Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:35:54 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 527/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DelayedArray 0.28.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the DelayedArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedArray.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: DelayedArray |
Version: 0.28.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DelayedArray_0.28.0.tar.gz |
StartedAt: 2024-04-15 21:57:15 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-15 22:11:03 -0400 (Mon, 15 Apr 2024) |
EllapsedTime: 828.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DelayedArray.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DelayedArray_0.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DelayedArray.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DelayedArray/DESCRIPTION’ ... OK * this is package ‘DelayedArray’ version ‘0.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'stats4', 'Matrix', 'BiocGenerics', 'MatrixGenerics', 'S4Vectors', 'IRanges', 'S4Arrays', 'SparseArray' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘DelayedArray’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 ... WARNING Subdirectory 'inst/doc' contains invalid file names: ‘02-Implementing_a_backend.Rmd’ ‘01-Working_with_large_arrays.Rnw’ ‘03-DelayedArray_HDF5Array_update.Rnw’ ‘02-Implementing_a_backend.html’ ‘01-Working_with_large_arrays.pdf’ ‘03-DelayedArray_HDF5Array_update.pdf’ Please remove or rename the files. See section ‘Package subdirectories’ in the ‘Writing R Extensions’ manual. * checking R 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 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 ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘defaultMultAutoGrids’ ‘multGrids’ Undocumented S4 methods: generic '[' and siglist 'DelayedArray,ANY,ANY,ANY' generic '[<-' and siglist 'DelayedArray,ANY,ANY,ANY' generic 'crossprod' and siglist 'ANY,DelayedMatrix' generic 'crossprod' and siglist 'DelayedMatrix,ANY' generic 'crossprod' and siglist 'DelayedMatrix,DelayedMatrix' generic 'crossprod' and siglist 'DelayedMatrix,missing' generic 'tcrossprod' and siglist 'ANY,DelayedMatrix' generic 'tcrossprod' and siglist 'DelayedMatrix,ANY' generic 'tcrossprod' and siglist 'DelayedMatrix,DelayedMatrix' generic 'tcrossprod' and siglist 'DelayedMatrix,missing' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 RleArray-class 41.635 4.836 46.473 DelayedMatrix-utils 16.110 1.784 17.896 DelayedArray-utils 10.114 0.232 10.357 DelayedArray-class 6.892 0.124 7.016 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘02-Implementing_a_backend.Rmd’ using ‘UTF-8’... OK ‘01-Working_with_large_arrays.Rnw’ using ‘UTF-8’... OK ‘03-DelayedArray_HDF5Array_update.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DelayedArray.Rcheck/00check.log’ for details.
DelayedArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DelayedArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘DelayedArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** 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 (DelayedArray)
DelayedArray.Rcheck/tests/run_unitTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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. > require("DelayedArray") || stop("unable to load DelayedArray package") Loading required package: DelayedArray Loading required package: stats4 Loading required package: Matrix 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, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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 [1] TRUE > DelayedArray:::.test() Attaching package: 'genefilter' The following object is masked from 'package:DelayedArray': rowVars The following objects are masked from 'package:SparseArray': rowSds, rowVars The following objects are masked from 'package:MatrixGenerics': rowSds, rowVars The following objects are masked from 'package:matrixStats': rowSds, rowVars Loading required package: stats4 Loading required package: Matrix 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, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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 Loading required package: stats4 Loading required package: Matrix 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, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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 Loading required package: stats4 Loading required package: Matrix 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, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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 Loading required package: stats4 Loading required package: Matrix 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, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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 Error in S4Arrays:::normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector In addition: Warning messages: 1: In log(a + 0.2) : NaNs produced 2: In OP(a) : NaNs produced Error in validObject(.Object) : invalid class "DelayedAperm" object: 'perm' cannot be an empty vector Error in validObject(.Object) : invalid class "DelayedAperm" object: only dimensions with an extent of 1 can be dropped Error in validObject(.Object) : invalid class "DelayedAperm" object: all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))' Error in validObject(.Object) : invalid class "DelayedAperm" object: only dimensions with an extent of 1 can be dropped Error in seed(x) : seed() is not supported on a DelayedArray object with multiple seeds at the moment. Note that you can check the number of seeds with nseed(). You can use 'seedApply(x, identity)' to extract all the seeds as a list. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"' Error in seed(x) : seed() is not supported on a DelayedArray object with multiple seeds at the moment. Note that you can check the number of seeds with nseed(). You can use 'seedApply(x, identity)' to extract all the seeds as a list. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"' Error in seed(x) : seed() is not supported on a DelayedArray object with multiple seeds at the moment. Note that you can check the number of seeds with nseed(). You can use 'seedApply(x, identity)' to extract all the seeds as a list. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"' Error in seed(x) : seed() is not supported on a DelayedArray object with multiple seeds at the moment. Note that you can check the number of seeds with nseed(). You can use 'seedApply(x, identity)' to extract all the seeds as a list. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"' Error in seed(x) : seed() is not supported on a DelayedArray object with multiple seeds at the moment. Note that you can check the number of seeds with nseed(). You can use 'seedApply(x, identity)' to extract all the seeds as a list. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"' Error in match.fun(OP) : 'NULL' is not a function, character or symbol Error in match.fun(OP) : 'list(NULL)' is not a function, character or symbol Error in get(as.character(FUN), mode = "function", envir = envir) : object 'not-an-existing-function' of mode 'function' was not found Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) : non-conformable array-like objects Error in S4Arrays:::normarg_dimnames(dimnames, seed_dim) : the supplied 'dimnames' must be NULL or a list Error in S4Arrays:::normarg_dimnames(dimnames, seed_dim) : the supplied 'dimnames' must have one list element per dimension Error in FUN(X[[i]], ...) : each list element in the supplied 'dimnames' must be NULL or a character vector Error in FUN(X[[i]], ...) : length of 'dimnames[[1]]' (26) must equal the array extent (5) Error in S4Arrays:::normalize_Nindex(Nindex, seed) : 'Nindex' must be a list with one list element per dimension in 'x' Error in S4Arrays:::normalize_Nindex(Nindex, seed) : 'Nindex' must be a list with one list element per dimension in 'x' Error : subscript contains out-of-bounds indices Error : subscript contains invalid names Error : subscript contains out-of-bounds ranges Error : subscript contains out-of-bounds ranges Error in new_DelayedUnaryIsoOpStack(.TEST_SAS3, NULL) : 'OPS' must be a list Error in FUN(X[[i]], ...) : 'OPS[[1L]]' is not a function, character or symbol Error in get(as.character(FUN), mode = "function", envir = envir) : object 'not-an-existing-function' of mode 'function' was not found RUNIT TEST PROTOCOL -- Mon Apr 15 22:10:10 2024 *********************************************** Number of test functions: 47 Number of errors: 0 Number of failures: 0 1 Test Suite : DelayedArray RUnit Tests - 47 test functions, 0 errors, 0 failures Number of test functions: 47 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 532.623 2.958 569.740
DelayedArray.Rcheck/DelayedArray-Ex.timings
name | user | system | elapsed | |
AutoBlock-global-settings | 0.190 | 0.001 | 0.190 | |
AutoGrid | 1.691 | 0.063 | 1.756 | |
ConstantArray-class | 0.056 | 0.008 | 0.063 | |
DelayedAbind-class | 0.103 | 0.007 | 0.110 | |
DelayedAperm-class | 0.025 | 0.011 | 0.038 | |
DelayedArray-class | 6.892 | 0.124 | 7.016 | |
DelayedArray-stats | 1.494 | 0.068 | 1.562 | |
DelayedArray-utils | 10.114 | 0.232 | 10.357 | |
DelayedMatrix-stats | 1.461 | 0.124 | 1.586 | |
DelayedMatrix-utils | 16.110 | 1.784 | 17.896 | |
DelayedNaryIsoOp-class | 0.034 | 0.000 | 0.035 | |
DelayedSetDimnames-class | 0.016 | 0.000 | 0.017 | |
DelayedSubassign-class | 0.064 | 0.000 | 0.065 | |
DelayedSubset-class | 0.057 | 0.000 | 0.058 | |
DelayedUnaryIsoOpStack-class | 0.047 | 0.003 | 0.051 | |
DelayedUnaryIsoOpWithArgs-class | 0.12 | 0.00 | 0.12 | |
RealizationSink-class | 2.654 | 0.056 | 2.710 | |
RleArray-class | 41.635 | 4.836 | 46.473 | |
SparseArraySeed-class | 0.304 | 0.016 | 0.319 | |
SparseArraySeed-utils | 0.002 | 0.000 | 0.002 | |
blockApply | 1.196 | 0.385 | 1.312 | |
chunkGrid | 0 | 0 | 0 | |
makeCappedVolumeBox | 0.220 | 0.008 | 0.228 | |
realize | 1.114 | 0.080 | 1.194 | |
showtree | 0.116 | 0.020 | 0.136 | |
simplify | 0.329 | 0.004 | 0.334 | |