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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2111/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeShiny 1.16.0  (landing page)
Le Zhang
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/systemPipeShiny
git_branch: RELEASE_3_20
git_last_commit: d1179e2
git_last_commit_date: 2024-10-29 10:51:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for systemPipeShiny on nebbiolo2

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.

raw results


Summary

Package: systemPipeShiny
Version: 1.16.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings systemPipeShiny_1.16.0.tar.gz
StartedAt: 2024-12-20 06:04:05 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:05:36 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 91.1 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeShiny.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings systemPipeShiny_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.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 ‘systemPipeShiny/DESCRIPTION’ ... OK
* this is package ‘systemPipeShiny’ version ‘1.16.0’
* 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 ‘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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.Rcheck/00check.log’
for details.


Installation output

systemPipeShiny.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL systemPipeShiny
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

systemPipeShiny.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(systemPipeShiny)
Loading required package: shiny
Loading required package: spsUtil
Loading required package: spsComps
Loading required package: drawer
> test_check('systemPipeShiny')
[SPS-INFO] 2024-12-20 06:05:11.54881 Created SPS encryption method container
[SPS-INFO] 2024-12-20 06:05:11.553636 Default SPS-db found and is working
[SPS-INFO] 2024-12-20 06:05:12.464663 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 
 14.406   0.957  15.671 

Example timings

systemPipeShiny.Rcheck/systemPipeShiny-Ex.timings

nameusersystemelapsed
canvasBtn0.0120.0020.015
dynamicFile0.0020.0010.001
genGallery000
genHrefTable0.0000.0000.001
loadDF0.0000.0000.001
removeSpsTab0.4650.0600.540
sps000
spsAccount0.6640.0060.670
spsCoreTabReplace0.0010.0000.000
spsDb0.3210.0020.323
spsEncryption0.6490.0040.653
spsEzUI000
spsInit000
spsNewTab0.6930.0130.707
spsOptDefaults000
spsTabInfo0.2620.0070.270