Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:24 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 292/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
celda 1.19.1 (landing page) Joshua Campbell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the celda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/celda.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: celda |
Version: 1.19.1 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings celda_1.19.1.tar.gz |
StartedAt: 2024-03-28 03:38:33 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 03:49:07 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 634.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: celda.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings celda_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/celda.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * 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 * using option ‘--no-vignettes’ * checking for file ‘celda/DESCRIPTION’ ... OK * this is package ‘celda’ version ‘1.19.1’ * 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 11.3Mb sub-directories of 1Mb or more: libs 9.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking Rd files ... NOTE checkRd: (-1) semiPheatmap.Rd:319-323: Lost braces 319 | callback = function(hc, mat) { | ^ * 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 41.708 0.379 42.180 plotDimReduceGrid 25.219 0.168 25.444 recursiveSplitCell 20.614 0.147 20.694 decontX 12.957 0.244 13.227 recursiveSplitModule 12.788 0.076 12.871 plotDimReduceModule 11.443 0.036 11.500 plotDimReduceCluster 11.146 0.139 11.310 plotDimReduceFeature 10.366 0.028 10.417 celda_CG 7.016 0.136 7.168 sceCeldaCG 6.153 0.032 6.172 moduleHeatmap 6.043 0.044 6.106 sceCeldaCGGridSearch 0.644 0.010 70.798 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: params [ FAIL 1 | WARN 1 | SKIP 2 | PASS 100 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-celda_CG.R:200:5'): Testing plotCeldaViolin with celda_CG ──── names(violin) not equal to c(...). Lengths differ: 11 is not 9 [ FAIL 1 | WARN 1 | SKIP 2 | PASS 100 ] Error: Test failures Execution halted * 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 ERROR, 5 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/celda.Rcheck/00check.log’ for details.
celda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL celda ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-celda/00new/celda/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (celda)
celda.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.unsetenv("R_TESTS") > library(testthat) > test_check("celda") Loading required package: celda Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics 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, 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 1 | WARN 1 | SKIP 2 | PASS 100 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-celda_CG.R:200:5'): Testing plotCeldaViolin with celda_CG ──── names(violin) not equal to c(...). Lengths differ: 11 is not 9 [ FAIL 1 | WARN 1 | SKIP 2 | PASS 100 ] Error: Test failures Execution halted
celda.Rcheck/celda-Ex.timings
name | user | system | elapsed | |
appendCeldaList | 0.006 | 0.000 | 0.007 | |
bestLogLikelihood | 0.14 | 0.00 | 0.14 | |
celda | 0.001 | 0.000 | 0.001 | |
celdaClusters | 0.095 | 0.006 | 0.101 | |
celdaGridSearch | 0 | 0 | 0 | |
celdaHeatmap | 0.709 | 0.060 | 0.772 | |
celdaModel | 0.096 | 0.004 | 0.100 | |
celdaModules | 0.063 | 0.007 | 0.071 | |
celdaPerplexity-celdaList-method | 0.003 | 0.000 | 0.003 | |
celdaPerplexity | 0.001 | 0.001 | 0.002 | |
celdaProbabilityMap | 3.345 | 0.141 | 3.501 | |
celdaTsne | 4.660 | 0.044 | 4.715 | |
celdaUmap | 4.242 | 0.136 | 4.382 | |
celda_C | 0.809 | 0.032 | 0.843 | |
celda_CG | 7.016 | 0.136 | 7.168 | |
celda_G | 3.954 | 0.067 | 4.031 | |
celdatosce | 1.682 | 0.008 | 1.694 | |
clusterProbability | 0.506 | 0.004 | 0.510 | |
compareCountMatrix | 0.011 | 0.000 | 0.010 | |
countChecksum-celdaList-method | 0.003 | 0.000 | 0.003 | |
countChecksum | 0.003 | 0.000 | 0.003 | |
decontX | 12.957 | 0.244 | 13.227 | |
distinctColors | 0 | 0 | 0 | |
factorizeMatrix | 0.317 | 0.008 | 0.325 | |
featureModuleLookup | 0.206 | 0.004 | 0.209 | |
featureModuleTable | 0.326 | 0.000 | 0.326 | |
geneSetEnrich | 41.708 | 0.379 | 42.180 | |
logLikelihood | 0.769 | 0.000 | 0.770 | |
logLikelihoodHistory | 0.058 | 0.000 | 0.057 | |
matrixNames | 0.003 | 0.000 | 0.003 | |
moduleHeatmap | 6.043 | 0.044 | 6.106 | |
normalizeCounts | 0.003 | 0.000 | 0.003 | |
params | 0.001 | 0.000 | 0.002 | |
perplexity | 0.594 | 0.000 | 0.595 | |
plotCeldaViolin | 0.983 | 0.020 | 1.005 | |
plotDimReduceCluster | 11.146 | 0.139 | 11.310 | |
plotDimReduceFeature | 10.366 | 0.028 | 10.417 | |
plotDimReduceGrid | 25.219 | 0.168 | 25.444 | |
plotDimReduceModule | 11.443 | 0.036 | 11.500 | |
plotGridSearchPerplexity | 1.065 | 0.004 | 1.064 | |
plotHeatmap | 0.165 | 0.000 | 0.165 | |
plotRPC | 0.982 | 0.008 | 0.985 | |
recodeClusterY | 0.258 | 0.008 | 0.267 | |
recodeClusterZ | 0.251 | 0.016 | 0.267 | |
recursiveSplitCell | 20.614 | 0.147 | 20.694 | |
recursiveSplitModule | 12.788 | 0.076 | 12.871 | |
reorderCelda | 2.059 | 0.000 | 2.064 | |
reportceldaCG | 0.000 | 0.001 | 0.001 | |
resList | 0.056 | 0.002 | 0.059 | |
resamplePerplexity | 0.965 | 0.000 | 0.960 | |
retrieveFeatureIndex | 0.003 | 0.000 | 0.003 | |
runParams | 0.067 | 0.000 | 0.067 | |
sampleLabel | 0.066 | 0.000 | 0.066 | |
sceCeldaC | 0.771 | 0.000 | 0.767 | |
sceCeldaCG | 6.153 | 0.032 | 6.172 | |
sceCeldaCGGridSearch | 0.644 | 0.010 | 70.798 | |
sceCeldaG | 1.344 | 0.000 | 1.347 | |
selectBestModel | 0.213 | 0.003 | 0.216 | |
selectFeatures | 0.465 | 0.004 | 0.470 | |
simulateCells | 0.445 | 0.004 | 0.449 | |
simulateContamination | 0.022 | 0.000 | 0.022 | |
splitModule | 0.282 | 0.000 | 0.283 | |
subsetCeldaList | 0.491 | 0.000 | 0.492 | |
topRank | 0.003 | 0.000 | 0.003 | |