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) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:25 -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: 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 |
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### 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
###
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* 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.
systemPipeShiny.Rcheck/00install.out
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###
### 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
###
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% 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
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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
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systemPipeShiny.Rcheck/examples_i386/systemPipeShiny-Ex.timings
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systemPipeShiny.Rcheck/examples_x64/systemPipeShiny-Ex.timings
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