Frederic Fournier
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/shinyTANDEM |
| Branch: RELEASE_3_12 |
| Last Commit: 0602b16 |
| Last Changed Date: 2020-10-27 10:53:37 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:29:06 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the shinyTANDEM package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1696/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Frederic Fournier
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| Package: shinyTANDEM |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:shinyTANDEM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings shinyTANDEM_1.28.0.tar.gz |
| StartedAt: 2021-05-06 06:01:14 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:02:23 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 68.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: shinyTANDEM.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:shinyTANDEM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings shinyTANDEM_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/shinyTANDEM.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 ‘shinyTANDEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘shinyTANDEM’ version ‘1.28.0’
* 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 ‘shinyTANDEM’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
Warning: Package 'shinyTANDEM' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.12-bioc/meat/shinyTANDEM.Rcheck/00install.out’ for details.
* 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 ... NOTE
Packages in Depends field not imported from:
‘methods’ ‘mixtools’ ‘rTANDEM’ ‘shiny’ ‘xtable’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Progress: no visible global function definition for ‘new’
analysis.ui: no visible global function definition for ‘div’
analysis.ui: no visible global function definition for ‘h2’
analysis.ui: no visible global function definition for ‘p’
biomart.ui: no visible global function definition for ‘div’
biomart.ui: no visible global function definition for ‘h2’
biomart.ui: no visible global function definition for ‘p’
convert.ui: no visible global function definition for ‘div’
convert.ui: no visible global function definition for ‘h2’
convert.ui: no visible global function definition for ‘p’
external.ui: no visible global function definition for ‘h3’
gominer.ui: no visible global function definition for ‘div’
gominer.ui: no visible global function definition for ‘h2’
gominer.ui: no visible global function definition for ‘p’
home.ui: no visible global function definition for ‘div’
home.ui: no visible binding for global variable ‘tags’
launch.ui: no visible global function definition for ‘div’
launch.ui: no visible global function definition for ‘h2’
launch.ui: no visible global function definition for ‘p’
load.ui: no visible global function definition for ‘div’
load.ui: no visible global function definition for ‘h4’
load.ui: no visible global function definition for ‘h5’
load.ui: no visible global function definition for ‘tag’
load.ui: no visible global function definition for ‘span’
load.ui: no visible binding for global variable ‘tags’
load.ui: no visible global function definition for ‘actionButton’
load.ui: no visible global function definition for ‘uiOutput’
navSection: no visible global function definition for ‘tagList’
navSection: no visible global function definition for ‘singleton’
navSection: no visible binding for global variable ‘tags’
navSection: no visible global function definition for ‘includeHTML’
overview.ui: no visible global function definition for ‘div’
overview.ui: no visible global function definition for ‘h3’
overview.ui: no visible global function definition for ‘htmlOutput’
param.ui: no visible global function definition for ‘div’
param.ui: no visible global function definition for ‘h2’
param.ui: no visible global function definition for ‘p’
peps.ui: no visible global function definition for ‘div’
peps.ui: no visible global function definition for ‘h3’
peps.ui: no visible global function definition for ‘textInput’
peps.ui: no visible global function definition for ‘uiOutput’
peps.ui: no visible binding for global variable ‘tags’
peps.ui: no visible global function definition for ‘htmlOutput’
progressInit: no visible global function definition for ‘tagList’
progressInit: no visible global function definition for ‘singleton’
progressInit: no visible binding for global variable ‘tags’
prots.ui: no visible global function definition for ‘div’
prots.ui: no visible global function definition for ‘h3’
prots.ui: no visible global function definition for ‘numericInput’
prots.ui: no visible global function definition for ‘textInput’
prots.ui: no visible global function definition for ‘uiOutput’
prots.ui: no visible binding for global variable ‘tags’
prots.ui: no visible global function definition for ‘htmlOutput’
shinyTANDEM: no visible global function definition for
‘addResourcePath’
shinyTANDEM: no visible global function definition for ‘is’
shinyTANDEM: no visible global function definition for ‘runApp’
shinyTandemServer: no visible global function definition for
‘reactiveValues’
shinyTandemServer: no visible global function definition for ‘reactive’
shinyTandemServer: no visible global function definition for ‘isolate’
shinyTandemServer: no visible global function definition for ‘is’
shinyTandemServer: no visible global function definition for
‘GetResultsFromXML’
shinyTandemServer: no visible binding for global variable ‘dataset’
shinyTandemServer: no visible global function definition for ‘observe’
shinyTandemServer: no visible global function definition for ‘renderUI’
shinyTandemServer: no visible global function definition for ‘div’
shinyTandemServer: no visible global function definition for
‘renderText’
shinyTandemServer: no visible binding for global variable
‘expect.value’
shinyTandemServer: no visible binding for global variable
‘num.peptides’
shinyTandemServer: no visible global function definition for ‘like’
shinyTandemServer: no visible binding for global variable ‘label’
shinyTandemServer: no visible global function definition for
‘selectInput’
shinyTandemServer: no visible binding for global variable ‘prot.uid’
shinyTandemServer: no visible global function definition for ‘HTML’
shinyTandemServer: no visible global function definition for
‘tabsetPanel’
shinyTandemServer: no visible global function definition for ‘tabPanel’
shinyTandemServer: no visible global function definition for
‘plotOutput’
shinyTandemServer: no visible global function definition for ‘helpText’
shinyTandemServer: no visible global function definition for
‘renderPlot’
shinyTandemServer: no visible global function definition for ‘points’
shinyTandemServer: no visible global function definition for ‘abline’
shinyTandemServer: no visible global function definition for ‘legend’
shinyTandemServer: no visible binding for global variable ‘tabsetPanel’
shinyTandemServer : plotChargeDis: no visible global function
definition for ‘normalmixEM’
shinyTandemServer : plotChargeDis: no visible global function
definition for ‘lines’
shinyTandemServer : plotChargeDis: no visible global function
definition for ‘density’
shinyTandemServer : plotChargeDis: no visible global function
definition for ‘legend’
shinyTandemServer: no visible binding for global variable ‘type’
shinyTandemServer: no visible binding for global variable ‘modified’
shinyTandemServer: no visible binding for global variable ‘pep.id’
shinyTandemServer: no visible binding for global variable ‘uid’
shinyTandemServer : <anonymous>: no visible binding for global variable
‘pep.id’
shinyTandemServer : <anonymous>: no visible binding for global variable
‘at’
shinyTandemServer : <anonymous>: no visible binding for global variable
‘type’
shinyTandemServer : <anonymous>: no visible binding for global variable
‘modified’
shinyTandemServer : <anonymous>: no visible global function definition
for ‘tabPanel’
shinyTandemServer : <anonymous>: no visible global function definition
for ‘plotOutput’
shinyUI: no visible global function definition for ‘basicPage’
shinyUI: no visible global function definition for ‘conditionalPanel’
stats.ui: no visible global function definition for ‘div’
stats.ui: no visible global function definition for ‘h3’
stats.ui: no visible global function definition for ‘uiOutput’
tableAsHTML: no visible global function definition for ‘capture.output’
tableAsHTML: no visible global function definition for ‘xtable’
Undefined global functions or variables:
GetResultsFromXML HTML abline actionButton addResourcePath at
basicPage capture.output conditionalPanel dataset density div
expect.value h2 h3 h4 h5 helpText htmlOutput includeHTML is isolate
label legend like lines modified new normalmixEM num.peptides
numericInput observe p pep.id plotOutput points prot.uid reactive
reactiveValues renderPlot renderText renderUI runApp selectInput
singleton span tabPanel tabsetPanel tag tagList tags textInput type
uiOutput uid xtable
Consider adding
importFrom("graphics", "abline", "legend", "lines", "points")
importFrom("methods", "is", "new")
importFrom("stats", "density")
importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/shinyTANDEM.Rcheck/00check.log’
for details.
shinyTANDEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL shinyTANDEM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘shinyTANDEM’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: Package 'rTANDEM' is deprecated and will be removed from Bioconductor version 3.13 ** help *** installing help indices ** building package indices ** installing vignettes ‘shinyTANDEM.Rnw’ ** testing if installed package can be loaded from temporary location Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor version 3.13 Warning: Package 'shinyTANDEM' is deprecated and will be removed from Bioconductor version 3.13 ** testing if installed package can be loaded from final location Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor version 3.13 Warning: Package 'shinyTANDEM' is deprecated and will be removed from Bioconductor version 3.13 ** testing if installed package keeps a record of temporary installation path * DONE (shinyTANDEM)
shinyTANDEM.Rcheck/shinyTANDEM-Ex.timings
| name | user | system | elapsed | |
| shinyTANDEM | 0.000 | 0.000 | 0.001 | |