Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 297/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
celda 1.25.0 (landing page) Joshua Campbell
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the celda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/celda.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: celda |
Version: 1.25.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings celda_1.25.0.tar.gz |
StartedAt: 2025-08-01 05:01:15 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 05:12:51 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 695.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: celda.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings celda_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/celda.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘celda/DESCRIPTION’ ... OK * this is package ‘celda’ version ‘1.25.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 32 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘celda’ can be installed ... WARNING Found the following significant warnings: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] See ‘/home/biocbuild/bbs-3.22-bioc/meat/celda.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 10.5Mb sub-directories of 1Mb or more: libs 8.9Mb * 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 ... NOTE .removeZeroVariance: no visible global function definition for ‘complete.cases’ .splitMetricIGpIGd: no visible global function definition for ‘model.matrix’ .splitMetricModF1: no visible global function definition for ‘model.matrix’ findMarkersTree: no visible global function definition for ‘Idents’ findMarkersTree: no visible global function definition for ‘RunUMAP’ findMarkersTree: no visible global function definition for ‘dendrapply’ plotDendro: no visible binding for global variable ‘xend’ plotDendro: no visible binding for global variable ‘y’ plotDendro: no visible binding for global variable ‘label’ plotMarkerHeatmap: no visible global function definition for ‘head’ plotMarkerHeatmap: no visible global function definition for ‘setNames’ Undefined global functions or variables: Idents RunUMAP complete.cases dendrapply head label model.matrix setNames xend y Consider adding importFrom("stats", "complete.cases", "dendrapply", "model.matrix", "setNames") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: bestLogLikelihood.Rd: SingleCellExperiment-class, altExp celdaClusters.Rd: SingleCellExperiment-class, altExp celdaGridSearch.Rd: SingleCellExperiment-class, assay, altExp, metadata celdaHeatmap.Rd: assay, altExp celdaModel.Rd: altExp celdaModules.Rd: SingleCellExperiment-class, altExp celdaProbabilityMap.Rd: assay, altExp celdaTsne.Rd: SingleCellExperiment-class, assay, altExp, reducedDim celdaUmap.Rd: assay, altExp, reducedDim celda_C.Rd: assay, altExp, SingleCellExperiment-class, metadata, colData celda_CG.Rd: assay, altExp, SingleCellExperiment-class, metadata, colData, rowData celda_G.Rd: assay, altExp, SingleCellExperiment-class, metadata, rowData celdatosce.Rd: SingleCellExperiment-class, assay, altExp, metadata, colData, rowData clusterProbability.Rd: SingleCellExperiment-class, assay, altExp decontX.Rd: SingleCellExperiment-class, Matrix decontXcounts.Rd: SingleCellExperiment-class, assay, assay<- factorizeMatrix.Rd: SingleCellExperiment-class, assay, altExp featureModuleLookup.Rd: SingleCellExperiment-class, altExp featureModuleTable.Rd: SingleCellExperiment-class, assay, altExp geneSetEnrich.Rd: SingleCellExperiment-class, assay, altExp logLikelihood.Rd: SingleCellExperiment-class, assay, altExp logLikelihoodHistory.Rd: SingleCellExperiment-class, altExp moduleHeatmap.Rd: SingleCellExperiment-class, assay, altExp perplexity.Rd: SingleCellExperiment-class, assay, altExp plotCeldaViolin.Rd: SingleCellExperiment-class, assay, altExp plotDecontXContamination.Rd: SingleCellExperiment-class plotDecontXMarkerExpression.Rd: SingleCellExperiment-class plotDecontXMarkerPercentage.Rd: SingleCellExperiment-class plotDimReduceCluster.Rd: SingleCellExperiment-class, altExp plotDimReduceFeature.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient2 plotDimReduceGrid.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient2 plotDimReduceModule.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient plotGridSearchPerplexity.Rd: SingleCellExperiment-class, altExp, geom_jitter plotRPC.Rd: SingleCellExperiment-class, altExp, geom_jitter recodeClusterY.Rd: SingleCellExperiment-class, rowData, altExp recodeClusterZ.Rd: SingleCellExperiment-class, colData, altExp recursiveSplitCell.Rd: SingleCellExperiment-class, assay, altExp, metadata recursiveSplitModule.Rd: SingleCellExperiment-class, assay, altExp, metadata reorderCelda.Rd: SingleCellExperiment-class, assay, altExp reportceldaCG.Rd: SingleCellExperiment-class, altExp, assay resList.Rd: SingleCellExperiment-class, altExp resamplePerplexity.Rd: SingleCellExperiment-class, assay, altExp retrieveFeatureIndex.Rd: SummarizedExperiment-class, SingleCellExperiment-class runParams.Rd: SingleCellExperiment-class, altExp sampleLabel.Rd: SingleCellExperiment-class, altExp sceCeldaC.Rd: SingleCellExperiment-class sceCeldaCG.Rd: SingleCellExperiment-class sceCeldaCGGridSearch.Rd: SingleCellExperiment-class sceCeldaG.Rd: SingleCellExperiment-class selectBestModel.Rd: SingleCellExperiment-class, altExp, metadata selectFeatures.Rd: SingleCellExperiment-class, altExp, assay, metadata simulateCells.Rd: SingleCellExperiment-class, metadata, colData, rowData splitModule.Rd: SingleCellExperiment-class, assay, altExp, rowData subsetCeldaList.Rd: SingleCellExperiment-class, altExp, metadata Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 LazyData ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed geneSetEnrich 44.331 0.259 78.660 plotDimReduceGrid 24.522 0.137 24.729 findMarkersTree 21.046 0.222 21.702 plotMarkerHeatmap 20.408 0.216 21.073 plotDendro 20.178 0.155 20.775 recursiveSplitCell 17.862 0.124 17.958 recursiveSplitModule 11.565 0.064 11.648 decontX 11.324 0.098 11.450 plotDimReduceModule 10.911 0.028 10.967 plotDimReduceFeature 8.760 0.040 8.826 plotDimReduceCluster 8.119 0.009 8.151 celda_CG 6.133 0.063 6.209 moduleHeatmap 5.801 0.025 5.848 sceCeldaCG 5.408 0.020 5.423 sceCeldaCGGridSearch 0.390 0.040 62.143 * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/celda.Rcheck/00check.log’ for details.
celda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL celda ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘celda’ ... ** this is package ‘celda’ version ‘1.25.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c DecontX.cpp -o DecontX.o In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25, from DecontX.cpp:1: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ DecontX.cpp: In function ‘Eigen::SparseMatrix<double, 0, int> calculateNativeMatrix(const Eigen::MappedSparseMatrix<double>&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::IntegerVector&, const double&)’: DecontX.cpp:321:10: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] 321 | double x; | ^ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c eigenMatMultInt.cpp -o eigenMatMultInt.o In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25, from eigenMatMultInt.cpp:3: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c matrixNorm.cpp -o matrixNorm.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c matrixSums.c -o matrixSums.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c matrixSumsSparse.cpp -o matrixSumsSparse.o In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25, from matrixSumsSparse.cpp:1: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c perplexity.c -o perplexity.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o celda.so DecontX.o RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o matrixSumsSparse.o perplexity.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-celda/00new/celda/libs ** R ** data *** moving datasets to lazyload DB ** 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 (celda)
celda.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > Sys.unsetenv("R_TESTS") > library(testthat) > test_check("celda") Loading required package: celda 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo 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: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'celda' The following object is masked from 'package:S4Vectors': params [ FAIL 0 | WARN 1 | SKIP 2 | PASS 101 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1' [ FAIL 0 | WARN 1 | SKIP 2 | PASS 101 ] > > proc.time() user system elapsed 72.488 1.103 86.051
celda.Rcheck/celda-Ex.timings
name | user | system | elapsed | |
appendCeldaList | 0.035 | 0.000 | 0.035 | |
bestLogLikelihood | 0.14 | 0.00 | 0.14 | |
celda | 0.001 | 0.000 | 0.001 | |
celdaClusters | 0.059 | 0.004 | 0.063 | |
celdaGridSearch | 0.001 | 0.000 | 0.000 | |
celdaHeatmap | 0.702 | 0.028 | 0.733 | |
celdaModel | 0.095 | 0.000 | 0.095 | |
celdaModules | 0.069 | 0.000 | 0.068 | |
celdaPerplexity-celdaList-method | 0.003 | 0.000 | 0.002 | |
celdaPerplexity | 0.003 | 0.000 | 0.002 | |
celdaProbabilityMap | 4.010 | 0.124 | 4.145 | |
celdaTsne | 4.427 | 0.044 | 4.483 | |
celdaUmap | 2.921 | 0.116 | 3.659 | |
celda_C | 0.564 | 0.004 | 0.569 | |
celda_CG | 6.133 | 0.063 | 6.209 | |
celda_G | 3.923 | 0.006 | 3.936 | |
celdatosce | 0.955 | 0.004 | 0.961 | |
clusterProbability | 0.506 | 0.000 | 0.508 | |
compareCountMatrix | 0.006 | 0.004 | 0.009 | |
countChecksum-celdaList-method | 0.002 | 0.000 | 0.003 | |
countChecksum | 0.002 | 0.000 | 0.003 | |
decontX | 11.324 | 0.098 | 11.450 | |
distinctColors | 0.001 | 0.000 | 0.001 | |
factorizeMatrix | 0.343 | 0.000 | 0.344 | |
featureModuleLookup | 0.226 | 0.004 | 0.231 | |
featureModuleTable | 0.357 | 0.000 | 0.357 | |
findMarkersTree | 21.046 | 0.222 | 21.702 | |
geneSetEnrich | 44.331 | 0.259 | 78.660 | |
logLikelihood | 0.832 | 0.000 | 0.836 | |
logLikelihoodHistory | 0.06 | 0.00 | 0.06 | |
matrixNames | 0.003 | 0.000 | 0.003 | |
moduleHeatmap | 5.801 | 0.025 | 5.848 | |
normalizeCounts | 0.003 | 0.000 | 0.003 | |
params | 0.001 | 0.000 | 0.001 | |
perplexity | 0.669 | 0.000 | 0.670 | |
plotCeldaViolin | 0.960 | 0.008 | 0.971 | |
plotDendro | 20.178 | 0.155 | 20.775 | |
plotDimReduceCluster | 8.119 | 0.009 | 8.151 | |
plotDimReduceFeature | 8.760 | 0.040 | 8.826 | |
plotDimReduceGrid | 24.522 | 0.137 | 24.729 | |
plotDimReduceModule | 10.911 | 0.028 | 10.967 | |
plotGridSearchPerplexity | 1.105 | 0.004 | 1.107 | |
plotHeatmap | 0.161 | 0.000 | 0.161 | |
plotMarkerHeatmap | 20.408 | 0.216 | 21.073 | |
plotRPC | 0.853 | 0.000 | 0.851 | |
recodeClusterY | 0.289 | 0.000 | 0.290 | |
recodeClusterZ | 0.264 | 0.000 | 0.265 | |
recursiveSplitCell | 17.862 | 0.124 | 17.958 | |
recursiveSplitModule | 11.565 | 0.064 | 11.648 | |
reorderCelda | 1.545 | 0.008 | 1.558 | |
reportceldaCG | 0.001 | 0.000 | 0.001 | |
resList | 0.063 | 0.000 | 0.063 | |
resamplePerplexity | 0.881 | 0.008 | 0.887 | |
retrieveFeatureIndex | 0.003 | 0.000 | 0.003 | |
runParams | 0.069 | 0.000 | 0.070 | |
sampleLabel | 0.07 | 0.00 | 0.07 | |
sceCeldaC | 0.495 | 0.000 | 0.493 | |
sceCeldaCG | 5.408 | 0.020 | 5.423 | |
sceCeldaCGGridSearch | 0.390 | 0.040 | 62.143 | |
sceCeldaG | 1.051 | 0.051 | 1.106 | |
selectBestModel | 0.209 | 0.039 | 0.250 | |
selectFeatures | 0.332 | 0.044 | 0.377 | |
simulateCells | 0.280 | 0.008 | 0.289 | |
simulateContamination | 0.021 | 0.000 | 0.020 | |
splitModule | 0.289 | 0.027 | 0.318 | |
subsetCeldaList | 0.442 | 0.047 | 0.490 | |
topRank | 0.000 | 0.002 | 0.003 | |