Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 857/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GOexpress 1.34.0 (landing page) Kevin Rue-Albrecht
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the GOexpress package: - 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: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2023-10-17 22:52:39 -0400 (Tue, 17 Oct 2023) |
EndedAt: 2023-10-17 22:56:33 -0400 (Tue, 17 Oct 2023) |
EllapsedTime: 234.9 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GOexpress.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GOexpress/DESCRIPTION’ ... OK * this is package ‘GOexpress’ version ‘1.34.0’ * 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 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 ... 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 ... OK * 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 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 | 0.181 | 0.016 | 0.306 | |
AlvMac_GOgenes | 0.413 | 0.008 | 0.639 | |
AlvMac_allGO | 0.024 | 0.003 | 0.041 | |
AlvMac_allgenes | 0.007 | 0.002 | 0.013 | |
AlvMac_results | 0.160 | 0.011 | 0.261 | |
AlvMac_results.pVal | 1.934 | 1.177 | 4.771 | |
GO_analyse | 2.780 | 0.079 | 4.438 | |
GOexpress-package | 0.004 | 0.005 | 0.009 | |
cluster_GO | 0.471 | 0.011 | 0.731 | |
expression_plot | 2.487 | 0.125 | 3.973 | |
expression_plot_symbol | 1.198 | 0.022 | 1.857 | |
expression_profiles | 0.850 | 0.014 | 1.327 | |
expression_profiles_symbol | 1.479 | 0.020 | 2.306 | |
heatmap_GO | 0.526 | 0.021 | 0.822 | |
hist_scores | 0.288 | 0.010 | 0.458 | |
list_genes | 0.133 | 0.004 | 0.194 | |
microarray2dataset | 0.010 | 0.011 | 0.031 | |
pValue_GO | 0 | 0 | 0 | |
plot_design | 0.606 | 0.016 | 0.951 | |
prefix2dataset | 0.008 | 0.005 | 0.022 | |
quantiles_scores | 0.146 | 0.003 | 0.228 | |
rerank | 0.250 | 0.012 | 0.398 | |
subEset | 0.051 | 0.002 | 0.083 | |
subset_scores | 0.212 | 0.017 | 0.348 | |
table_genes | 0.119 | 0.005 | 0.188 | |