Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 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 136/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
batchelor 1.21.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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. |
Package: batchelor |
Version: 1.21.1 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:batchelor.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings batchelor_1.21.1.tar.gz |
StartedAt: 2024-07-15 21:56:18 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 22:03:01 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 403.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: batchelor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:batchelor.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings batchelor_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/batchelor.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'batchelor/DESCRIPTION' ... OK * this is package 'batchelor' version '1.21.1' * 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 whether package 'batchelor' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/batchelor/libs/x64/batchelor.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed applyMultiSCE 7.19 0.24 7.44 correctExperiments 6.38 0.17 6.63 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/batchelor.Rcheck/00check.log' for details.
batchelor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL batchelor ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'batchelor' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 118 | for (size_t other=0; other<restrict1.size(); ++other) { | ~~~~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_mutual_nns.cpp -o find_mutual_nns.o g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 18 | if (nmnn!=index.size()) { | ~~~~^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -shared -s -static-libgcc -o batchelor.dll tmp.def RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-batchelor/00new/batchelor/libs/x64 ** 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 ** 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 22 | SKIP 0 | PASS 1024 ] [ FAIL 0 | WARN 22 | SKIP 0 | PASS 1024 ] > > proc.time() user system elapsed 190.51 5.21 195.85
batchelor.Rcheck/batchelor-Ex.timings
name | user | system | elapsed | |
BatchelorParam | 0.06 | 0.01 | 0.08 | |
applyMultiSCE | 7.19 | 0.24 | 7.44 | |
batchCorrect | 1.24 | 0.04 | 1.29 | |
batchelor-restrict | 0.25 | 0.00 | 0.25 | |
checkInputs | 0 | 0 | 0 | |
clusterMNN | 3.04 | 0.08 | 3.13 | |
convertPCsToSCE | 0.61 | 0.00 | 0.61 | |
correctExperiments | 6.38 | 0.17 | 6.63 | |
cosineNorm | 0.01 | 0.00 | 0.01 | |
diagnostics-cluster | 0.91 | 0.05 | 0.96 | |
divideIntoBatches | 0 | 0 | 0 | |
fastMNN | 0.95 | 0.02 | 0.96 | |
intersectRows | 0 | 0 | 0 | |
mnnCorrect | 0.24 | 0.00 | 0.24 | |
mnnDeltaVariance | 1.39 | 0.00 | 1.39 | |
multiBatchNorm | 0.64 | 0.00 | 0.64 | |
multiBatchPCA | 1.67 | 0.00 | 2.00 | |
noCorrect | 0.11 | 0.00 | 0.11 | |
quickCorrect | 2.09 | 0.03 | 2.12 | |
reducedMNN | 0.5 | 0.0 | 0.5 | |
regressBatches | 0.11 | 0.00 | 0.11 | |
rescaleBatches | 0.13 | 0.00 | 0.13 | |