Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
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. |
Package: GOexpress |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GOexpress_1.40.0.tar.gz |
StartedAt: 2024-11-20 03:56:22 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:58:32 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 130.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GOexpress.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GOexpress_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ‘/media/volume/teran2_disk/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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck/00check.log’ for details.
GOexpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GOexpress ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 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 | 0.060 | 0.007 | 0.066 | |
AlvMac_GOgenes | 0.478 | 0.015 | 0.519 | |
AlvMac_allGO | 0.013 | 0.001 | 0.013 | |
AlvMac_allgenes | 0.003 | 0.000 | 0.004 | |
AlvMac_results | 0.079 | 0.015 | 0.095 | |
AlvMac_results.pVal | 0.519 | 0.336 | 0.880 | |
GO_analyse | 1.916 | 0.051 | 2.026 | |
GOexpress-package | 0.001 | 0.001 | 0.003 | |
cluster_GO | 0.079 | 0.012 | 0.092 | |
expression_plot | 1.364 | 0.069 | 1.807 | |
expression_plot_symbol | 0.530 | 0.015 | 0.545 | |
expression_profiles | 0.477 | 0.002 | 0.498 | |
expression_profiles_symbol | 0.391 | 0.001 | 0.396 | |
heatmap_GO | 0.319 | 0.006 | 0.335 | |
hist_scores | 0.639 | 0.023 | 0.676 | |
list_genes | 0.053 | 0.014 | 0.067 | |
microarray2dataset | 0.004 | 0.002 | 0.006 | |
pValue_GO | 0 | 0 | 0 | |
plot_design | 0.091 | 0.012 | 0.103 | |
prefix2dataset | 0.004 | 0.001 | 0.005 | |
quantiles_scores | 0.077 | 0.001 | 0.078 | |
rerank | 0.119 | 0.002 | 0.121 | |
subEset | 0.027 | 0.001 | 0.028 | |
subset_scores | 0.113 | 0.000 | 0.113 | |
table_genes | 0.058 | 0.000 | 0.058 | |