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CHECK report for MSGFgui on malbec2

This page was generated on 2020-10-17 11:55:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MSGFgui PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1137/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFgui 1.22.0
Thomas Lin Pedersen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MSGFgui
Branch: RELEASE_3_11
Last Commit: 2ef7364
Last Changed Date: 2020-04-27 14:43:55 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: MSGFgui
Version: 1.22.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSGFgui.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSGFgui_1.22.0.tar.gz
StartedAt: 2020-10-17 03:27:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:29:10 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MSGFgui.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSGFgui.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSGFgui_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MSGFgui.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSGFgui/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSGFgui’ version ‘1.22.0’
* 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 ‘MSGFgui’ 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 ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/MSGFgui.Rcheck/00check.log’
for details.



Installation output

MSGFgui.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSGFgui
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MSGFgui’ ...
** 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 (MSGFgui)

Tests output

MSGFgui.Rcheck/tests/test-all.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> test_check('MSGFgui')
Loading required package: MSGFgui
Loading required package: mzR
Loading required package: Rcpp
Loading required package: xlsx
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  5.347   0.417   4.985 

Example timings

MSGFgui.Rcheck/MSGFgui-Ex.timings

nameusersystemelapsed
MSGFgui000
currentData0.0020.0000.001