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CHECK report for systemPipeShiny on malbec1

This page was generated on 2021-05-06 12:29:23 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the systemPipeShiny package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1833/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeShiny 1.0.20  (landing page)
Le Zhang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/systemPipeShiny
Branch: RELEASE_3_12
Last Commit: 51f0dac
Last Changed Date: 2021-03-15 14:31:44 -0400 (Mon, 15 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeShiny
Version: 1.0.20
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings systemPipeShiny_1.0.20.tar.gz
StartedAt: 2021-05-06 06:32:45 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:34:53 -0400 (Thu, 06 May 2021)
EllapsedTime: 127.9 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeShiny.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings systemPipeShiny_1.0.20.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/systemPipeShiny.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeShiny/DESCRIPTION’ ... OK
* this is package ‘systemPipeShiny’ version ‘1.0.20’
* 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 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’
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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/systemPipeShiny.Rcheck/00check.log’
for details.



Installation output

systemPipeShiny.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL systemPipeShiny
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output

systemPipeShiny.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] 2021-05-06 06:34:47 App starts ...
Loading required package: shinyTree
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)
• Skip on checks (1)

[ FAIL 0 | WARN 4 | SKIP 2 | PASS 71 ]
> identical(Sys.getenv("NOT_CRAN"), "true")
[1] FALSE
> 
> proc.time()
   user  system elapsed 
 28.464   1.008  32.335 

Example timings

systemPipeShiny.Rcheck/systemPipeShiny-Ex.timings

nameusersystemelapsed
canvasBtn0.0160.0000.019
genGallery0.0000.0000.001
genHrefTable0.0000.0000.001
removeSpsTab0.2080.0360.367
sps000
spsCoreTabReplace0.0000.0000.001
spsEzUI0.0000.0000.001
spsInit0.0000.0000.001
spsNewTab0.3120.0240.350
spsOptDefaults0.0000.0000.001
spsTabInfo0.2920.0160.312