Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:07 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 802/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemini 1.23.0 (landing page) Sidharth Jain
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: gemini |
Version: 1.23.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemini_1.23.0.tar.gz |
StartedAt: 2025-09-23 07:27:31 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 07:30:47 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 196.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemini_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gemini.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gemini/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gemini’ version ‘1.23.0’ * 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 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 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 35.463 0.367 35.913 update_tau_pb 15.806 0.259 16.106 update_x_pb 13.200 0.028 13.263 gemini_initialize 6.301 0.077 6.392 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/gemini.Rcheck/00check.log’ for details.
gemini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gemini ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘gemini’ ... ** this is package ‘gemini’ version ‘1.23.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 8.390 0.307 8.706
gemini.Rcheck/gemini-Ex.timings
name | user | system | elapsed | |
Sgene2Pguides_hash | 0 | 0 | 0 | |
Sguide2Pguides_hash | 0 | 0 | 0 | |
compound | 0.001 | 0.000 | 0.000 | |
dot-median_normalize | 0 | 0 | 0 | |
gemini_boxplot | 3.133 | 0.415 | 3.558 | |
gemini_calculate_lfc | 0.408 | 0.032 | 0.442 | |
gemini_create_input | 0.323 | 0.000 | 0.323 | |
gemini_inference | 35.463 | 0.367 | 35.913 | |
gemini_initialize | 6.301 | 0.077 | 6.392 | |
gemini_plot_mae | 0.853 | 0.004 | 0.858 | |
gemini_prepare_input | 0.376 | 0.008 | 0.384 | |
gemini_score | 0.792 | 0.008 | 0.801 | |
initialize_s | 1.652 | 0.000 | 1.656 | |
initialize_tau | 2.049 | 0.000 | 2.054 | |
initialize_x | 4.072 | 0.012 | 4.093 | |
initialize_y | 0.638 | 0.000 | 0.640 | |
pipe | 0 | 0 | 0 | |
update_mae | 1.203 | 0.004 | 1.210 | |
update_s_pb | 2.618 | 0.020 | 2.645 | |
update_tau_pb | 15.806 | 0.259 | 16.106 | |
update_x_pb | 13.200 | 0.028 | 13.263 | |
update_y_pb | 4.206 | 0.004 | 4.222 | |