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 1349/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MultiDataSet 1.33.0 (landing page) Xavier EscribĂ Montagut
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MultiDataSet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiDataSet.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: MultiDataSet |
Version: 1.33.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MultiDataSet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MultiDataSet_1.33.0.tar.gz |
StartedAt: 2024-08-21 03:08:06 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:11:29 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 202.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MultiDataSet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MultiDataSet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MultiDataSet_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MultiDataSet.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 'MultiDataSet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MultiDataSet' version '1.33.0' * 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 'MultiDataSet' 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 ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: o Add function to add matrices to MDS. Cannot process chunk/lines: o Add vignettes published in scientific article. Cannot process chunk/lines: o Remove non-critical dependencies. Cannot process chunk/lines: o Add wrappers for two functions to integrate omic data: mcia (from omicade4 package) and iClusterPlus. Cannot process chunk/lines: o Add advanced subsetting by phenotype and feature. Cannot process chunk/lines: BUG FIXES Cannot process chunk/lines: o Solve subsetting issues when sampleNames is different from ID column. * 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: 'Biobase:::assayDataEnvLock' 'Biobase:::assayDataStorageMode' 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 ... NOTE downloadGEO : <anonymous>: no visible global function definition for 'methylationSet' lambdaClayton: no visible global function definition for 'qnorm' lambdaClayton: no visible global function definition for 'qchisq' qq_plot: no visible global function definition for 'qbeta' Undefined global functions or variables: methylationSet qbeta qchisq qnorm Consider adding importFrom("stats", "qbeta", "qchisq", "qnorm") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'ResultSet-class.Rd': \S4method{getAssociation}{ResultSet} Code: function(object, rid = 1, coef = 2, contrast = NULL, fNames = NULL, robust = FALSE, ...) Docs: function(object, rid = 1, coef = 2, contrast = NULL, fNames = NULL, ...) Argument names in code not in docs: robust Mismatches in argument names: Position: 6 Code: robust Docs: ... * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed add_methy 17.61 1.33 19.14 * 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: 1 WARNING, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/MultiDataSet.Rcheck/00check.log' for details.
MultiDataSet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MultiDataSet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MultiDataSet' ... ** using staged installation Warning in .write_description(db, file.path(outDir, "DESCRIPTION")) : Unknown encoding with non-ASCII data: converting to ASCII ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for 'add_methy' with signature '"MultiDataSet","GenomicRatioSet"': no definition for class "GenomicRatioSet" ** help *** installing help indices ** 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 (MultiDataSet)
MultiDataSet.Rcheck/MultiDataSet-Ex.timings
name | user | system | elapsed | |
MultiDataSet-class | 0 | 0 | 0 | |
ResultSet-class | 0 | 0 | 0 | |
add_eset | 0.08 | 0.00 | 0.08 | |
add_genexp | 0.14 | 0.00 | 0.14 | |
add_methy | 17.61 | 1.33 | 19.14 | |
add_rnaseq-methods | 0.11 | 0.00 | 0.11 | |
add_rse | 0.24 | 0.03 | 0.28 | |
add_se | 0.06 | 0.00 | 0.06 | |
add_snps | 0.08 | 0.01 | 0.09 | |
add_table | 0.01 | 0.00 | 0.02 | |
chrNumToChar | 0 | 0 | 0 | |
commonIds | 0.16 | 0.02 | 0.17 | |
commonSamples | 0.2 | 0.0 | 0.2 | |
getAssociation-methods | 0.03 | 0.02 | 0.05 | |
lambdaClayton | 0 | 0 | 0 | |
opt-methods | 0 | 0 | 0 | |
qq_plot | 0.52 | 0.11 | 0.67 | |
rowRangesElements | 0.12 | 0.01 | 0.14 | |
volcano_plot | 0.25 | 0.02 | 0.26 | |