Joshua Campbell
| Snapshot Date: 2025-11-16 13:40 -0500 (Sun, 16 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 2025-11-17 11:39 -0500 (Mon, 17 Nov 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 298/2325 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: 2025-11-17 01:43:48 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 01:53:43 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 595.2 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) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* 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 32.424 0.517 52.834
plotDimReduceGrid 19.176 0.179 19.394
plotDendro 16.010 0.465 16.493
findMarkersTree 15.783 0.325 16.135
plotMarkerHeatmap 15.158 0.350 15.535
recursiveSplitCell 13.131 0.307 13.466
decontX 12.378 0.168 12.580
recursiveSplitModule 9.318 0.233 9.572
plotDimReduceModule 6.575 0.073 6.665
plotDimReduceFeature 5.462 0.093 5.585
plotDimReduceCluster 5.160 0.088 5.276
sceCeldaCGGridSearch 0.289 0.016 45.967
* 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:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL celda
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘celda’ ...
** this is package ‘celda’ version ‘1.27.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixNorm.cpp -o matrixNorm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixSums.c -o matrixSums.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c perplexity.c -o perplexity.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.
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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
70.118 1.369 82.680
celda.Rcheck/celda-Ex.timings
| name | user | system | elapsed | |
| appendCeldaList | 0.006 | 0.003 | 0.009 | |
| bestLogLikelihood | 0.119 | 0.008 | 0.128 | |
| celda | 0.001 | 0.000 | 0.001 | |
| celdaClusters | 0.059 | 0.015 | 0.074 | |
| celdaGridSearch | 0.000 | 0.000 | 0.001 | |
| celdaHeatmap | 0.592 | 0.044 | 0.637 | |
| celdaModel | 0.084 | 0.004 | 0.088 | |
| celdaModules | 0.062 | 0.003 | 0.065 | |
| celdaPerplexity-celdaList-method | 0.002 | 0.002 | 0.004 | |
| celdaPerplexity | 0.001 | 0.002 | 0.004 | |
| celdaProbabilityMap | 3.421 | 0.079 | 3.506 | |
| celdaTsne | 2.342 | 0.065 | 2.420 | |
| celdaUmap | 3.640 | 0.068 | 3.709 | |
| celda_C | 0.425 | 0.008 | 0.434 | |
| celda_CG | 4.086 | 0.136 | 4.227 | |
| celda_G | 2.980 | 0.050 | 3.035 | |
| celdatosce | 0.792 | 0.028 | 0.825 | |
| clusterProbability | 0.397 | 0.014 | 0.412 | |
| compareCountMatrix | 0.009 | 0.008 | 0.016 | |
| countChecksum-celdaList-method | 0.003 | 0.002 | 0.005 | |
| countChecksum | 0.003 | 0.003 | 0.007 | |
| decontX | 12.378 | 0.168 | 12.580 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| factorizeMatrix | 0.269 | 0.013 | 0.282 | |
| featureModuleLookup | 0.159 | 0.003 | 0.162 | |
| featureModuleTable | 0.283 | 0.006 | 0.289 | |
| findMarkersTree | 15.783 | 0.325 | 16.135 | |
| geneSetEnrich | 32.424 | 0.517 | 52.834 | |
| logLikelihood | 0.577 | 0.008 | 0.585 | |
| logLikelihoodHistory | 0.052 | 0.007 | 0.059 | |
| matrixNames | 0.003 | 0.007 | 0.010 | |
| moduleHeatmap | 4.310 | 0.063 | 4.379 | |
| normalizeCounts | 0.003 | 0.003 | 0.006 | |
| params | 0.001 | 0.003 | 0.004 | |
| perplexity | 0.617 | 0.026 | 0.643 | |
| plotCeldaViolin | 0.998 | 0.021 | 1.020 | |
| plotDendro | 16.010 | 0.465 | 16.493 | |
| plotDimReduceCluster | 5.160 | 0.088 | 5.276 | |
| plotDimReduceFeature | 5.462 | 0.093 | 5.585 | |
| plotDimReduceGrid | 19.176 | 0.179 | 19.394 | |
| plotDimReduceModule | 6.575 | 0.073 | 6.665 | |
| plotGridSearchPerplexity | 0.969 | 0.011 | 0.982 | |
| plotHeatmap | 0.120 | 0.004 | 0.126 | |
| plotMarkerHeatmap | 15.158 | 0.350 | 15.535 | |
| plotRPC | 0.988 | 0.027 | 1.017 | |
| recodeClusterY | 0.211 | 0.005 | 0.215 | |
| recodeClusterZ | 0.196 | 0.005 | 0.202 | |
| recursiveSplitCell | 13.131 | 0.307 | 13.466 | |
| recursiveSplitModule | 9.318 | 0.233 | 9.572 | |
| reorderCelda | 1.133 | 0.021 | 1.157 | |
| reportceldaCG | 0.001 | 0.002 | 0.003 | |
| resList | 0.043 | 0.006 | 0.047 | |
| resamplePerplexity | 0.878 | 0.012 | 0.891 | |
| retrieveFeatureIndex | 0.002 | 0.003 | 0.005 | |
| runParams | 0.054 | 0.008 | 0.062 | |
| sampleLabel | 0.063 | 0.018 | 0.080 | |
| sceCeldaC | 0.343 | 0.008 | 0.352 | |
| sceCeldaCG | 3.532 | 0.087 | 3.623 | |
| sceCeldaCGGridSearch | 0.289 | 0.016 | 45.967 | |
| sceCeldaG | 0.780 | 0.021 | 0.802 | |
| selectBestModel | 0.159 | 0.007 | 0.166 | |
| selectFeatures | 0.217 | 0.007 | 0.224 | |
| simulateCells | 0.202 | 0.002 | 0.205 | |
| simulateContamination | 0.013 | 0.000 | 0.013 | |
| splitModule | 0.157 | 0.003 | 0.161 | |
| subsetCeldaList | 0.276 | 0.006 | 0.283 | |
| topRank | 0.002 | 0.004 | 0.007 | |