Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 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" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
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 24/32 | Hostname | OS / Arch | CHECK | |||||||
HDF5Array 1.33.3 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino6 | Windows Server 2022 Datacenter / x64 | WARNINGS | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | WARNINGS | ||||||||
To the developers/maintainers of the HDF5Array package: - 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: HDF5Array |
Version: 1.33.3 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.33.3.tar.gz |
StartedAt: 2024-07-06 16:20:14 -0400 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 16:39:08 -0400 (Sat, 06 Jul 2024) |
EllapsedTime: 1133.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HDF5Array.Rcheck |
Warnings: 1 |
HDF5Array.Rcheck/tests/run_longtests.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. > require("HDF5Array") || stop("unable to load HDF5Array package") Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls [1] TRUE > setAutoRealizationBackend("HDF5Array") > ## The tests in DelayedArray require the DelayedMatrixStats and genefilter > ## packages so HDF5Array must have them in Suggests. > BiocGenerics:::testPackage("DelayedArray") Error in S4Arrays:::normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector In addition: Warning messages: 1: In OLD_extract_sparse_array(A3, list(1:10, 1:20)) : OLD_extract_sparse_array() is deprecated in BioC >= 3.20. Please use SparseArray::extract_sparse_array() instead. 2: In OLD_extract_sparse_array(x@seed, index) : OLD_extract_sparse_array() is deprecated in BioC >= 3.20. Please use SparseArray::extract_sparse_array() instead. 3: In SparseArraySeed(ans_dim, nzdata = ans_nzdata, check = FALSE) : SparseArraySeed objects are deprecated in BioC >= 3.20 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 Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Loading required package: HDF5Array Loading required package: SparseArray 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, 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 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: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls 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 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. In addition: Warning messages: 1: In log(a + 0.2) : NaNs produced 2: In OP(a) : NaNs produced Error : unable to find an inherited method for function 'is_noop' for signature 'x = "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 : unable to find an inherited method for function 'is_noop' for signature 'x = "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 : unable to find an inherited method for function 'is_noop' for signature 'x = "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 : unable to find an inherited method for function 'is_noop' for signature 'x = "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 : unable to find an inherited method for function 'is_noop' for signature 'x = "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_SVT3, 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 -- Sat Jul 6 16:39:06 2024 *********************************************** Number of test functions: 42 Number of errors: 0 Number of failures: 0 1 Test Suite : DelayedArray RUnit Tests - 42 test functions, 0 errors, 0 failures Number of test functions: 42 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 410.68 51.03 985.20
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.33.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/HDF5Array.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 options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'HDF5Array/DESCRIPTION' ... OK * this is package 'HDF5Array' version '1.33.3' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'HDF5Array' can be installed ... WARNING Found the following significant warnings: H5DSetDescriptor.c:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=] H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] See 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/HDF5Array.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 15.3Mb sub-directories of 1Mb or more: extdata 7.7Mb libs 6.6Mb * checking package 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 ... NOTE Unexported object imported by a ':::' call: 'rhdf5:::h5checktypeOrOpenLocS3' 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'run_longtests.R' OK * DONE Status: 1 WARNING, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/HDF5Array.Rcheck/00check.log' for details.
HDF5Array.Rcheck/00install.out
* installing *source* package 'HDF5Array' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c H5File.c -o H5File.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c H5DSetDescriptor.c -o H5DSetDescriptor.o H5DSetDescriptor.c: In function 'print_H5TypeDescriptor': H5DSetDescriptor.c:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=] 698 | Rprintf("%s * h5type_id = %ld\n", margin, h5type->h5type_id); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 700 | Rprintf("%s * h5type_size = %lu\n", margin, h5type->h5type_size); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 740 | Rprintf("%s * Rtype_size = %lu\n", margin, h5type->Rtype_size); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 755 | Rprintf("%s * native_type_size = %lu\n", margin, | ~~^ | | | long unsigned int | %llu 756 | h5type->native_type_size); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long long unsigned int} H5DSetDescriptor.c: In function 'C_show_H5DSetDescriptor_xp': H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1166 | Rprintf("- dset_id = %ld\n", h5dset->dset_id); | ~~^ ~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1184 | Rprintf("- h5space_id = %ld\n", h5dset->h5space_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1188 | Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 1210 | Rprintf(" %lu", h5dset->h5nchunk[h5along]); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5dimscales.c -o h5dimscales.o In file included from h5dimscales.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/R_ext/Memory.h:36, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/Rdefines.h:37, from h5dimscales.h:4, from h5dimscales.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uaselection.c -o uaselection.o In file included from uaselection.c:7: uaselection.c: In function 'get_untrusted_elt': uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ^~~~~~~~~~~~~~~ ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:53:51: note: format string is defined here 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ~~^ | | | long int | %lld uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ^~~~~~~~~~~~~~~ ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:53:51: note: format string is defined here 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ~~^ | | | long int | %lld uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ^~~~~~~~~~~~~~~~~~~~~ 56 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:55:57: note: format string is defined here 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ~~^ | | | long int | %lld uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ^~~~~~~~~~~~~~~~~~~~~ 56 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:55:57: note: format string is defined here 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ~~^ | | | long int | %lld uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~ 65 | "or not a finite number", 66 | what, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:64:51: note: format string is defined here 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~ 65 | "or not a finite number", 66 | what, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:64:51: note: format string is defined here 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | "or not a finite number", 70 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:68:57: note: format string is defined here 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | "or not a finite number", 70 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:68:57: note: format string is defined here 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 | what, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:75:51: note: format string is defined here 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 | what, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:75:51: note: format string is defined here 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 | what, along + 1, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:78:57: note: format string is defined here 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 | what, along + 1, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:78:57: note: format string is defined here 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c: In function 'set_errmsg_for_uaselection_beyond_dim': uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 199 | "%s starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~ 200 | "> dimension %d in array", 201 | msg, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:199:44: note: format string is defined here 199 | "%s starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 199 | "%s starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~ 200 | "> dimension %d in array", 201 | msg, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:199:44: note: format string is defined here 199 | "%s starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:44: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:64: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:44: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:64: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c: In function 'set_errmsg_for_non_strictly_ascending_uaselection': uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:56: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:77: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:56: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:77: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:56: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:76: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:56: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:76: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c: In function 'get_untrusted_start': uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:233:53: note: format string is defined here 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ~~^ | | | long int | %lld uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:233:53: note: format string is defined here 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ~~^ | | | long int | %lld uaselection.c: In function 'check_uaselection_along': uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:288:61: note: format string is defined here 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:288:61: note: format string is defined here 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c: In function 'check_ordered_uaselection_along': uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 429 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:428:69: note: format string is defined here 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 429 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:428:69: note: format string is defined here 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChunkIterator.c -o ChunkIterator.o ChunkIterator.c: In function '_print_tchunk_info': ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]); | ~~^ ~ | | | | | size_t {aka long long unsigned int} | long unsigned int | %llu ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_index.c -o h5mread_index.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_sparse.c -o h5mread_sparse.o gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o In file included from h5mread.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/R_ext/Memory.h:36, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/Rdefines.h:37, from h5mread.h:4, from h5mread.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5summarize.c -o h5summarize.o In file included from h5summarize.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/R_ext/Memory.h:36, from C:/Users/BIOCBU~1/BBS-3~1.20-/R/include/Rdefines.h:37, from h5summarize.h:4, from h5summarize.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"C:/Users/BIOCBU~1/BBS-3~1.20-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_HDF5Array.c -o R_init_HDF5Array.o gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o -LC:/Users/BIOCBU~1/BBS-3~1.20-/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/BIOCBU~1/BBS-3~1.20-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/HDF5Array.Rcheck/00LOCK-HDF5AR~1/00new/HDF5Array/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (HDF5Array)