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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for systemPipeShiny on tokay2

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.

raw results

Package 1889/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeShiny 1.2.0  (landing page)
Le Zhang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/systemPipeShiny
git_branch: RELEASE_3_13
git_last_commit: 6765e8d
git_last_commit_date: 2021-05-19 12:56:05 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: systemPipeShiny
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeShiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeShiny_1.2.0.tar.gz
StartedAt: 2021-10-15 06:25:56 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:29:10 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 193.7 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeShiny.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeShiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeShiny_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck/00check.log'
for details.



Installation output

systemPipeShiny.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/systemPipeShiny_1.2.0.tar.gz && rm -rf systemPipeShiny.buildbin-libdir && mkdir systemPipeShiny.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeShiny.buildbin-libdir systemPipeShiny_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL systemPipeShiny_1.2.0.zip && rm systemPipeShiny_1.2.0.tar.gz systemPipeShiny_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 55 2612k   55 1451k    0     0  1902k      0  0:00:01 --:--:--  0:00:01 1902k
100 2612k  100 2612k    0     0  2237k      0  0:00:01  0:00:01 --:--:-- 2240k

install for i386

* installing *source* package 'systemPipeShiny' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'systemPipeShiny'
    finding HTML links ... done
    canvasBtn                               html  
    dynamicFile                             html  
    finding level-2 HTML links ... done

    genGallery                              html  
    genHrefTable                            html  
    loadDF                                  html  
    removeSpsTab                            html  
    sps                                     html  
    spsAccount                              html  
    spsCoreTabReplace                       html  
    spsDb                                   html  
    spsEncryption                           html  
    spsEzUI                                 html  
    spsInit                                 html  
    spsNewTab                               html  
    spsOptDefaults                          html  
    spsTabInfo                              html  
** 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

install for x64

* installing *source* package 'systemPipeShiny' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeShiny' as systemPipeShiny_1.2.0.zip
* DONE (systemPipeShiny)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'systemPipeShiny' successfully unpacked and MD5 sums checked

Tests output

systemPipeShiny.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 06:27:57 Created SPS encryption method container
[SPS-INFO] 2021-10-15 06:27:57 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"))
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("esquisse"))
Error in gzfile(file, "rb") : 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`
[SPS-INFO] 2021-10-15 06:28:05 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 
  24.64    4.90   31.14 

systemPipeShiny.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 06:28:29 Created SPS encryption method container
[SPS-INFO] 2021-10-15 06:28:29 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"))
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("esquisse"))
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`
[SPS-INFO] 2021-10-15 06:28:36 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 
  25.62    3.45   29.59 

Example timings

systemPipeShiny.Rcheck/examples_i386/systemPipeShiny-Ex.timings

nameusersystemelapsed
canvasBtn0.020.000.02
dynamicFile000
genGallery000
genHrefTable000
loadDF000
removeSpsTab1.380.062.43
sps000
spsAccount0.670.020.69
spsCoreTabReplace000
spsDb0.240.000.23
spsEncryption0.810.030.84
spsEzUI000
spsInit000
spsNewTab0.500.030.61
spsOptDefaults000
spsTabInfo1.110.061.18

systemPipeShiny.Rcheck/examples_x64/systemPipeShiny-Ex.timings

nameusersystemelapsed
canvasBtn0.020.000.02
dynamicFile000
genGallery000
genHrefTable000
loadDF000
removeSpsTab0.860.071.35
sps000
spsAccount0.390.010.41
spsCoreTabReplace000
spsDb0.210.020.22
spsEncryption0.200.010.23
spsEzUI000
spsInit000
spsNewTab0.700.030.73
spsOptDefaults000
spsTabInfo0.380.030.41