Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1756/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RNAseqCovarImpute 1.3.0 (landing page) Brennan Baker
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the RNAseqCovarImpute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAseqCovarImpute.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: RNAseqCovarImpute |
Version: 1.3.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAseqCovarImpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RNAseqCovarImpute_1.3.0.tar.gz |
StartedAt: 2024-08-21 04:33:03 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 04:37:35 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 272.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RNAseqCovarImpute.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAseqCovarImpute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RNAseqCovarImpute_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RNAseqCovarImpute/DESCRIPTION' ... OK * this is package 'RNAseqCovarImpute' version '1.3.0' * 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 whether package 'RNAseqCovarImpute' 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 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 combine_rubins: no visible binding for global variable 'probe' combine_rubins: no visible binding for global variable 'i' combine_rubins: no visible binding for global variable 'coef_combined' combine_rubins: no visible binding for global variable 'rubins_t_bayes' combine_rubins: no visible binding for global variable 'combined_p' combine_rubins: no visible binding for global variable 'combined_p_bayes' limmavoom_imputed_data_list_helper: no visible binding for global variable 'i' limmavoom_imputed_data_list_helper: no visible binding for global variable 'lm_predictor' limmavoom_imputed_data_pca: no visible binding for global variable 'probe' lowess_all_gene_bins: no visible binding for global variable 'gene_bin' lowess_all_gene_bins: no visible binding for global variable 'i' voom_master_lowess: no visible global function definition for 'is' voom_master_lowess: no visible global function definition for 'new' voom_master_lowess: no visible global function definition for 'lowess' voom_master_lowess: no visible global function definition for 'approxfun' voom_sx_sy: no visible global function definition for 'is' voom_sx_sy: no visible global function definition for 'new' Undefined global functions or variables: approxfun coef_combined combined_p combined_p_bayes gene_bin i is lm_predictor lowess new probe rubins_t_bayes Consider adding importFrom("methods", "is", "new") importFrom("stats", "approxfun", "lowess") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Documented arguments not in \usage in Rd file 'impute_gene_bin_helper.Rd': 'DGE' 'param' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 limmavoom_imputed_data_pca 11.17 0.65 45.52 combine_rubins 1.60 0.03 29.51 impute_by_gene_bin 1.03 0.09 25.83 get_gene_bin_intervals 0.97 0.14 26.01 limmavoom_imputed_data_list 0.94 0.13 25.06 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck/00check.log' for details.
RNAseqCovarImpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RNAseqCovarImpute ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'RNAseqCovarImpute' ... ** using staged installation ** R ** data ** 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 (RNAseqCovarImpute)
RNAseqCovarImpute.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(RNAseqCovarImpute) > > test_check("RNAseqCovarImpute") iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a 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4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b iter imp variable 1 1 y z a b 1 2 y z a b 2 1 y z a b 2 2 y z a b 3 1 y z a b 3 2 y z a b 4 1 y z a b 4 2 y z a b 5 1 y z a b 5 2 y z a b 6 1 y z a b 6 2 y z a b 7 1 y z a b 7 2 y z a b 8 1 y z a b 8 2 y z a b 9 1 y z a b 9 2 y z a b 10 1 y z a b 10 2 y z a b [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 18.51 2.10 30.46
RNAseqCovarImpute.Rcheck/RNAseqCovarImpute-Ex.timings
name | user | system | elapsed | |
combine_rubins | 1.60 | 0.03 | 29.51 | |
example_DGE | 0.07 | 0.05 | 0.14 | |
example_data | 0.00 | 0.00 | 0.05 | |
get_gene_bin_intervals | 0.97 | 0.14 | 26.01 | |
impute_by_gene_bin | 1.03 | 0.09 | 25.83 | |
limmavoom_imputed_data_list | 0.94 | 0.13 | 25.06 | |
limmavoom_imputed_data_pca | 11.17 | 0.65 | 45.52 | |