Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:04 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the gemini package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 736/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemini 1.13.0 (landing page) Sidharth Jain
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: gemini |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gemini_1.13.0.tar.gz |
StartedAt: 2023-02-07 02:10:18 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 02:14:26 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 247.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gemini_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/gemini.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘gemini/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gemini’ version ‘1.13.0’ * 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 ... 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 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 ... 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 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 37.283 0.605 41.020 update_tau_pb 16.826 0.028 17.610 update_x_pb 14.561 0.011 15.404 gemini_initialize 6.686 0.020 7.513 gemini_boxplot 5.963 0.059 6.301 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘gemini-quickstart.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/gemini.Rcheck/00check.log’ for details.
gemini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gemini ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 11.728 0.235 12.353
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 | 5.963 | 0.059 | 6.301 | |
gemini_calculate_lfc | 0.435 | 0.012 | 0.457 | |
gemini_create_input | 0.389 | 0.000 | 0.421 | |
gemini_inference | 37.283 | 0.605 | 41.020 | |
gemini_initialize | 6.686 | 0.020 | 7.513 | |
gemini_plot_mae | 0.813 | 0.004 | 0.924 | |
gemini_prepare_input | 0.443 | 0.004 | 0.448 | |
gemini_score | 0.841 | 0.000 | 0.874 | |
initialize_s | 1.617 | 0.004 | 1.837 | |
initialize_tau | 2.421 | 0.008 | 2.817 | |
initialize_x | 3.576 | 0.001 | 3.956 | |
initialize_y | 0.693 | 0.008 | 0.726 | |
pipe | 0 | 0 | 0 | |
update_mae | 1.330 | 0.008 | 1.365 | |
update_s_pb | 2.897 | 0.004 | 3.176 | |
update_tau_pb | 16.826 | 0.028 | 17.610 | |
update_x_pb | 14.561 | 0.011 | 15.404 | |
update_y_pb | 3.990 | 0.004 | 4.199 | |