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 527/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DelayedMatrixStats 1.29.0 (landing page) Peter Hickey
| 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 DelayedMatrixStats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedMatrixStats.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: DelayedMatrixStats |
Version: 1.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DelayedMatrixStats_1.29.0.tar.gz |
StartedAt: 2024-12-24 06:01:45 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:08:36 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 411.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DelayedMatrixStats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DelayedMatrixStats_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DelayedMatrixStats.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 ‘DelayedMatrixStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DelayedMatrixStats’ version ‘1.29.0’ * 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 ‘DelayedMatrixStats’ can be installed ... OK * 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 ... NOTE Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’ Unexported objects imported by ':::' calls: ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’ ‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’ ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’ ‘DelayedArray:::to_linear_index’ See the note in ?`:::` about the use of this operator. * 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: colAlls.Rd: DelayedMatrix-class colAnyNAs.Rd: DelayedMatrix-class colAvgsPerRowSet.Rd: DelayedMatrix-class colCollapse.Rd: DelayedMatrix-class colCounts.Rd: DelayedMatrix-class colCummaxs.Rd: DelayedMatrix-class colDiffs.Rd: DelayedMatrix-class colIQRDiffs.Rd: DelayedMatrix-class colIQRs.Rd: DelayedMatrix-class colLogSumExps.Rd: DelayedMatrix-class colMads.Rd: DelayedMatrix-class colMeans2.Rd: DelayedMatrix-class colMedians.Rd: DelayedMatrix-class colOrderStats.Rd: DelayedMatrix-class colProds.Rd: DelayedMatrix-class colQuantiles.Rd: DelayedMatrix-class colRanks.Rd: DelayedMatrix-class colSums2.Rd: DelayedMatrix-class colTabulates.Rd: DelayedMatrix-class colVars.Rd: DelayedMatrix-class colWeightedMads.Rd: DelayedMatrix-class colWeightedMeans.Rd: DelayedMatrix-class colWeightedMedians.Rd: DelayedMatrix-class colWeightedVars.Rd: DelayedMatrix-class from_DelayedArray_to_simple_seed_class.Rd: DelayedArray-class 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/DelayedMatrixStats.Rcheck/00check.log’ for details.
DelayedMatrixStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DelayedMatrixStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘DelayedMatrixStats’ ... ** using staged installation ** 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 (DelayedMatrixStats)
DelayedMatrixStats.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(DelayedMatrixStats) 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: DelayedArray Loading required package: stats4 Loading required package: Matrix 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 objects are masked from 'package:Matrix': expand, unname 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: 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 > > test_check("DelayedMatrixStats") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14108 ] > > proc.time() user system elapsed 242.499 7.475 254.945
DelayedMatrixStats.Rcheck/DelayedMatrixStats-Ex.timings
name | user | system | elapsed | |
colAlls | 0.119 | 0.004 | 0.123 | |
colAnyNAs | 1.165 | 0.008 | 1.176 | |
colAvgsPerRowSet | 0.292 | 0.028 | 0.320 | |
colCollapse | 0.129 | 0.020 | 0.149 | |
colCounts | 0.123 | 0.020 | 0.143 | |
colCummaxs | 0.139 | 0.004 | 0.143 | |
colDiffs | 0.140 | 0.004 | 0.145 | |
colIQRDiffs | 0.141 | 0.000 | 0.141 | |
colIQRs | 0.006 | 0.004 | 0.010 | |
colLogSumExps | 0.03 | 0.00 | 0.03 | |
colMads | 0.136 | 0.000 | 0.138 | |
colMeans2 | 0.032 | 0.000 | 0.032 | |
colMedians | 0.027 | 0.000 | 0.026 | |
colOrderStats | 0.071 | 0.000 | 0.072 | |
colProds | 0.102 | 0.004 | 0.107 | |
colQuantiles | 0.031 | 0.000 | 0.031 | |
colRanks | 0.025 | 0.000 | 0.025 | |
colSums2 | 0.017 | 0.000 | 0.017 | |
colTabulates | 0.155 | 0.012 | 0.167 | |
colVars | 0.086 | 0.008 | 0.094 | |
colWeightedMads | 0.005 | 0.000 | 0.006 | |
colWeightedMeans | 0.048 | 0.004 | 0.053 | |
colWeightedMedians | 0.023 | 0.004 | 0.027 | |
colWeightedVars | 0.105 | 0.004 | 0.109 | |