Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1136/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mariner 1.5.0 (landing page) Eric Davis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the mariner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mariner.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: mariner |
Version: 1.5.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mariner.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mariner_1.5.0.tar.gz |
StartedAt: 2024-08-21 02:16:25 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:33:36 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 1031.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mariner.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mariner.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mariner_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mariner.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'mariner/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'mariner' version '1.5.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'mariner' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'plotgardener:::check_page' 'plotgardener:::convert_page' 'plotgardener:::current_viewports' 'plotgardener:::defaultUnits' 'plotgardener:::pgEnv' 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 ... NOTE checkRd: (-1) mariner-package.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) mariner-package.Rd:20-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) mariner-package.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) mariner-package.Rd:26-28: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'MatrixSelection.Rd': 'object' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CountMatrix-class 12.03 3.28 18.42 adjustEnrichment 11.68 1.16 33.11 calcLoopEnrichment 8.89 1.33 52.18 aggHicMatrices 8.48 0.78 50.42 changePixelRes 6.35 1.09 9.53 pullHicMatrices 6.25 0.73 11.03 selectPixel 5.87 0.98 8.72 pullHicPixels 5.09 0.85 7.64 aggPairMcols 4.70 0.67 6.63 counts 4.03 0.69 5.91 path 3.48 0.67 5.80 getPairClusters 3.42 0.54 5.03 sources 3.41 0.47 5.02 selectionMethod 3.30 0.50 5.06 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/mariner.Rcheck/00check.log' for details.
mariner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mariner ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'mariner' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mariner)
mariner.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(mariner) > > test_check("mariner") see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache class: InteractionMatrix dim: count matrix with 3 interactions and 2 file(s) metadata(3): binSize norm matrix assays(1): counts rownames: NULL rowData names(0): colnames(2): FS WT colData names(2): files fileNames type: GInteractions regions: 4 class: InteractionMatrix dim: count matrix with 3 interactions and 2 file(s) metadata(3): binSize norm matrix assays(1): counts rownames: NULL rowData names(0): colnames(2): FS WT colData names(2): files fileNames type: GInteractions regions: 4 class: InteractionMatrix dim: count matrix with 3 interactions and 2 file(s) metadata(3): binSize norm matrix assays(1): counts rownames: NULL rowData names(0): colnames(2): FS WT colData names(2): files fileNames type: GInteractions regions: 4 Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache '0' = foreground; 'X' = background; '*' = both; '-' = unselected X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - - - - - - 0 - - - - - - - - - 0 0 0 - - - - - - - - - 0 - - - - - - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X / reading and realizing block 1/5 ... ok \ processing it ... ok / reading and realizing block 2/5 ... ok \ processing it ... ok / reading and realizing block 5/5 ... ok \ processing it ... ok / reading and realizing block 3/5 ... ok \ processing it ... ok / reading and realizing block 4/5 ... ok \ processing it ... ok see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache '0' = selected; '- ' = unselected 0 0 0 - - - 0 0 0 '0' = selected; '- ' = unselected - - - 0 0 0 - - - '0' = selected; '- ' = unselected - - - - - - - - - - - - - - - - - - - 0 - 0 - 0 0 0 - - 0 - 0 - - 0 - - - 0 0 0 - - 0 - - - 0 - 0 - - 0 - - - 0 - 0 - 0 0 0 - - - - - - - - - - - - - - - - - - - '0' = selected; '- ' = unselected 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 0 - 0 - - - 0 0 - 0 - 0 0 - 0 0 0 - - - 0 0 - 0 0 0 - 0 - 0 0 - 0 0 0 - 0 - 0 - - - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 '0' = foreground; 'X' = background; '*' = both; '-' = unselected X X X X X X X X X X X X X X X X X 0 X X X X X 0 0 0 X X X X X 0 X X X X X X X X X X X X X X X X X '0' = foreground; 'X' = background; '*' = both; '-' = unselected X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - - - - - - 0 - - - - - - - - - 0 0 0 - - - - - - - - - 0 - - - - - - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X - - - - - - - X X X X / reading and realizing block 1/5 ... ok \ processing it ... ok / reading and realizing block 2/5 ... ok \ processing it ... ok / reading and realizing block 3/5 ... ok \ processing it ... ok / reading and realizing block 4/5 ... ok \ processing it ... ok / reading and realizing block 5/5 ... ok \ processing it ... ok see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache / Reading and realizing block 1/5 ... OK \ Processing it ... OK / Reading and realizing block 2/5 ... OK \ Processing it ... OK / Reading and realizing block 3/5 ... OK \ Processing it ... OK / Reading and realizing block 4/5 ... OK \ Processing it ... OK / Reading and realizing block 5/5 ... OK \ Processing it ... OK / Reading and realizing block 1/5 ... OK \ Processing it ... OK / Reading and realizing block 2/5 ... OK \ Processing it ... OK / Reading and realizing block 3/5 ... OK \ Processing it ... OK / Reading and realizing block 4/5 ... OK \ Processing it ... OK / Reading and realizing block 5/5 ... OK \ Processing it ... OK Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep / Reading and realizing block 1/10 ... OK \ Processing it ... OK / Reading and realizing block 2/10 ... OK \ Processing it ... OK / Reading and realizing block 3/10 ... OK \ Processing it ... OK / Reading and realizing block 4/10 ... OK \ Processing it ... OK / Reading and realizing block 5/10 ... OK \ Processing it ... OK / Reading and realizing block 6/10 ... OK \ Processing it ... OK / Reading and realizing block 7/10 ... OK \ Processing it ... OK / Reading and realizing block 8/10 ... OK \ Processing it ... OK / Reading and realizing block 9/10 ... OK \ Processing it ... OK / Reading and realizing block 10/10 ... OK \ Processing it ... OK see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache Attaching package: 'plotgardener' The following object is masked from 'package:base': c MatrixPlot[MatrixPlot1] MatrixPlot[MatrixPlot1] MatrixPlot[MatrixPlot1] MatrixPlot[MatrixPlot1] MatrixPlot[MatrixPlot1] see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache see ?marinerData and browseVignettes('marinerData') for documentation loading from cache Attaching package: 'rlang' The following object is masked from 'package:data.table': := The following object is masked from 'package:Biobase': exprs The following objects are masked from 'package:testthat': is_false, is_null, is_true Attaching package: 'assertthat' The following object is masked from 'package:rlang': has_name see ?marinerData and browseVignettes('marinerData') for documentation loading from cache [ FAIL 0 | WARN 0 | SKIP 4 | PASS 899 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test_InteractionArray.R:39:5', 'test_InteractionArray.R:97:5', 'test_InteractionMatrix.R:74:5', 'test_MergedGInteractions.R:61:5' [ FAIL 0 | WARN 0 | SKIP 4 | PASS 899 ] > > proc.time() user system elapsed 264.15 29.98 489.04
mariner.Rcheck/mariner-Ex.timings
name | user | system | elapsed | |
CountMatrix-class | 12.03 | 3.28 | 18.42 | |
GInteractions-accessors | 0.53 | 0.05 | 0.58 | |
InteractionArray-class | 0.14 | 0.00 | 0.14 | |
InteractionMatrix-class | 0.11 | 0.00 | 0.11 | |
MatrixSelection-class | 0.03 | 0.13 | 0.16 | |
MergedGInteractions-class | 3.12 | 0.40 | 4.72 | |
adjustEnrichment | 11.68 | 1.16 | 33.11 | |
aggHicMatrices | 8.48 | 0.78 | 50.42 | |
aggPairMcols | 4.70 | 0.67 | 6.63 | |
as_ginteractions | 0.94 | 0.06 | 1.00 | |
binPairs | 1.28 | 0.05 | 1.34 | |
binRanges | 0.72 | 0.05 | 0.79 | |
calcLoopEnrichment | 8.89 | 1.33 | 52.18 | |
changePixelRes | 6.35 | 1.09 | 9.53 | |
counts | 4.03 | 0.69 | 5.91 | |
getPairClusters | 3.42 | 0.54 | 5.03 | |
hdf5BlockApply | 0.64 | 0.07 | 0.80 | |
mergePairs | 3.22 | 0.62 | 4.98 | |
path | 3.48 | 0.67 | 5.80 | |
pixelsToMatrices | 0.53 | 0.05 | 0.58 | |
plotMatrix | 0.24 | 0.03 | 0.30 | |
pullHicMatrices | 6.25 | 0.73 | 11.03 | |
pullHicPixels | 5.09 | 0.85 | 7.64 | |
removeShortPairs | 0.13 | 0.00 | 0.13 | |
selectPixel | 5.87 | 0.98 | 8.72 | |
selection-functions | 0.28 | 1.48 | 1.76 | |
selectionMethod | 3.30 | 0.50 | 5.06 | |
shiftRanges | 0.53 | 0.04 | 0.57 | |
snapToBins | 1.75 | 0.09 | 1.84 | |
sources | 3.41 | 0.47 | 5.02 | |
subsetBySource | 0.54 | 0.06 | 0.60 | |