Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1007/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IHW 1.35.0 (landing page) Nikos Ignatiadis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the IHW package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IHW.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: IHW |
Version: 1.35.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings IHW_1.35.0.tar.gz |
StartedAt: 2024-12-23 23:00:26 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:02:32 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 126.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IHW.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings IHW_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/IHW.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘IHW/DESCRIPTION’ ... OK * this is package ‘IHW’ version ‘1.35.0’ * 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 ‘IHW’ 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 filter_pvals_for_optim: no visible global function definition for ‘p.adjust’ groups_by_filter: no visible global function definition for ‘runif’ ihw.DESeqResults: no visible global function definition for ‘mcols’ ihw.DESeqResults: no visible global function definition for ‘mcols<-’ ihw.DESeqResults: no visible global function definition for ‘metadata’ ihw.DESeqResults: no visible global function definition for ‘metadata<-’ ihw.default: no visible global function definition for ‘runif’ ihw.default: no visible global function definition for ‘p.adjust’ ihw_convex: no visible global function definition for ‘gurobi’ ihw_internal: no visible global function definition for ‘p.adjust’ ihw_milp: no visible global function definition for ‘str’ ihw_milp: no visible global function definition for ‘gurobi’ plot_decisionboundary: no visible binding for global variable ‘stratum’ plot_decisionboundary: no visible binding for global variable ‘covariate’ plot_decisionboundary: no visible binding for global variable ‘pvalue’ plot_decisionboundary: no visible binding for global variable ‘fold’ thresholds_ihwResult: no visible global function definition for ‘na.exclude’ thresholds,ihwResult: no visible global function definition for ‘na.exclude’ Undefined global functions or variables: covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude p.adjust pvalue runif str stratum Consider adding importFrom("stats", "na.exclude", "p.adjust", "runif") importFrom("utils", "str") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/IHW.Rcheck/00check.log’ for details.
IHW.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL IHW ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘IHW’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IHW’ ** 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 (IHW)
IHW.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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("IHW") > > test_check("IHW") List of 3 $ solution: num [1:2000] 0 0 0 0 0 0 0 0 0 0 ... $ objval : num 70 $ status : Named int 0 ..- attr(*, "names")= chr "TM_OPTIMAL_SOLUTION_FOUND" NULL [ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 9.436 0.276 9.702
IHW.Rcheck/IHW-Ex.timings
name | user | system | elapsed | |
get_bh_threshold | 0.002 | 0.000 | 0.002 | |
groups_by_filter | 0.002 | 0.000 | 0.002 | |
ihw.DESeqResults | 0 | 0 | 0 | |
ihw.default | 3.411 | 0.050 | 3.460 | |
ihwResult-class | 1.898 | 0.008 | 1.905 | |
plot-ihwResult-method | 3.007 | 0.016 | 3.023 | |