Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MultiDataSet package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1222/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MultiDataSet 1.20.2 (landing page) Xavier Escribà Montagut
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: MultiDataSet |
Version: 1.20.2 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MultiDataSet_1.20.2.tar.gz |
StartedAt: 2021-10-14 10:44:23 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:46:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 143.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MultiDataSet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MultiDataSet_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MultiDataSet.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MultiDataSet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MultiDataSet’ version ‘1.20.2’ * 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 for sufficient/correct file permissions ... 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 ... OK * checking R 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 documentation object 'ResultSet': \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 14.235 0.937 15.181 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/MultiDataSet.Rcheck/00check.log’ for details.
MultiDataSet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MultiDataSet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 | 0.001 | 0.000 | 0.001 | |
ResultSet-class | 0.002 | 0.000 | 0.002 | |
add_eset | 0.080 | 0.012 | 0.092 | |
add_genexp | 0.122 | 0.008 | 0.130 | |
add_methy | 14.235 | 0.937 | 15.181 | |
add_rnaseq-methods | 0.094 | 0.000 | 0.093 | |
add_rse | 0.246 | 0.000 | 0.246 | |
add_se | 0.053 | 0.000 | 0.052 | |
add_snps | 0.050 | 0.000 | 0.049 | |
add_table | 0.008 | 0.000 | 0.007 | |
chrNumToChar | 0.000 | 0.000 | 0.001 | |
commonIds | 0.112 | 0.000 | 0.112 | |
commonSamples | 0.128 | 0.004 | 0.132 | |
getAssociation-methods | 0.022 | 0.016 | 0.039 | |
lambdaClayton | 0.002 | 0.000 | 0.002 | |
opt-methods | 0.002 | 0.000 | 0.001 | |
qq_plot | 0.347 | 0.019 | 0.367 | |
rowRangesElements | 0.091 | 0.000 | 0.090 | |
volcano_plot | 0.121 | 0.000 | 0.121 | |