Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 140/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
batchelor 1.23.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the batchelor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/batchelor.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: batchelor |
Version: 1.23.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:batchelor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings batchelor_1.23.0.tar.gz |
StartedAt: 2024-12-24 03:51:37 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 04:00:05 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 507.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: batchelor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:batchelor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings batchelor_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/batchelor.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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 ‘batchelor/DESCRIPTION’ ... OK * this is package ‘batchelor’ version ‘1.23.0’ * 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 ‘batchelor’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BatchelorParam.Rd: SimpleList-class applyMultiSCE.Rd: applySCE, SingleCellExperiment, SingleCellExperiment-class, altExps, simplifyToSCE batchCorrect.Rd: SingleCellExperiment-class checkInputs.Rd: SingleCellExperiment-class clusterMNN.Rd: SingleCellExperiment-class, BiocSingularParam-class, BiocNeighborParam-class, BiocParallelParam-class, colData, metadata convertPCsToSCE.Rd: SingleCellExperiment-class, DataFrame-class, metadata, reducedDims, LowRankMatrix-class, colData, rowData correctExperiments.Rd: SingleCellExperiment-class, rowRanges, colData, mcols, assays, reducedDims, rowData, metadata cosineNorm.Rd: BiocParallelParam-class, DelayedArray-class, DelayedMatrix-class diagnostics-cluster.Rd: normalizeCounts fastMNN.Rd: SingleCellExperiment-class, BiocSingularParam-class, BiocNeighborParam-class, BiocParallelParam-class, DataFrame-class, List-class, altExps intersectRows.Rd: SingleCellExperiment-class mnnCorrect.Rd: SingleCellExperiment-class, BiocSingularParam-class, BiocNeighborParam-class, BiocParallelParam-class, List-class mnnDeltaVariance.Rd: SingleCellExperiment-class, DataFrame-class, BiocParallelParam-class, metadata multiBatchNorm.Rd: SingleCellExperiment-class, BiocParallelParam-class, logNormCounts, altExps multiBatchPCA.Rd: SingleCellExperiment-class, BiocSingularParam-class, runSVD, BiocParallelParam-class, List-class, IrlbaParam, RandomParam, bsdeferred noCorrect.Rd: SingleCellExperiment-class, colData quickCorrect.Rd: SingleCellExperiment-class, DataFrame, DataFrame-class reducedMNN.Rd: BiocNeighborParam-class, BiocParallelParam-class, DataFrame-class regressBatches.Rd: SingleCellExperiment-class, ResidualMatrix, BiocSingularParam-class, BiocParallelParam-class, ResidualMatrix-class, reducedDims, altExps rescaleBatches.Rd: SingleCellExperiment-class, altExps 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 line endings in C/C++/Fortran sources/headers ... 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 correctExperiments 9.332 0.039 9.431 applyMultiSCE 6.564 0.136 6.944 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/batchelor.Rcheck/00check.log’ for details.
batchelor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL batchelor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘batchelor’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++11 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c adjust_shift_variance.cpp -o adjust_shift_variance.o adjust_shift_variance.cpp: In function ‘Rcpp::NumericVector adjust_shift_variance(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::IntegerVector, Rcpp::IntegerVector)’: adjust_shift_variance.cpp:34:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (ngenes != data2.nrow() || ngenes != vect.ncol()) { | ~~~~~~~^~~~~~~~~~~~~~~ adjust_shift_variance.cpp:34:42: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (ngenes != data2.nrow() || ngenes != vect.ncol()) { | ~~~~~~~^~~~~~~~~~~~~~ adjust_shift_variance.cpp:39:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare] 39 | if (ncells != vect.nrow()) { | ~~~~~~~^~~~~~~~~~~~~~ adjust_shift_variance.cpp:118:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 118 | for (size_t other=0; other<restrict1.size(); ++other) { | ~~~~~^~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c find_mutual_nns.cpp -o find_mutual_nns.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o smooth_gaussian_kernel.cpp: In function ‘SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::NumericMatrix, double)’: smooth_gaussian_kernel.cpp:18:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 18 | if (nmnn!=index.size()) { | ~~~~^~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c utils.cpp -o utils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o batchelor.so RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-batchelor/00new/batchelor/libs ** R ** 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 (batchelor)
batchelor.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "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. > library(testthat) > library(batchelor) 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: 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 > test_check("batchelor") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep [ FAIL 0 | WARN 15 | SKIP 0 | PASS 1048 ] [ FAIL 0 | WARN 15 | SKIP 0 | PASS 1048 ] > > proc.time() user system elapsed 214.086 1.290 225.070
batchelor.Rcheck/batchelor-Ex.timings
name | user | system | elapsed | |
BatchelorParam | 0.143 | 0.000 | 0.143 | |
applyMultiSCE | 6.564 | 0.136 | 6.944 | |
batchCorrect | 1.828 | 0.008 | 2.022 | |
batchelor-restrict | 0.238 | 0.000 | 0.274 | |
checkInputs | 0.003 | 0.000 | 0.002 | |
clusterMNN | 3.628 | 0.020 | 3.690 | |
convertPCsToSCE | 0.988 | 0.000 | 0.997 | |
correctExperiments | 9.332 | 0.039 | 9.431 | |
cosineNorm | 0.012 | 0.000 | 0.013 | |
diagnostics-cluster | 1.600 | 0.003 | 1.611 | |
divideIntoBatches | 0.002 | 0.000 | 0.002 | |
fastMNN | 1.698 | 0.000 | 1.855 | |
intersectRows | 0.005 | 0.000 | 0.005 | |
mnnCorrect | 0.233 | 0.000 | 0.233 | |
mnnDeltaVariance | 2.352 | 0.020 | 2.377 | |
multiBatchNorm | 0.515 | 0.016 | 0.532 | |
multiBatchPCA | 1.956 | 0.000 | 1.968 | |
noCorrect | 0.094 | 0.000 | 0.093 | |
quickCorrect | 2.824 | 0.008 | 3.304 | |
reducedMNN | 0.831 | 0.000 | 0.833 | |
regressBatches | 0.082 | 0.004 | 0.086 | |
rescaleBatches | 0.105 | 0.000 | 0.105 | |