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This page was generated on 2021-12-03 13:05:23 -0500 (Fri, 03 Dec 2021).

CHECK results for MSGFgui on tokay2

To the developers/maintainers of the MSGFgui package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSGFgui.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 1217/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFgui 1.28.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/MSGFgui
git_branch: RELEASE_3_14
git_last_commit: 2725a95
git_last_commit_date: 2021-10-26 12:16:30 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: MSGFgui
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MSGFgui.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSGFgui_1.28.0.tar.gz
StartedAt: 2021-12-02 23:55:53 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 23:57:46 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 113.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSGFgui.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MSGFgui.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSGFgui_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFgui.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSGFgui/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSGFgui' 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MSGFgui' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MSGFgui' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFgui.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
Package in Depends field not imported from: 'xlsx'
  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
getAAtable: no visible global function definition for 'read.csv'
getAdductTable: no visible global function definition for 'read.csv'
getIonTrace: no visible global function definition for 'predict'
getIonTrace: no visible global function definition for 'loess'
getIonTrace : gauss: no visible global function definition for 'dnorm'
getIonTrace: no visible global function definition for 'optimize'
getScoreDistribution: no visible global function definition for
  'density'
renderMzID: no visible global function definition for 'scans'
renderMzID: no visible global function definition for 'peptides'
renderMzID: no visible global function definition for 'modifications'
renderMzID: no visible global function definition for 'database'
server: no visible global function definition for 'scans'
server : <anonymous>: no visible global function definition for
  'createWorkbook'
server : <anonymous>: no visible global function definition for
  'createSheet'
server : <anonymous>: no visible global function definition for
  'addDataFrame'
server : <anonymous>: no visible global function definition for
  'saveWorkbook'
server : <anonymous>: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  addDataFrame createSheet createWorkbook database density dnorm loess
  modifications optimize peptides predict read.csv saveWorkbook scans
  write.table
Consider adding
  importFrom("stats", "density", "dnorm", "loess", "optimize", "predict")
  importFrom("utils", "read.csv", "write.table")
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 'test-all.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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFgui.Rcheck/00check.log'
for details.



Installation output

MSGFgui.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MSGFgui
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'MSGFgui' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSGFgui'
    finding HTML links ... done
    MSGFgui-package                         html  
    MSGFgui                                 html  
    currentData                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'MSGFgui' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'MSGFgui' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (MSGFgui)
Making 'packages.html' ... done

Tests output

MSGFgui.Rcheck/tests/test-all.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> test_check('MSGFgui')
Loading required package: MSGFgui
Loading required package: mzR
Loading required package: Rcpp
Loading required package: xlsx
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
Warning message:
Package 'MSGFgui' is deprecated and will be removed from Bioconductor
  version 3.15 
> 
> proc.time()
   user  system elapsed 
   5.85    0.37    6.01 

Example timings

MSGFgui.Rcheck/MSGFgui-Ex.timings

nameusersystemelapsed
MSGFgui000
currentData000