Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-10-25 11:41:17 -0400 (Wed, 25 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4727
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4465
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4476
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 290/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celda 1.18.0  (landing page)
Joshua Campbell
Snapshot Date: 2023-10-24 14:05:06 -0400 (Tue, 24 Oct 2023)
git_url: https://git.bioconductor.org/packages/celda
git_branch: RELEASE_3_18
git_last_commit: f35400e
git_last_commit_date: 2023-10-24 11:13:56 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  NO, package depends on 'multipanelfigure' which is not available
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'multipanelfigure' which is not available
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'multipanelfigure' which is not available
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for celda on kunpeng2


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: 1.18.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings celda_1.18.0.tar.gz
StartedAt: 2023-10-25 08:23:40 -0000 (Wed, 25 Oct 2023)
EndedAt: 2023-10-25 08:43:05 -0000 (Wed, 25 Oct 2023)
EllapsedTime: 1165.0 seconds
RetCode: 0
Status:   OK  
CheckDir: celda.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings celda_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/celda.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘celda/DESCRIPTION’ ... OK
* this is package ‘celda’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘celda’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
* 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 R 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking 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        47.538  0.328  47.975
plotDimReduceGrid    24.451  0.132  24.635
recursiveSplitCell   21.776  0.155  21.871
recursiveSplitModule 13.831  0.044  13.886
decontX              13.122  0.063  13.213
plotDimReduceModule  11.727  0.052  11.805
plotDimReduceCluster 10.803  0.035  10.861
plotDimReduceFeature 10.717  0.016  10.756
celda_CG              7.200  0.280   7.495
moduleHeatmap         6.100  0.047   6.151
sceCeldaCG            6.108  0.019   6.115
sceCeldaCGGridSearch  0.636  0.173  69.969
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘celda.Rmd’ using ‘UTF-8’... OK
  ‘decontX.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/celda.Rcheck/00check.log’
for details.



Installation output

celda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL celda
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘celda’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c DecontX.cpp -o DecontX.o
DecontX.cpp: In function ‘Eigen::SparseMatrix<double, 0, int> calculateNativeMatrix(const Eigen::MappedSparseMatrix<double>&, const NumericVector&, const NumericMatrix&, const NumericMatrix&, const IntegerVector&, const double&)’:
DecontX.cpp:321:10: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
  321 |   double x;
      |          ^
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c eigenMatMultInt.cpp -o eigenMatMultInt.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c matrixNorm.cpp -o matrixNorm.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c matrixSums.c -o matrixSums.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -c matrixSumsSparse.cpp -o matrixSumsSparse.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c perplexity.c -o perplexity.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/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 -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

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 
 94.928   2.192 109.362 

Example timings

celda.Rcheck/celda-Ex.timings

nameusersystemelapsed
appendCeldaList0.0070.0000.007
bestLogLikelihood0.1280.0220.150
celda000
celdaClusters0.1350.0000.135
celdaGridSearch000
celdaHeatmap0.7240.0030.729
celdaModel0.1000.0010.100
celdaModules0.0720.0000.072
celdaPerplexity-celdaList-method0.0170.0000.017
celdaPerplexity0.0000.0030.003
celdaProbabilityMap3.4110.0483.466
celdaTsne4.8690.0164.894
celdaUmap4.3210.1844.506
celda_C0.8760.0000.878
celda_CG7.2000.2807.495
celda_G4.3030.0404.353
celdatosce1.8470.0041.855
clusterProbability0.5420.0040.547
compareCountMatrix0.0080.0040.011
countChecksum-celdaList-method0.0030.0000.003
countChecksum0.0030.0000.003
decontX13.122 0.06313.213
distinctColors0.0010.0000.001
factorizeMatrix0.3540.0040.359
featureModuleLookup0.2470.0000.248
featureModuleTable0.3850.0000.386
geneSetEnrich47.538 0.32847.975
logLikelihood0.8800.0040.885
logLikelihoodHistory0.0650.0000.065
matrixNames0.0030.0000.003
moduleHeatmap6.1000.0476.151
normalizeCounts0.0040.0000.004
params0.0020.0000.002
perplexity0.6360.0040.640
plotCeldaViolin1.1180.0041.125
plotDimReduceCluster10.803 0.03510.861
plotDimReduceFeature10.717 0.01610.756
plotDimReduceGrid24.451 0.13224.635
plotDimReduceModule11.727 0.05211.805
plotGridSearchPerplexity1.2120.0081.215
plotHeatmap0.1640.0000.165
plotRPC0.9780.0040.978
recodeClusterY0.2980.0080.307
recodeClusterZ0.2670.0000.268
recursiveSplitCell21.776 0.15521.871
recursiveSplitModule13.831 0.04413.886
reorderCelda3.2440.0563.309
reportceldaCG0.0010.0000.001
resList0.0640.0000.065
resamplePerplexity1.0560.0001.052
retrieveFeatureIndex0.0000.0030.003
runParams0.0630.0050.067
sampleLabel0.0660.0000.066
sceCeldaC0.7700.0040.771
sceCeldaCG6.1080.0196.115
sceCeldaCGGridSearch 0.636 0.17369.969
sceCeldaG1.4350.1071.545
selectBestModel0.2180.0120.230
selectFeatures0.4410.0200.462
simulateCells0.4320.0280.460
simulateContamination0.0240.0000.024
splitModule0.2690.0160.286
subsetCeldaList0.4900.0120.503
topRank0.0020.0000.002