Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:40 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 1843/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
S4Arrays 1.7.3 (landing page) Hervé Pagès
| 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 | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the S4Arrays package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/S4Arrays.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: S4Arrays |
Version: 1.7.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings S4Arrays_1.7.3.tar.gz |
StartedAt: 2025-03-16 21:14:40 -0400 (Sun, 16 Mar 2025) |
EndedAt: 2025-03-16 21:15:31 -0400 (Sun, 16 Mar 2025) |
EllapsedTime: 51.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: S4Arrays.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings S4Arrays_1.7.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Arrays.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘S4Arrays/DESCRIPTION’ ... OK * this is package ‘S4Arrays’ version ‘1.7.3’ * 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 ‘S4Arrays’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 whether startup messages can be suppressed ... 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: extract_array.Rd: dgCMatrix-class is_sparse.Rd: dgCMatrix-class read_block.Rd: dgCMatrix-class, lgCMatrix-class type.Rd: dgCMatrix-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 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 ... ERROR Running examples in ‘S4Arrays-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: array_recycling > ### Title: Multidimensional array recycling > ### Aliases: array_recycling class:tile tile-class tile as_tile > ### Ops,array,tile-method Ops,tile,array-method Ops,tile,tile-method > ### Keywords: array methods > > ### ** Examples > > ## --------------------------------------------------------------------- > ## 2D EXAMPLES > ## --------------------------------------------------------------------- > m0 <- matrix(1:54, nrow=6) > x <- c(-1, 0, 100) > > ## Arithmetic operations in base R recycle 'x' along the first dimension > ## of the matrix ("vertical recycling"): > m0 * x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] -1 -7 -13 -19 -25 -31 -37 -43 -49 [2,] 0 0 0 0 0 0 0 0 0 [3,] 300 900 1500 2100 2700 3300 3900 4500 5100 [4,] -4 -10 -16 -22 -28 -34 -40 -46 -52 [5,] 0 0 0 0 0 0 0 0 0 [6,] 600 1200 1800 2400 3000 3600 4200 4800 5400 > > ## To recycle 'x' along the second dimension of the matrix ("horizontal > ## recycling"), we turn it into an "horizontal" tile: > t <- as_tile(x, along=2) > t An object of class "tile" [,1] [,2] [,3] [1,] -1 0 100 > > m0 * t [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] -1 0 1300 -19 0 3100 -37 0 4900 [2,] -2 0 1400 -20 0 3200 -38 0 5000 [3,] -3 0 1500 -21 0 3300 -39 0 5100 [4,] -4 0 1600 -22 0 3400 -40 0 5200 [5,] -5 0 1700 -23 0 3500 -41 0 5300 [6,] -6 0 1800 -24 0 3600 -42 0 5400 > > ## The above produces the same result as the double-transposition trick > ## but is more efficient (and also makes code easier to read): > stopifnot(identical(m0 * t, t(t(m0) * x))) > > ## A less artificial example: > cs0 <- colSums(m0) > m <- m0 / as_tile(cs0, along=2) > > stopifnot(all(colSums(m) == 1)) # sanity check Error: all(colSums(m) == 1) is not TRUE Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed Array-kronecker-methods 4.909 0.133 5.051 * 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: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Arrays.Rcheck/00check.log’ for details.
S4Arrays.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL S4Arrays ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘S4Arrays’ ... ** this is package ‘S4Arrays’ version ‘1.7.3’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_S4Arrays.c -o R_init_S4Arrays.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c abind.c -o abind.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array_selection.c -o array_selection.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dim_tuning_utils.c -o dim_tuning_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowsum.c -o rowsum.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** 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 (S4Arrays)
S4Arrays.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(S4Arrays) Loading required package: Matrix Loading required package: abind 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 Loading required package: stats4 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 Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum > > test_check("S4Arrays") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 514 ] > > proc.time() user system elapsed 10.521 0.166 10.707
S4Arrays.Rcheck/S4Arrays-Ex.timings
name | user | system | elapsed | |
Array-class | 0 | 0 | 0 | |
Array-kronecker-methods | 4.909 | 0.133 | 5.051 | |
ArrayGrid-class | 0.170 | 0.011 | 0.181 | |
abind | 0.002 | 0.002 | 0.004 | |
aperm2 | 0.005 | 0.005 | 0.010 | |
arep | 0 | 0 | 0 | |