Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2066/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
systemPipeShiny 1.15.0 (landing page) Le Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the systemPipeShiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/systemPipeShiny.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: systemPipeShiny |
Version: 1.15.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeShiny.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings systemPipeShiny_1.15.0.tar.gz |
StartedAt: 2024-06-10 10:58:06 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 11:06:45 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 519.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeShiny.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeShiny.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings systemPipeShiny_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'systemPipeShiny/DESCRIPTION' ... OK * this is package 'systemPipeShiny' version '1.15.0' * 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 'systemPipeShiny' 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 whether startup messages can be suppressed ... 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 core_topServer : module : <anonymous>: warning in eval(code, env = .GlobalEnv): partial argument match of 'env' to 'envir' .validateGuide: no visible binding for global variable 'guide_ui' .validateGuide: no visible binding for global variable 'guide_content' .validateGuide : <anonymous>: no visible binding for global variable 'guide_content' admin_infoServer : timeDiffString: no visible binding for global variable 'time_start' admin_infoServer : getCPU: no visible binding for global variable 'V2' appLoadingTime: no visible binding for global variable 'time_start' core_topServer : module : <anonymous>: no visible global function definition for 'dev.off' core_topServer : module : <anonymous>: no visible binding for '<<-' assignment to '.cur_plot' core_topServer : module : <anonymous>: no visible global function definition for 'dev.cur' core_topServer : module : <anonymous>: no visible binding for global variable '.cur_plot' core_topServer : module : <anonymous>: no visible global function definition for 'recordPlot' core_topServer : module : <anonymous>: no visible global function definition for 'png' core_topServer : module : <anonymous>: no visible binding for global variable '.rs_dir' core_topServer : module : <anonymous>: no visible binding for global variable '.plot_num' core_topServer : module : <anonymous>: no visible global function definition for 'replayPlot' core_topServer : module : <anonymous>: no visible binding for '<<-' assignment to '.plot_num' findTabInfo: no visible binding for global variable 'tab_info' makeSort: no visible binding for global variable 'session' parseGuide: no visible binding for global variable 'guide_ui' parseGuide: no visible binding for global variable 'guide_content' removeSpsTab: no visible binding for global variable 'type' removeSpsTab: no visible binding for global variable 'tab_file_name' vs_rnaseq_degServer : module: no visible binding for global variable 'trans_table' vs_rnaseq_degServer : module: no visible binding for global variable 'Sample' vs_rnaseq_degServer : module: no visible binding for global variable 'log2FoldChange' vs_rnaseq_degServer : module: no visible binding for global variable 'padj' vs_rnaseq_degServer : module: no visible binding for global variable 'cmp' vs_rnaseq_degServer : module: no visible binding for global variable 'direction' vs_rnaseq_degServer : module: no visible binding for global variable 'pass_filter' vs_rnaseq_degServer : module : <anonymous>: no visible binding for global variable 'pass_filter' vs_rnaseq_degServer : module : <anonymous>: no visible binding for global variable 'cmp' vs_rnaseq_degServer : module: no visible binding for global variable 'baseMean' vs_rnaseq_degServer : module: no visible global function definition for 'png' vs_rnaseq_degServer : module: no visible global function definition for 'dev.off' vs_rnaseq_dendroServer : module: no visible global function definition for 'hcl.colors' vs_rnaseq_dendroServer : module: no visible global function definition for 'title' vs_rnaseq_glmServer : module: no visible binding for global variable 'dim1' vs_rnaseq_glmServer : module: no visible binding for global variable 'dim2' vs_rnaseq_heatmapServer : module: no visible global function definition for 'png' vs_rnaseq_heatmapServer : module: no visible global function definition for 'dev.off' vs_rnaseq_mdsServer : module: no visible binding for global variable 'spsRNA_trans' vs_rnaseq_mdsServer : module: no visible binding for global variable 'X1' vs_rnaseq_mdsServer : module: no visible binding for global variable 'X2' vs_rnaseq_normalServer : module: no visible binding for '<<-' assignment to 'spsRNA_trans' vs_rnaseq_normalServer : module: no visible binding for global variable 'spsRNA_trans' vs_rnaseq_normalServer : module: no visible binding for '<<-' assignment to 'spsDEG' vs_rnaseq_normalServer : module : <anonymous>: no visible binding for global variable 'spsRNA_trans' vs_rnaseq_pcaServer : module: no visible binding for global variable 'spsRNA_trans' vs_rnaseq_pcaServer : module: no visible binding for global variable 'PC1' vs_rnaseq_pcaServer : module: no visible binding for global variable 'PC2' vs_rnaseq_tsneServer : module: no visible binding for global variable 'dim1' vs_rnaseq_tsneServer : module: no visible binding for global variable 'dim2' wf_runServer : module : <anonymous> : <anonymous>: no visible global function definition for 'png' wf_runServer : module : <anonymous> : <anonymous>: no visible binding for global variable '.rs_dir' wf_runServer : module : <anonymous> : <anonymous>: no visible binding for global variable '.plot_num' wf_runServer : module : <anonymous> : <anonymous>: no visible global function definition for 'dev.cur' wf_runServer : module : <anonymous> : <anonymous>: no visible global function definition for 'dev.new' wf_runServer : module : <anonymous> : <anonymous>: no visible global function definition for 'dev.control' wf_runServer : module : <anonymous> : <anonymous>: no visible binding for '<<-' assignment to '.plot_num' wf_runServer : module : <anonymous>: no visible binding for '<<-' assignment to '.rs_dir' wf_runServer : module : <anonymous>: no visible binding for '<<-' assignment to '.plot_num' wf_runServer : module : <anonymous>: no visible binding for '<<-' assignment to '.cur_plot' wf_wfServer : module: no visible binding for global variable 'input_code' Undefined global functions or variables: .cur_plot .plot_num .rs_dir PC1 PC2 Sample V2 X1 X2 baseMean cmp dev.control dev.cur dev.new dev.off dim1 dim2 direction guide_content guide_ui hcl.colors input_code log2FoldChange padj pass_filter png recordPlot replayPlot session spsRNA_trans tab_file_name tab_info time_start title trans_table type Consider adding importFrom("grDevices", "dev.control", "dev.cur", "dev.new", "dev.off", "hcl.colors", "png", "recordPlot", "replayPlot") importFrom("graphics", "title") 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.Rcheck/00check.log' for details.
systemPipeShiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL systemPipeShiny ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'systemPipeShiny' ... ** using staged installation ** 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 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 (systemPipeShiny)
systemPipeShiny.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > library(testthat) > library(systemPipeShiny) Loading required package: shiny Loading required package: spsUtil Loading required package: spsComps Loading required package: drawer > test_check('systemPipeShiny') [SPS-INFO] 2024-06-10 11:04:26.581734 Created SPS encryption method container [SPS-INFO] 2024-06-10 11:04:26.590078 Default SPS-db found and is working [SPS-INFO] 2024-06-10 11:04:28.018098 App starts ... create a new R6 [ FAIL 0 | WARN 0 | SKIP 2 | PASS 75 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test-04imports.R:57:5' • Skip on checks (1): 'test-02interactive_funcs.R:31:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 75 ] > identical(Sys.getenv("NOT_CRAN"), "true") [1] FALSE > > proc.time() user system elapsed 17.39 110.75 130.06
systemPipeShiny.Rcheck/systemPipeShiny-Ex.timings
name | user | system | elapsed | |
canvasBtn | 0.02 | 0.03 | 0.05 | |
dynamicFile | 0 | 0 | 0 | |
genGallery | 0 | 0 | 0 | |
genHrefTable | 0 | 0 | 0 | |
loadDF | 0 | 0 | 0 | |
removeSpsTab | 0.68 | 0.29 | 1.06 | |
sps | 0 | 0 | 0 | |
spsAccount | 0.40 | 0.05 | 0.45 | |
spsCoreTabReplace | 0.02 | 0.00 | 0.02 | |
spsDb | 0.33 | 0.00 | 0.34 | |
spsEncryption | 0.23 | 0.02 | 0.27 | |
spsEzUI | 0 | 0 | 0 | |
spsInit | 0 | 0 | 0 | |
spsNewTab | 0.27 | 0.09 | 0.45 | |
spsOptDefaults | 0 | 0 | 0 | |
spsTabInfo | 0.28 | 0.08 | 0.42 | |