Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the systemPipeShiny package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1889/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
systemPipeShiny 1.2.0 (landing page) Le Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: systemPipeShiny |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeShiny_1.2.0.tar.gz |
StartedAt: 2021-10-15 00:34:57 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:37:21 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 143.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeShiny.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeShiny_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘systemPipeShiny/DESCRIPTION’ ... OK * this is package ‘systemPipeShiny’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... 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 R 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 core_topServer : module : <anonymous>: warning in eval(code, env = .GlobalEnv): partial argument match of 'env' to 'envir' vs_rnaseq_normalServer : module: warning in read.delim(targetspath, comment = "#"): partial argument match of 'comment' to 'comment.char' .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’ 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_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_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’ 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 log2FoldChange padj pass_filter png recordPlot replayPlot spsRNA_trans tab_file_name tab_info time_start trans_table type Consider adding importFrom("grDevices", "dev.control", "dev.cur", "dev.new", "dev.off", "png", "recordPlot", "replayPlot") 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 in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck/00check.log’ for details.
systemPipeShiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL systemPipeShiny ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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] 2021-10-15 00:36:43 Created SPS encryption method container [SPS-INFO] 2021-10-15 00:36:43 Default SPS-db found and is working if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c("DOT", "R.utils", "callr", "fs", "networkD3", "openssl", "pushbar", "readr", "rhandsontable", "shinyTree", "systemPipeR", "systemPipeRdata", "zip")) if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c("DESeq2", "Rtsne", "SummarizedExperiment", "UpSetR", "ape", "ggtree", "glmpca", "grid", "pheatmap", "systemPipeR", "tidyr")) Error in getOption("encoding") : reached elapsed time limit This Font Awesome icon ('warning') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('gears') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('gear') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('file-image-o') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('file-pdf-o') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('file-image-o') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('file-powerpoint-o') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('gear') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('remove') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('remove') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('gears') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('close') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` [SPS-INFO] 2021-10-15 00:36:50 App starts ... This Font Awesome icon ('') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` This Font Awesome icon ('') does not exist: * if providing a custom `html_dependency` these `name` checks can be deactivated with `verify_fa = FALSE` Loading required package: shinyTree create a new R6 ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (2) • Skip on checks (1) [ FAIL 0 | WARN 0 | SKIP 3 | PASS 76 ] > identical(Sys.getenv("NOT_CRAN"), "true") [1] FALSE > > proc.time() user system elapsed 29.763 2.880 33.916
systemPipeShiny.Rcheck/systemPipeShiny-Ex.timings
name | user | system | elapsed | |
canvasBtn | 0.020 | 0.001 | 0.021 | |
dynamicFile | 0.004 | 0.002 | 0.006 | |
genGallery | 0.001 | 0.000 | 0.001 | |
genHrefTable | 0.001 | 0.000 | 0.001 | |
loadDF | 0.002 | 0.001 | 0.002 | |
removeSpsTab | 0.698 | 0.089 | 0.800 | |
sps | 0.001 | 0.000 | 0.001 | |
spsAccount | 0.414 | 0.022 | 0.438 | |
spsCoreTabReplace | 0.001 | 0.000 | 0.000 | |
spsDb | 0.347 | 0.011 | 0.359 | |
spsEncryption | 0.314 | 0.010 | 0.326 | |
spsEzUI | 0.000 | 0.001 | 0.000 | |
spsInit | 0.001 | 0.000 | 0.000 | |
spsNewTab | 0.332 | 0.052 | 0.383 | |
spsOptDefaults | 0.001 | 0.001 | 0.001 | |
spsTabInfo | 0.545 | 0.052 | 0.597 | |