Joshua Campbell
| Snapshot Date: 2025-11-30 13:40 -0500 (Sun, 30 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/celda |
| git_branch: devel |
| git_last_commit: 9bcee6f |
| git_last_commit_date: 2025-10-29 10:52:12 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-01 11:35 -0500 (Mon, 01 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 299/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| celda 1.27.0 (landing page) Joshua Campbell
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: celda |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celda_1.27.0.tar.gz |
| StartedAt: 2025-11-30 18:56:14 -0500 (Sun, 30 Nov 2025) |
| EndedAt: 2025-11-30 19:00:13 -0500 (Sun, 30 Nov 2025) |
| EllapsedTime: 239.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: celda.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celda_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/celda.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘celda/DESCRIPTION’ ... OK
* this is package ‘celda’ version ‘1.27.0’
* 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 ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 ... 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 ... INFO
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 9.764 0.263 26.328
plotDimReduceGrid 6.946 0.110 7.427
findMarkersTree 5.896 0.191 6.654
plotDendro 5.714 0.217 6.489
plotMarkerHeatmap 5.457 0.207 6.439
sceCeldaCGGridSearch 0.093 0.008 17.334
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/celda.Rcheck/00check.log’
for details.
celda.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL celda
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘celda’ ...
** this is package ‘celda’ version ‘1.27.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecontX.cpp -o DecontX.o
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
DecontX.cpp:321:10: warning: variable 'x' set but not used [-Wunused-but-set-variable]
double x;
^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c eigenMatMultInt.cpp -o eigenMatMultInt.o
In file included from eigenMatMultInt.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from eigenMatMultInt.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from eigenMatMultInt.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from eigenMatMultInt.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixNorm.cpp -o matrixNorm.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixSums.c -o matrixSums.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixSumsSparse.cpp -o matrixSumsSparse.o
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c perplexity.c -o perplexity.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o celda.so DecontX.o RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o matrixSumsSparse.o perplexity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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.
> 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
29.196 0.431 35.399
celda.Rcheck/celda-Ex.timings
| name | user | system | elapsed | |
| appendCeldaList | 0.002 | 0.002 | 0.003 | |
| bestLogLikelihood | 0.032 | 0.002 | 0.034 | |
| celda | 0.001 | 0.000 | 0.001 | |
| celdaClusters | 0.014 | 0.005 | 0.020 | |
| celdaGridSearch | 0.000 | 0.001 | 0.000 | |
| celdaHeatmap | 0.171 | 0.011 | 0.194 | |
| celdaModel | 0.022 | 0.001 | 0.027 | |
| celdaModules | 0.016 | 0.002 | 0.018 | |
| celdaPerplexity-celdaList-method | 0.001 | 0.001 | 0.002 | |
| celdaPerplexity | 0.001 | 0.002 | 0.003 | |
| celdaProbabilityMap | 1.188 | 0.029 | 1.300 | |
| celdaTsne | 1.039 | 0.074 | 1.202 | |
| celdaUmap | 1.825 | 0.035 | 2.313 | |
| celda_C | 0.137 | 0.004 | 0.159 | |
| celda_CG | 1.407 | 0.053 | 1.573 | |
| celda_G | 0.845 | 0.025 | 0.944 | |
| celdatosce | 0.226 | 0.011 | 0.254 | |
| clusterProbability | 0.116 | 0.006 | 0.130 | |
| compareCountMatrix | 0.004 | 0.003 | 0.006 | |
| countChecksum-celdaList-method | 0.000 | 0.001 | 0.002 | |
| countChecksum | 0.000 | 0.001 | 0.002 | |
| decontX | 4.162 | 0.060 | 4.536 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| factorizeMatrix | 0.084 | 0.004 | 0.098 | |
| featureModuleLookup | 0.061 | 0.002 | 0.063 | |
| featureModuleTable | 0.078 | 0.003 | 0.087 | |
| findMarkersTree | 5.896 | 0.191 | 6.654 | |
| geneSetEnrich | 9.764 | 0.263 | 26.328 | |
| logLikelihood | 0.178 | 0.003 | 0.192 | |
| logLikelihoodHistory | 0.013 | 0.003 | 0.016 | |
| matrixNames | 0.001 | 0.002 | 0.003 | |
| moduleHeatmap | 1.406 | 0.029 | 1.554 | |
| normalizeCounts | 0.001 | 0.001 | 0.002 | |
| params | 0.000 | 0.002 | 0.002 | |
| perplexity | 0.141 | 0.006 | 0.166 | |
| plotCeldaViolin | 0.300 | 0.007 | 0.314 | |
| plotDendro | 5.714 | 0.217 | 6.489 | |
| plotDimReduceCluster | 2.235 | 0.074 | 2.460 | |
| plotDimReduceFeature | 2.326 | 0.075 | 2.579 | |
| plotDimReduceGrid | 6.946 | 0.110 | 7.427 | |
| plotDimReduceModule | 3.280 | 0.049 | 3.473 | |
| plotGridSearchPerplexity | 0.752 | 0.024 | 0.848 | |
| plotHeatmap | 0.039 | 0.005 | 0.052 | |
| plotMarkerHeatmap | 5.457 | 0.207 | 6.439 | |
| plotRPC | 0.305 | 0.022 | 0.341 | |
| recodeClusterY | 0.065 | 0.002 | 0.067 | |
| recodeClusterZ | 0.056 | 0.001 | 0.063 | |
| recursiveSplitCell | 3.920 | 0.175 | 4.493 | |
| recursiveSplitModule | 2.815 | 0.159 | 3.231 | |
| reorderCelda | 0.338 | 0.014 | 0.370 | |
| reportceldaCG | 0.000 | 0.001 | 0.001 | |
| resList | 0.014 | 0.002 | 0.017 | |
| resamplePerplexity | 0.271 | 0.005 | 0.304 | |
| retrieveFeatureIndex | 0.001 | 0.001 | 0.002 | |
| runParams | 0.015 | 0.003 | 0.018 | |
| sampleLabel | 0.015 | 0.004 | 0.018 | |
| sceCeldaC | 0.104 | 0.005 | 0.114 | |
| sceCeldaCG | 1.159 | 0.055 | 1.292 | |
| sceCeldaCGGridSearch | 0.093 | 0.008 | 17.334 | |
| sceCeldaG | 0.251 | 0.015 | 0.281 | |
| selectBestModel | 0.050 | 0.002 | 0.053 | |
| selectFeatures | 0.071 | 0.003 | 0.079 | |
| simulateCells | 0.058 | 0.002 | 0.063 | |
| simulateContamination | 0.005 | 0.000 | 0.005 | |
| splitModule | 0.059 | 0.002 | 0.063 | |
| subsetCeldaList | 0.086 | 0.003 | 0.091 | |
| topRank | 0.001 | 0.001 | 0.002 | |