Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:36 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 704/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemini 1.6.0 (landing page) Sidharth Jain
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: gemini |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.6.0.tar.gz |
StartedAt: 2021-10-14 19:17:27 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:20:52 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 205.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/gemini.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gemini/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gemini’ version ‘1.6.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt .github 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 ‘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 29.814 4.508 34.341 update_tau_pb 11.863 1.764 13.640 update_x_pb 11.372 1.387 12.767 gemini_initialize 8.606 0.089 8.700 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/gemini.Rcheck/00check.log’ for details.
gemini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gemini ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 9.690 0.371 10.051
gemini.Rcheck/gemini-Ex.timings
name | user | system | elapsed | |
Sgene2Pguides_hash | 0 | 0 | 0 | |
Sguide2Pguides_hash | 0 | 0 | 0 | |
compound | 0.000 | 0.001 | 0.001 | |
dot-median_normalize | 0 | 0 | 0 | |
gemini_boxplot | 3.411 | 0.059 | 3.473 | |
gemini_calculate_lfc | 0.461 | 0.023 | 0.488 | |
gemini_create_input | 0.439 | 0.017 | 0.459 | |
gemini_inference | 29.814 | 4.508 | 34.341 | |
gemini_initialize | 8.606 | 0.089 | 8.700 | |
gemini_plot_mae | 0.933 | 0.009 | 0.943 | |
gemini_prepare_input | 0.512 | 0.006 | 0.518 | |
gemini_score | 0.887 | 0.010 | 0.898 | |
initialize_s | 1.766 | 0.021 | 1.789 | |
initialize_tau | 3.113 | 0.046 | 3.163 | |
initialize_x | 4.589 | 0.023 | 4.614 | |
initialize_y | 0.831 | 0.009 | 0.840 | |
pipe | 0.001 | 0.000 | 0.000 | |
update_mae | 1.555 | 0.009 | 1.568 | |
update_s_pb | 2.484 | 0.175 | 2.663 | |
update_tau_pb | 11.863 | 1.764 | 13.640 | |
update_x_pb | 11.372 | 1.387 | 12.767 | |
update_y_pb | 3.733 | 0.074 | 3.810 | |