Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -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 876/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GOexpress 1.41.0 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the GOexpress package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOexpress.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: GOexpress |
Version: 1.41.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GOexpress_1.41.0.tar.gz |
StartedAt: 2024-12-24 07:20:10 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:22:47 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 157.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GOexpress.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GOexpress_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GOexpress.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 ‘GOexpress/DESCRIPTION’ ... OK * this is package ‘GOexpress’ version ‘1.41.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml 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 ‘GOexpress’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) See ‘/home/biocbuild/bbs-3.21-bioc/meat/GOexpress.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 ... 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 GO_analyse: no visible binding for global variable ‘microarray2dataset’ GO_analyse: no visible binding for global variable ‘prefix2dataset’ mart_from_ensembl: no visible binding for global variable ‘prefix2dataset’ microarray2dataset.build: possible error in getBM(attributes = microarray.header, mart = mart.loop, curl = curlHandle): unused argument (curl = curlHandle) sampleEnsemblGeneId: possible error in getBM(attributes = "ensembl_gene_id", mart = mart.loop, curl = curl): unused argument (curl = curl) Undefined global functions or variables: microarray2dataset prefix2dataset * checking Rd files ... NOTE checkRd: (-1) AlvMac_GOgenes.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_GOgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allGO.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allGO.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allGO.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allgenes.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) AlvMac_allgenes.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) hist_scores.Rd:11: Lost braces; missing escapes or markup? 11 | variable of the {GO_analyse()} function. | ^ * 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 ... 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 * 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/GOexpress.Rcheck/00check.log’ for details.
GOexpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GOexpress ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GOexpress’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) ** 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 (GOexpress)
GOexpress.Rcheck/GOexpress-Ex.timings
name | user | system | elapsed | |
AlvMac | 0.126 | 0.001 | 0.129 | |
AlvMac_GOgenes | 0.641 | 0.000 | 0.644 | |
AlvMac_allGO | 0.022 | 0.000 | 0.022 | |
AlvMac_allgenes | 0.003 | 0.014 | 0.017 | |
AlvMac_results | 0.160 | 0.009 | 0.170 | |
AlvMac_results.pVal | 1.234 | 0.258 | 1.500 | |
GO_analyse | 2.466 | 0.066 | 2.548 | |
GOexpress-package | 0.003 | 0.000 | 0.003 | |
cluster_GO | 0.173 | 0.016 | 0.190 | |
expression_plot | 3.125 | 0.129 | 3.276 | |
expression_plot_symbol | 1.173 | 0.008 | 1.188 | |
expression_profiles | 0.722 | 0.000 | 0.726 | |
expression_profiles_symbol | 1.357 | 0.000 | 1.364 | |
heatmap_GO | 0.621 | 0.027 | 0.653 | |
hist_scores | 0.320 | 0.012 | 0.333 | |
list_genes | 0.156 | 0.000 | 0.156 | |
microarray2dataset | 0.003 | 0.004 | 0.007 | |
pValue_GO | 0 | 0 | 0 | |
plot_design | 0.190 | 0.008 | 0.198 | |
prefix2dataset | 0.008 | 0.000 | 0.007 | |
quantiles_scores | 0.207 | 0.004 | 0.212 | |
rerank | 0.264 | 0.008 | 0.273 | |
subEset | 0.052 | 0.000 | 0.053 | |
subset_scores | 0.240 | 0.000 | 0.242 | |
table_genes | 0.165 | 0.000 | 0.166 | |