Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1789/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RNAseqCovarImpute 1.7.0 (landing page) Brennan Baker
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: RNAseqCovarImpute |
Version: 1.7.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAseqCovarImpute_1.7.0.tar.gz |
StartedAt: 2025-08-01 10:27:46 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 11:07:46 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 2400.3 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: RNAseqCovarImpute.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAseqCovarImpute_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RNAseqCovarImpute.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 ‘RNAseqCovarImpute/DESCRIPTION’ ... OK * this is package ‘RNAseqCovarImpute’ version ‘1.7.0’ * 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 ‘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 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 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 ...
RNAseqCovarImpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RNAseqCovarImpute ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘RNAseqCovarImpute’ ... ** this is package ‘RNAseqCovarImpute’ version ‘1.7.0’ ** 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/RNAseqCovarImpute-Ex.timings
name | user | system | elapsed | |
combine_rubins | 21.351 | 1.162 | 11.233 | |
example_DGE | 0.090 | 0.004 | 0.094 | |
example_data | 0.003 | 0.000 | 0.003 | |
get_gene_bin_intervals | 20.708 | 1.161 | 10.297 | |
impute_by_gene_bin | 20.738 | 1.057 | 10.036 | |