Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1444/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OMICsPCA 1.25.0 (landing page) Subhadeep Das
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the OMICsPCA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OMICsPCA.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: OMICsPCA |
Version: 1.25.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OMICsPCA_1.25.0.tar.gz |
StartedAt: 2024-12-24 09:28:00 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 09:35:57 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 476.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: OMICsPCA.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:OMICsPCA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OMICsPCA_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OMICsPCA.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OMICsPCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OMICsPCA’ version ‘1.25.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OMICsPCA’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/OMICsPCA.Rcheck/00install.out’ for details. * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: version 0.99.0 * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'cluster_boxplot.Rd': ‘name’ * 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 analyse_individuals 8.655 0.427 9.205 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/OMICsPCA.Rcheck/00check.log’ for details.
OMICsPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OMICsPCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘OMICsPCA’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (OMICsPCA)
OMICsPCA.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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(OMICsPCAdata) > BiocGenerics:::testPackage("OMICsPCA") 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 Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname 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 Warning: program compiled against libxml 212 using older 211 Attaching package: 'OMICsPCA' The following object is masked from 'package:GenomicRanges': intersect The following object is masked from 'package:GenomeInfoDb': intersect The following object is masked from 'package:IRanges': intersect The following object is masked from 'package:S4Vectors': intersect The following object is masked from 'package:BiocGenerics': intersect The following object is masked from 'package:generics': intersect The following object is masked from 'package:base': intersect [1] "Running intersect... This may take some time" [1] "Merging cell lines... This may take some time" [1] "Total time taken is: 0.577132225036621" [1] "time taken to run intersect() is: 0.567632913589478" [1] "time taken to run merge_cells() is: 0.00949931144714355" RUNIT TEST PROTOCOL -- Tue Dec 24 09:35:53 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : OMICsPCA RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 20.579 0.925 21.542
OMICsPCA.Rcheck/OMICsPCA-Ex.timings
name | user | system | elapsed | |
analyse_individuals | 8.655 | 0.427 | 9.205 | |
analyse_integrated_individuals | 3.225 | 0.123 | 3.355 | |
analyse_integrated_variables | 1.877 | 0.064 | 1.945 | |
analyse_variables | 0.688 | 0.000 | 0.691 | |
chart_correlation | 0.035 | 0.000 | 0.035 | |
cluster | 1.661 | 0.068 | 1.733 | |
cluster_boxplot | 0.875 | 0.012 | 0.890 | |
cluster_parameters | 2.071 | 0.028 | 2.103 | |
create_group | 1.116 | 0.000 | 1.118 | |
descriptor | 1.517 | 0.008 | 1.527 | |
extract | 2.972 | 0.088 | 3.066 | |
extract_assay | 0.616 | 0.132 | 0.751 | |
integrate_pca | 1.544 | 0.016 | 1.563 | |
integrate_variables | 0.350 | 0.000 | 0.357 | |
intersect | 0.594 | 0.004 | 0.603 | |
merge_cells | 0.288 | 0.008 | 0.298 | |
plot_density | 2.103 | 0.032 | 2.142 | |
plot_density_3D | 0.231 | 0.000 | 0.231 | |
plot_integrated_density | 2.135 | 0.000 | 2.142 | |
plot_integrated_density_3D | 1.971 | 0.007 | 1.984 | |
prepare_dataset | 0.273 | 0.000 | 0.274 | |