Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 882/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GOexpress 1.40.0 (landing page) Kevin Rue-Albrecht
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: GOexpress |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOexpress_1.40.0.tar.gz |
StartedAt: 2024-12-20 04:12:37 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:16:56 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 259.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GOexpress.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOexpress_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GOexpress/DESCRIPTION’ ... OK * this is package ‘GOexpress’ version ‘1.40.0’ * 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: 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 ‘/Users/biocbuild/bbs-3.20-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 ... 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 ... NOTE 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 ... 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlvMac_results.pVal 3.145 3.598 6.769 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck/00check.log’ for details.
GOexpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GOexpress ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GOexpress’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GOexpress)
GOexpress.Rcheck/GOexpress-Ex.timings
name | user | system | elapsed | |
AlvMac | 0.212 | 0.038 | 0.250 | |
AlvMac_GOgenes | 0.653 | 0.016 | 0.670 | |
AlvMac_allGO | 0.029 | 0.005 | 0.034 | |
AlvMac_allgenes | 0.011 | 0.004 | 0.015 | |
AlvMac_results | 0.223 | 0.021 | 0.244 | |
AlvMac_results.pVal | 3.145 | 3.598 | 6.769 | |
GO_analyse | 3.593 | 0.170 | 3.769 | |
GOexpress-package | 0.004 | 0.006 | 0.010 | |
cluster_GO | 0.575 | 0.017 | 0.593 | |
expression_plot | 4.304 | 0.153 | 4.464 | |
expression_plot_symbol | 1.781 | 0.021 | 1.808 | |
expression_profiles | 1.134 | 0.011 | 1.148 | |
expression_profiles_symbol | 1.236 | 0.010 | 1.250 | |
heatmap_GO | 1.637 | 0.028 | 1.672 | |
hist_scores | 0.396 | 0.009 | 0.406 | |
list_genes | 0.147 | 0.004 | 0.153 | |
microarray2dataset | 0.017 | 0.031 | 0.047 | |
pValue_GO | 0.000 | 0.000 | 0.001 | |
plot_design | 0.254 | 0.013 | 0.268 | |
prefix2dataset | 0.015 | 0.014 | 0.029 | |
quantiles_scores | 0.743 | 0.008 | 0.754 | |
rerank | 0.318 | 0.020 | 0.338 | |
subEset | 0.085 | 0.003 | 0.088 | |
subset_scores | 0.300 | 0.016 | 0.317 | |
table_genes | 0.189 | 0.008 | 0.198 | |