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 12:07 -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 786/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemini 1.20.0 (landing page) Sidharth Jain
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 gemini package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemini.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: gemini |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemini_1.20.0.tar.gz |
StartedAt: 2024-12-20 20:10:44 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 20:13:20 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 155.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemini_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gemini.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gemini/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gemini’ version ‘1.20.0’ * package encoding: UTF-8 * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gemini’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 gemini_boxplot : <anonymous>: no visible binding for global variable ‘.’ gemini_boxplot: no visible binding for global variable ‘.’ gemini_boxplot : <anonymous>: no visible binding for global variable ‘gi’ gemini_boxplot : <anonymous>: no visible binding for global variable ‘hj’ gemini_boxplot: no visible binding for global variable ‘label’ gemini_boxplot: no visible binding for global variable ‘y’ gemini_calculate_lfc: no visible binding for global variable ‘.’ update_s_pb: no visible binding for global variable ‘.’ update_tau_pb: no visible binding for global variable ‘.’ Undefined global functions or variables: . gi hj label y * checking Rd files ... NOTE checkRd: (-1) gemini_initialize.Rd:81-83: Lost braces 81 | \strong{Use of negative control}{ | ^ * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gemini_inference 18.381 3.993 22.480 update_tau_pb 9.195 2.215 11.434 update_x_pb 7.146 1.645 8.863 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/gemini.Rcheck/00check.log’ for details.
gemini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gemini ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘gemini’ ... ** using staged installation ** R ** data ** 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 (gemini)
gemini.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(gemini) > > test_check("gemini") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 7.751 0.347 8.092
gemini.Rcheck/gemini-Ex.timings
name | user | system | elapsed | |
Sgene2Pguides_hash | 0 | 0 | 0 | |
Sguide2Pguides_hash | 0 | 0 | 0 | |
compound | 0 | 0 | 0 | |
dot-median_normalize | 0.000 | 0.000 | 0.001 | |
gemini_boxplot | 2.007 | 0.057 | 2.065 | |
gemini_calculate_lfc | 0.448 | 0.017 | 0.466 | |
gemini_create_input | 0.314 | 0.010 | 0.324 | |
gemini_inference | 18.381 | 3.993 | 22.480 | |
gemini_initialize | 3.720 | 0.109 | 3.846 | |
gemini_plot_mae | 0.943 | 0.013 | 0.957 | |
gemini_prepare_input | 0.409 | 0.009 | 0.417 | |
gemini_score | 0.823 | 0.008 | 0.830 | |
initialize_s | 1.308 | 0.038 | 1.348 | |
initialize_tau | 1.490 | 0.021 | 1.511 | |
initialize_x | 2.162 | 0.056 | 2.253 | |
initialize_y | 0.794 | 0.010 | 0.804 | |
pipe | 0 | 0 | 0 | |
update_mae | 1.087 | 0.016 | 1.104 | |
update_s_pb | 1.611 | 0.204 | 1.820 | |
update_tau_pb | 9.195 | 2.215 | 11.434 | |
update_x_pb | 7.146 | 1.645 | 8.863 | |
update_y_pb | 2.575 | 0.117 | 2.700 | |