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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 297/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celda 1.25.0  (landing page)
Joshua Campbell
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/celda
git_branch: devel
git_last_commit: b623680
git_last_commit_date: 2025-04-15 11:46:22 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'scran' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for celda on taishan

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.

raw results


Summary

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

Command output

##############################################################################
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###
### 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.


Installation output

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)

Tests output

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

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> 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 

Example timings

celda.Rcheck/celda-Ex.timings

nameusersystemelapsed
appendCeldaList0.0350.0000.035
bestLogLikelihood0.140.000.14
celda0.0010.0000.001
celdaClusters0.0590.0040.063
celdaGridSearch0.0010.0000.000
celdaHeatmap0.7020.0280.733
celdaModel0.0950.0000.095
celdaModules0.0690.0000.068
celdaPerplexity-celdaList-method0.0030.0000.002
celdaPerplexity0.0030.0000.002
celdaProbabilityMap4.0100.1244.145
celdaTsne4.4270.0444.483
celdaUmap2.9210.1163.659
celda_C0.5640.0040.569
celda_CG6.1330.0636.209
celda_G3.9230.0063.936
celdatosce0.9550.0040.961
clusterProbability0.5060.0000.508
compareCountMatrix0.0060.0040.009
countChecksum-celdaList-method0.0020.0000.003
countChecksum0.0020.0000.003
decontX11.324 0.09811.450
distinctColors0.0010.0000.001
factorizeMatrix0.3430.0000.344
featureModuleLookup0.2260.0040.231
featureModuleTable0.3570.0000.357
findMarkersTree21.046 0.22221.702
geneSetEnrich44.331 0.25978.660
logLikelihood0.8320.0000.836
logLikelihoodHistory0.060.000.06
matrixNames0.0030.0000.003
moduleHeatmap5.8010.0255.848
normalizeCounts0.0030.0000.003
params0.0010.0000.001
perplexity0.6690.0000.670
plotCeldaViolin0.9600.0080.971
plotDendro20.178 0.15520.775
plotDimReduceCluster8.1190.0098.151
plotDimReduceFeature8.7600.0408.826
plotDimReduceGrid24.522 0.13724.729
plotDimReduceModule10.911 0.02810.967
plotGridSearchPerplexity1.1050.0041.107
plotHeatmap0.1610.0000.161
plotMarkerHeatmap20.408 0.21621.073
plotRPC0.8530.0000.851
recodeClusterY0.2890.0000.290
recodeClusterZ0.2640.0000.265
recursiveSplitCell17.862 0.12417.958
recursiveSplitModule11.565 0.06411.648
reorderCelda1.5450.0081.558
reportceldaCG0.0010.0000.001
resList0.0630.0000.063
resamplePerplexity0.8810.0080.887
retrieveFeatureIndex0.0030.0000.003
runParams0.0690.0000.070
sampleLabel0.070.000.07
sceCeldaC0.4950.0000.493
sceCeldaCG5.4080.0205.423
sceCeldaCGGridSearch 0.390 0.04062.143
sceCeldaG1.0510.0511.106
selectBestModel0.2090.0390.250
selectFeatures0.3320.0440.377
simulateCells0.2800.0080.289
simulateContamination0.0210.0000.020
splitModule0.2890.0270.318
subsetCeldaList0.4420.0470.490
topRank0.0000.0020.003