Package: MSGFgui

Version: 1.16.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFgui.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSGFgui_1.16.1.tar.gz

StartedAt: 2019-04-13 04:00:27 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:03:13 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 166.3 seconds

RetCode: 0

Status:  OK

CheckDir: MSGFgui.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFgui.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSGFgui_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSGFgui.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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 ... 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 ...
** 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 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSGFgui.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MSGFgui_1.16.1.tar.gz && rm -rf MSGFgui.buildbin-libdir && mkdir MSGFgui.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSGFgui.buildbin-libdir MSGFgui_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MSGFgui_1.16.1.zip && rm MSGFgui_1.16.1.tar.gz MSGFgui_1.16.1.zip
###
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100 1345k  100 1345k    0     0  15.1M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'MSGFgui' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'MSGFgui' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSGFgui' as MSGFgui_1.16.1.zip
* DONE (MSGFgui)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MSGFgui' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
> 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.37    0.31    4.18 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
== testthat results  ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.00    0.32    4.14