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 786/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemini 1.20.0 (landing page) Sidharth Jain
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. |
Package: gemini |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gemini_1.20.0.tar.gz |
StartedAt: 2024-11-20 03:22:21 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:24:32 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 130.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gemini_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/gemini.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 ‘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 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 14.571 0.040 14.938 update_tau_pb 5.871 0.303 6.549 update_x_pb 5.651 0.003 5.883 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/gemini.Rcheck/00check.log’ for details.
gemini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gemini ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-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 4.894 0.273 5.230
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 | 0.001 | 0.000 | 0.000 | |
gemini_boxplot | 1.321 | 0.075 | 1.414 | |
gemini_calculate_lfc | 0.238 | 0.012 | 0.253 | |
gemini_create_input | 0.163 | 0.003 | 0.171 | |
gemini_inference | 14.571 | 0.040 | 14.938 | |
gemini_initialize | 3.074 | 0.041 | 3.673 | |
gemini_plot_mae | 0.406 | 0.000 | 0.549 | |
gemini_prepare_input | 0.215 | 0.001 | 0.288 | |
gemini_score | 0.401 | 0.002 | 0.403 | |
initialize_s | 0.739 | 0.005 | 0.744 | |
initialize_tau | 1.291 | 0.000 | 1.880 | |
initialize_x | 1.741 | 0.012 | 1.854 | |
initialize_y | 0.340 | 0.003 | 0.345 | |
pipe | 0 | 0 | 0 | |
update_mae | 0.608 | 0.008 | 0.616 | |
update_s_pb | 1.042 | 0.001 | 1.061 | |
update_tau_pb | 5.871 | 0.303 | 6.549 | |
update_x_pb | 5.651 | 0.003 | 5.883 | |
update_y_pb | 2.251 | 0.002 | 2.258 | |