Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 286/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cbpManager 1.14.0 (landing page) Arsenij Ustjanzew
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cbpManager package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cbpManager.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: cbpManager |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cbpManager.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cbpManager_1.14.0.tar.gz |
StartedAt: 2024-11-19 23:57:55 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:58:44 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 49.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cbpManager.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cbpManager.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cbpManager_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/cbpManager.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘cbpManager/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cbpManager’ version ‘1.14.0’ * 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 ‘cbpManager’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/cbpManager.Rcheck/00install.out’ for details. * 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 ... NOTE Namespace in Imports field not imported from: ‘markdown’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cbpManager: no visible binding for '<<-' assignment to ‘cbpManager.options’ generateUIwidgets: no visible global function definition for ‘selectizeInput’ saveResource_Server: no visible global function definition for ‘runif’ saveTimeline_Server: no visible global function definition for ‘runif’ shinyAppServer: no visible binding for '<<-' assignment to ‘study_dir’ shinyAppServer: no visible binding for '<<-' assignment to ‘logDir’ shinyAppServer: no visible binding for '<<-' assignment to ‘oncotree’ shinyAppServer: no visible binding for '<<-' assignment to ‘tumor_tissue_site’ shinyAppServer: no visible binding for '<<-' assignment to ‘cancer_type’ shinyAppServer: no visible binding for '<<-' assignment to ‘oncotree_code’ shinyAppServer: no visible binding for '<<-' assignment to ‘cancer_type_detailed’ Undefined global functions or variables: runif selectizeInput Consider adding importFrom("stats", "runif") 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 ... WARNING Undocumented arguments in Rd file 'generateUIwidgets.Rd' ‘sampleIDs’ 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 line endings in shell scripts ... 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 WARNING, 3 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/cbpManager.Rcheck/00check.log’ for details.
cbpManager.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cbpManager ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘cbpManager’ ... ** using non-staged installation via StagedInstall field ** R ** 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 * DONE (cbpManager)
cbpManager.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(cbpManager) Loading required package: shiny Loading required package: shinydashboard Attaching package: 'shinydashboard' The following object is masked from 'package:graphics': box > > test_check("cbpManager") ##---------------------------------------------------------------------------## ## Launching cbpManager ##---------------------------------------------------------------------------## ##---------------------------------------------------------------------------## ## Launching cbpManager ##---------------------------------------------------------------------------## [ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test_functions.R:46:3' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ] > > proc.time() user system elapsed 1.589 0.199 1.776
cbpManager.Rcheck/cbpManager-Ex.timings
name | user | system | elapsed | |
IsDate | 0.001 | 0.000 | 0.000 | |
cBioPortalToDataFrame | 0.003 | 0.000 | 0.003 | |
cbpManager | 0 | 0 | 0 | |
check_input_dates | 0.001 | 0.000 | 0.001 | |
convertDataFrame | 0.002 | 0.001 | 0.002 | |
create_name | 0 | 0 | 0 | |
fncols | 0.001 | 0.000 | 0.001 | |
generateOncotreeUIwidgets | 0.071 | 0.011 | 0.085 | |
generateUIwidgets | 0.001 | 0.001 | 0.002 | |
getSampleIDs | 0.002 | 0.000 | 0.002 | |
setupConda_cbpManager | 0 | 0 | 0 | |
writeLogfile | 0.001 | 0.000 | 0.001 | |