Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 690/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
extraChIPs 1.10.0 (landing page) Stevie Pederson
| teran2 | Linux (Ubuntu 24.04.1 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 | OK | OK | OK | |||||||||
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 extraChIPs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/extraChIPs.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: extraChIPs |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.10.0.tar.gz |
StartedAt: 2024-11-09 02:05:43 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 02:12:09 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 385.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: extraChIPs.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/extraChIPs.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘extraChIPs/DESCRIPTION’ ... OK * this is package ‘extraChIPs’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE Depends: includes the non-default packages: 'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside', 'SummarizedExperiment', 'tibble' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... 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 for sufficient/correct file permissions ... OK * checking whether package ‘extraChIPs’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/extraChIPs.Rcheck/00check.log’ for details.
extraChIPs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL extraChIPs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘extraChIPs’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FMStable.c -o FMStable.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o extraChIPs.so FMStable.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-extraChIPs/00new/extraChIPs/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (extraChIPs)
extraChIPs.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(extraChIPs) Loading required package: BiocParallel Loading required package: GenomicRanges 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, saveRDS, 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 Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: ggside 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 Loading required package: tibble > > test_check("extraChIPs") Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Getting coverage across all 1 peaks...done (0.15s) Finding centres by chromosome...done (0.09s) Getting coverage across all 1 peaks...done (0.15s) Finding centres by chromosome...done (0.09s) Getting coverage across all 1 peaks...done (0.14s) Finding centres by chromosome...done (0.08s) Getting coverage across all 1 peaks...done (0.11s) Finding centres by chromosome...done (0.09s) Creating DESeqDataSet... converting counts to integer mode Calculating none normalisation factors... Estimating dispersions using fitType = local... gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895 Creating DGE list... Calculating experiment-wide normalisation factors... Estimating dispersions... Running glmQLFit... Creating DGE list... Calculating experiment-wide normalisation factors... Estimating dispersions... Running glmQLFit... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 591 ] > > proc.time() user system elapsed 25.481 1.802 27.116
extraChIPs.Rcheck/extraChIPs-Ex.timings
name | user | system | elapsed | |
addDiffStatus-methods | 0.068 | 0.005 | 0.073 | |
as_tibble | 0.568 | 0.005 | 0.572 | |
bestOverlap-methods | 0.247 | 0.009 | 0.257 | |
centrePeaks-methods | 0.149 | 0.006 | 0.156 | |
chopMC | 0.044 | 0.001 | 0.045 | |
colToRanges-methods | 0.075 | 0.001 | 0.076 | |
collapseGenes | 0.001 | 0.000 | 0.001 | |
cytobands | 0.004 | 0.002 | 0.006 | |
defineRegions | 0.922 | 0.003 | 0.925 | |
defineSeqinfo | 0.003 | 0.001 | 0.004 | |
distinctMC | 0.087 | 0.000 | 0.088 | |
dualFilter | 0 | 0 | 0 | |
ex_datasets | 0.005 | 0.002 | 0.006 | |
fitAssayDiff-methods | 0.057 | 0.001 | 0.059 | |
fixed_width_datasets | 0.012 | 0.002 | 0.013 | |
getProfileData-methods | 0.760 | 0.014 | 0.797 | |
grlToSE-methods | 0.121 | 0.001 | 0.122 | |
importPeaks | 0.036 | 0.001 | 0.037 | |
makeConsensus | 0.250 | 0.008 | 0.258 | |
mapByFeature | 0.178 | 0.001 | 0.179 | |
mapGrlCols | 0.405 | 0.002 | 0.407 | |
mergeByCol-methods | 0.079 | 0.001 | 0.080 | |
mergeByHMP-methods | 0.122 | 0.000 | 0.123 | |
mergeBySig-methods | 0.145 | 0.002 | 0.146 | |
partitionRanges-methods | 0.265 | 0.000 | 0.265 | |
plotAssayDensities-methods | 0.249 | 0.005 | 0.254 | |
plotAssayHeatmap-methods | 0.105 | 0.001 | 0.106 | |
plotAssayPCA-methods | 0.203 | 0.003 | 0.206 | |
plotAssayRle-methods | 0.212 | 0.003 | 0.215 | |
plotGrlCol | 0.385 | 0.005 | 0.391 | |
plotHFGC | 0 | 0 | 0 | |
plotOverlaps-methods | 0.811 | 0.009 | 0.821 | |
plotPairwise | 0.851 | 0.006 | 0.858 | |
plotPie-methods | 0.380 | 0.006 | 0.387 | |
plotProfileHeatmap-methods | 0 | 0 | 0 | |
plotSplitDonut-methods | 0.319 | 0.002 | 0.321 | |
propOverlap-methods | 0.07 | 0.00 | 0.07 | |
reduceMC | 0.075 | 0.001 | 0.075 | |
setoptsMC-methods | 0.232 | 0.001 | 0.233 | |
stitchRanges | 0.078 | 0.000 | 0.078 | |
voomWeightsFromCPM | 0.048 | 0.002 | 0.051 | |