Joshua Campbell
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/celda |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7e5755c |
| git_last_commit_date: 2024-04-30 11:14:54 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:39 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 294/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| celda 1.20.0 (landing page) Joshua Campbell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.20.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings celda_1.20.0.tar.gz |
| StartedAt: 2024-05-09 05:38:28 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 05:49:00 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 632.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: celda.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:celda.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings celda_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/celda.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.20.0’
* 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 installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
libs 9.7Mb
* 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 41.172 0.328 41.588
plotDimReduceGrid 25.672 0.184 25.907
recursiveSplitCell 21.425 0.167 21.541
decontX 13.951 0.199 14.183
recursiveSplitModule 12.449 0.045 12.495
plotDimReduceModule 11.437 0.032 11.492
plotDimReduceFeature 10.487 0.035 10.544
plotDimReduceCluster 10.394 0.055 10.472
celda_CG 6.957 0.132 7.103
sceCeldaCG 6.839 0.008 6.837
moduleHeatmap 5.901 0.027 5.937
sceCeldaCGGridSearch 0.591 0.049 70.679
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/celda.Rcheck/00check.log’
for details.
celda.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL celda
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c eigenMatMultInt.cpp -o eigenMatMultInt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c matrixSums.c -o matrixSums.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c perplexity.c -o perplexity.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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 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
88.908 1.883 102.594
celda.Rcheck/celda-Ex.timings
| name | user | system | elapsed | |
| appendCeldaList | 0.002 | 0.004 | 0.006 | |
| bestLogLikelihood | 0.137 | 0.000 | 0.137 | |
| celda | 0.001 | 0.000 | 0.001 | |
| celdaClusters | 0.096 | 0.000 | 0.096 | |
| celdaGridSearch | 0 | 0 | 0 | |
| celdaHeatmap | 0.642 | 0.100 | 0.743 | |
| celdaModel | 0.094 | 0.004 | 0.098 | |
| celdaModules | 0.056 | 0.012 | 0.068 | |
| celdaPerplexity-celdaList-method | 0.002 | 0.000 | 0.003 | |
| celdaPerplexity | 0.002 | 0.000 | 0.003 | |
| celdaProbabilityMap | 3.250 | 0.147 | 3.406 | |
| celdaTsne | 4.705 | 0.024 | 4.736 | |
| celdaUmap | 4.047 | 0.192 | 4.238 | |
| celda_C | 0.842 | 0.012 | 0.856 | |
| celda_CG | 6.957 | 0.132 | 7.103 | |
| celda_G | 3.903 | 0.048 | 3.959 | |
| celdatosce | 1.726 | 0.008 | 1.738 | |
| clusterProbability | 0.491 | 0.007 | 0.499 | |
| compareCountMatrix | 0.01 | 0.00 | 0.01 | |
| countChecksum-celdaList-method | 0.002 | 0.000 | 0.002 | |
| countChecksum | 0.002 | 0.000 | 0.002 | |
| decontX | 13.951 | 0.199 | 14.183 | |
| distinctColors | 0 | 0 | 0 | |
| factorizeMatrix | 0.318 | 0.008 | 0.326 | |
| featureModuleLookup | 0.220 | 0.000 | 0.221 | |
| featureModuleTable | 0.329 | 0.016 | 0.346 | |
| geneSetEnrich | 41.172 | 0.328 | 41.588 | |
| logLikelihood | 0.719 | 0.004 | 0.724 | |
| logLikelihoodHistory | 0.053 | 0.002 | 0.055 | |
| matrixNames | 0.000 | 0.003 | 0.003 | |
| moduleHeatmap | 5.901 | 0.027 | 5.937 | |
| normalizeCounts | 0.000 | 0.003 | 0.003 | |
| params | 0.002 | 0.000 | 0.002 | |
| perplexity | 0.636 | 0.024 | 0.661 | |
| plotCeldaViolin | 0.937 | 0.012 | 0.952 | |
| plotDimReduceCluster | 10.394 | 0.055 | 10.472 | |
| plotDimReduceFeature | 10.487 | 0.035 | 10.544 | |
| plotDimReduceGrid | 25.672 | 0.184 | 25.907 | |
| plotDimReduceModule | 11.437 | 0.032 | 11.492 | |
| plotGridSearchPerplexity | 1.079 | 0.008 | 1.083 | |
| plotHeatmap | 0.170 | 0.000 | 0.171 | |
| plotRPC | 0.892 | 0.012 | 0.900 | |
| recodeClusterY | 0.293 | 0.000 | 0.294 | |
| recodeClusterZ | 0.257 | 0.000 | 0.258 | |
| recursiveSplitCell | 21.425 | 0.167 | 21.541 | |
| recursiveSplitModule | 12.449 | 0.045 | 12.495 | |
| reorderCelda | 2.012 | 0.000 | 2.016 | |
| reportceldaCG | 0.000 | 0.001 | 0.001 | |
| resList | 0.059 | 0.002 | 0.061 | |
| resamplePerplexity | 0.916 | 0.004 | 0.916 | |
| retrieveFeatureIndex | 0.003 | 0.000 | 0.003 | |
| runParams | 0.063 | 0.000 | 0.063 | |
| sampleLabel | 0.062 | 0.000 | 0.062 | |
| sceCeldaC | 0.721 | 0.004 | 0.722 | |
| sceCeldaCG | 6.839 | 0.008 | 6.837 | |
| sceCeldaCGGridSearch | 0.591 | 0.049 | 70.679 | |
| sceCeldaG | 1.272 | 0.120 | 1.395 | |
| selectBestModel | 0.215 | 0.004 | 0.219 | |
| selectFeatures | 0.426 | 0.020 | 0.447 | |
| simulateCells | 0.440 | 0.028 | 0.469 | |
| simulateContamination | 0.023 | 0.000 | 0.022 | |
| splitModule | 0.245 | 0.004 | 0.248 | |
| subsetCeldaList | 0.433 | 0.012 | 0.446 | |
| topRank | 0.002 | 0.000 | 0.003 | |