Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 890/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GOexpress 1.38.0 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | 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: 1.38.0 |
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_1.38.0.tar.gz |
StartedAt: 2024-07-22 05:59:14 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 06:04:43 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 328.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GOexpress.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GOexpress.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GOexpress/DESCRIPTION’ ... OK * this is package ‘GOexpress’ version ‘1.38.0’ * 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 ... 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 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’ 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 3.194 3.838 8.909 expression_plot 4.791 0.193 6.488 GO_analyse 4.027 0.164 5.495 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-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 ** 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 | 0.227 | 0.039 | 0.309 | |
AlvMac_GOgenes | 0.729 | 0.021 | 0.917 | |
AlvMac_allGO | 0.033 | 0.006 | 0.047 | |
AlvMac_allgenes | 0.013 | 0.004 | 0.017 | |
AlvMac_results | 0.226 | 0.027 | 0.301 | |
AlvMac_results.pVal | 3.194 | 3.838 | 8.909 | |
GO_analyse | 4.027 | 0.164 | 5.495 | |
GOexpress-package | 0.006 | 0.008 | 0.016 | |
cluster_GO | 0.643 | 0.018 | 0.886 | |
expression_plot | 4.791 | 0.193 | 6.488 | |
expression_plot_symbol | 1.941 | 0.024 | 2.437 | |
expression_profiles | 1.257 | 0.020 | 1.517 | |
expression_profiles_symbol | 1.318 | 0.015 | 1.649 | |
heatmap_GO | 1.734 | 0.036 | 2.232 | |
hist_scores | 0.434 | 0.013 | 0.610 | |
list_genes | 0.154 | 0.006 | 0.198 | |
microarray2dataset | 0.017 | 0.031 | 0.062 | |
pValue_GO | 0.001 | 0.000 | 0.001 | |
plot_design | 0.275 | 0.015 | 0.373 | |
prefix2dataset | 0.015 | 0.013 | 0.037 | |
quantiles_scores | 0.779 | 0.012 | 0.994 | |
rerank | 0.342 | 0.025 | 0.484 | |
subEset | 0.091 | 0.004 | 0.117 | |
subset_scores | 0.300 | 0.016 | 0.375 | |
table_genes | 0.189 | 0.008 | 0.244 | |