Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 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" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1238/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miloR 2.1.0 (landing page) Mike Morgan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the miloR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.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: miloR |
Version: 2.1.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miloR_2.1.0.tar.gz |
StartedAt: 2024-07-16 01:44:59 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 01:53:20 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 501.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miloR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miloR_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'miloR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'miloR' version '2.1.0' * 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 whether package 'miloR' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... NOTE Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotDAbeeswarm: no visible binding for global variable 'SpatialFDR' plotDAbeeswarm: no visible binding for global variable 'logFC' plotDAbeeswarm: no visible binding for global variable 'is_signif' plotDAbeeswarm: no visible binding for global variable 'Nhood' plotDAbeeswarm: no visible binding for global variable 'logFC_color' plotNhoodCounts: no visible binding for global variable 'cond' plotNhoodCounts: no visible binding for global variable 'values' plotNhoodCounts: no visible binding for global variable 'y' plotNhoodExpressionDA: no visible binding for global variable 'Nhood' plotNhoodExpressionDA: no visible binding for global variable 'logFC' plotNhoodExpressionDA: no visible binding for global variable 'SpatialFDR' plotNhoodExpressionDA: no visible binding for global variable 'logFC_rank' plotNhoodExpressionDA: no visible binding for global variable '.' plotNhoodExpressionDA: no visible binding for global variable 'is_signif' plotNhoodExpressionDA: no visible binding for global variable 'feature' plotNhoodExpressionDA: no visible binding for global variable 'avg_expr' plotNhoodExpressionDA: no visible binding for global variable 'label' plotNhoodExpressionGroups: no visible binding for global variable 'Nhood' plotNhoodExpressionGroups: no visible binding for global variable 'NhoodGroup' plotNhoodExpressionGroups: no visible binding for global variable 'logFC' plotNhoodExpressionGroups: no visible binding for global variable 'feature' plotNhoodExpressionGroups: no visible binding for global variable 'logFC_rank' plotNhoodExpressionGroups: no visible binding for global variable 'avg_expr' plotNhoodExpressionGroups: no visible binding for global variable '.' plotNhoodExpressionGroups: no visible binding for global variable 'label' plotNhoodGraph: no visible binding for global variable 'weight' plotNhoodGraph: no visible binding for global variable 'size' plotNhoodGraphDA: no visible binding for global variable 'layout' plotNhoodGroups: no visible binding for global variable 'layout' plotNhoodMA: no visible binding for global variable 'logCPM' plotNhoodMA: no visible binding for global variable 'logFC' plotNhoodMA: no visible binding for global variable 'Sig' plotNhoodSizeHist: no visible binding for global variable 'nh_size' testNhoods: no visible global function definition for 'type' Undefined global functions or variables: . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif label layout logCPM logFC logFC_color logFC_rank nh_size size type values weight y Consider adding importFrom("graphics", "layout") to your NAMESPACE file. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/miloR/libs/x64/miloR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck/00check.log' for details.
miloR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miloR ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'miloR' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeMatrices.cpp -o computeMatrices.o computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)': computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 135 | for(unsigned long k=0; k < stot; k++){ | ~~^~~~~~ computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 143 | for(int l=0; l < q; l++){ | ~~^~~ computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)': computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 327 | for(unsigned long k=0; k < stot; k++){ | ~~^~~~~~ computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 335 | for(int l=0; l < q; l++){ | ~~^~~ g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o fitGeneticPLGlmm.cpp: In function 'Rcpp::List fitGeneticPLGlmm(const arma::mat&, const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)': fitGeneticPLGlmm.cpp:197:10: warning: unused variable '_phi_est' [-Wunused-variable] 197 | bool _phi_est = true; // control if we re-estimate phi or not | ^~~~~~~~ g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitPLGlmm.cpp -o fitPLGlmm.o fitPLGlmm.cpp: In function 'Rcpp::List fitPLGlmm(const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)': fitPLGlmm.cpp:177:10: warning: unused variable '_phi_est' [-Wunused-variable] 177 | bool _phi_est = true; // control if we re-estimate phi or not | ^~~~~~~~ g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inference.cpp -o inference.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c invertPseudoVar.cpp -o invertPseudoVar.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multiP.cpp -o multiP.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c paramEst.cpp -o paramEst.o paramEst.cpp:46: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 46 | #pragma omp parallel for | paramEst.cpp:50: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 50 | #pragma omp parallel for | paramEst.cpp:257: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 257 | #pragma omp parallel for private(i, j, _ycovij) | paramEst.cpp:301: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 301 | #pragma omp parallel for private(i, j, _ycovij) | paramEst.cpp:380: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 380 | #pragma omp parallel for private(i, j, _ycovij) | paramEst.cpp:489: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 489 | #pragma omp parallel for private(i, j, _ycovij) | paramEst.cpp:714: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 714 | #pragma omp parallel for reduction(+:temp_value) | paramEst.cpp:729: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 729 | #pragma omp parallel for reduction(+:temp_value) | paramEst.cpp: In function 'arma::vec sigmaScoreREML_arma(const Rcpp::List&, const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const arma::mat&)': paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value] 29 | double rhs = 0.5 * mid1[0, 0]; | ^ paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)': paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 258 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 259 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable] 252 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable] 252 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable] 253 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&)': paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 302 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 303 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable] 294 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable] 294 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable] 295 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function 'arma::vec estHasemanElstonConstrained(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, arma::vec, const int&)': paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 381 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 382 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable] 373 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable] 373 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable] 374 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)': paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 490 | for (int i = 0; i < n; i++) { | ~~^~~ paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 491 | for (int j = i; j < n; j++) { | ~~^~~ paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable] 484 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable] 484 | unsigned int i, j; // Declare loop variables i and j for OpenMP | ^ paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable] 485 | double _ycovij; // Declare temp_value | ^~~~~~~ paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)': paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 549 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 559 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 587 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 623 | for(int i=0; i < m; i++){ | ~~^~~ paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable] 543 | unsigned int inner_count = 0; | ^~~~~~~~~~~ paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable] 544 | unsigned int outer_count = 0; | ^~~~~~~~~~~ paramEst.cpp: In function 'arma::mat vectoriseZ(const arma::mat&, const Rcpp::List&, const arma::mat&)': paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable] 688 | int j, k, l, a; | ^ paramEst.cpp: In function 'double phiLineSearch(double, double, double, const int&, const arma::vec&, const arma::mat&, double, const arma::vec&, const arma::vec&, const arma::vec&)': paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable] 866 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood; | ^~~~~~~~~~ paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable] 871 | bool comp_vals = false; | ^~~~~~~~~ g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pseudovarPartial.cpp -o pseudovarPartial.o pseudovarPartial.cpp:60: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 60 | #pragma omp parallel for reduction(+:temp_value) | pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)': pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 58 | for (int j = 0; j < n; j++) { | ~~^~~ pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 61 | for (int k = 0; k < n; k++) { | ~~^~~ pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 64 | for(int a=0; a < n; a++){ | ~~^~~ g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -s -static-libgcc -o miloR.dll tmp.def RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-miloR/00new/miloR/libs/x64 ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for 'graph' in package 'miloR' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (miloR)
miloR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(miloR) Loading required package: edgeR Loading required package: limma > require(mvtnorm) Loading required package: mvtnorm > require(scran) Loading required package: 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 object is masked from 'package:limma': plotMA 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, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 Attaching package: 'SingleCellExperiment' The following object is masked from 'package:edgeR': cpm Loading required package: scuttle > require(scater) Loading required package: scater Loading required package: ggplot2 Attaching package: 'scater' The following object is masked from 'package:limma': plotMDS > require(MASS) Loading required package: MASS > > test_check("miloR") A patchwork composed of 2 patches - Autotagging is turned off - Guides are collected Layout: 2 patch areas, spanning 2 columns and 1 rows t l b r 1: 1 1 1 1 2: 1 2 1 2 A patchwork composed of 2 patches - Autotagging is turned off - Guides are collected Layout: 2 patch areas, spanning 2 columns and 1 rows t l b r 1: 1 1 1 1 2: 1 2 1 2 Coefficients not estimable: ConditionA warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution [ FAIL 0 | WARN 0 | SKIP 0 | PASS 213 ] > > proc.time() user system elapsed 253.09 12.50 266.84
miloR.Rcheck/miloR-Ex.timings
name | user | system | elapsed | |
Milo | 1.50 | 0.03 | 1.53 | |
Satterthwaite_df | 0 | 0 | 0 | |
annotateNhoods | 0 | 0 | 0 | |
buildFromAdjacency | 1.10 | 0.05 | 1.13 | |
buildGraph | 0.53 | 0.05 | 0.57 | |
buildNhoodGraph | 0 | 0 | 0 | |
calcNhoodDistance | 1.17 | 0.04 | 1.22 | |
calcNhoodExpression | 0.80 | 0.02 | 0.81 | |
checkSeparation | 2.78 | 0.05 | 2.84 | |
computePvalue | 0 | 0 | 0 | |
countCells | 0.69 | 0.03 | 0.72 | |
findNhoodGroupMarkers | 0 | 0 | 0 | |
findNhoodMarkers | 3.50 | 0.07 | 3.56 | |
fitGLMM | 0.34 | 0.15 | 0.50 | |
fitGeneticPLGlmm | 0 | 0 | 0 | |
fitPLGlmm | 0 | 0 | 0 | |
glmmControl.defaults | 0 | 0 | 0 | |
graphSpatialFDR | 0 | 0 | 0 | |
initialiseG | 0.00 | 0.02 | 0.02 | |
initializeFullZ | 0 | 0 | 0 | |
makeNhoods | 0.49 | 0.03 | 0.52 | |
matrix.trace | 0 | 0 | 0 | |
methods | 0.37 | 0.02 | 0.40 | |
plotDAbeeswarm | 0 | 0 | 0 | |
plotNhoodCounts | 2.60 | 0.06 | 2.66 | |
plotNhoodExpressionDA | 0 | 0 | 0 | |
plotNhoodGraph | 0 | 0 | 0 | |
plotNhoodGraphDA | 0 | 0 | 0 | |
plotNhoodGroups | 0 | 0 | 0 | |
plotNhoodMA | 0 | 0 | 0 | |
plotNhoodSizeHist | 0.56 | 0.08 | 0.64 | |
sim_discrete | 0 | 0 | 0 | |
sim_family | 0 | 0 | 0 | |
sim_nbglmm | 0.02 | 0.00 | 0.02 | |
sim_trajectory | 0 | 0 | 0 | |
testDiffExp | 3.39 | 0.03 | 3.42 | |
testNhoods | 2.98 | 0.08 | 3.06 | |