007 | 0.003 | 0.012 | |
overdispersion_shrinkage | 0.162 | 0.001 | 0.162 | |
predict.glmGamPoi | 0.066 | 0.008 | 0.074 | |
pseudobulk | 1.124 | 0.068 | 1.192 | |
test_de | 0.557 | 0.008 | 0.565 | |