Thomas Lin Pedersen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MSGFgui |
| Branch: RELEASE_3_6 |
| Last Commit: 7a95439 |
| Last Changed Date: 2017-10-30 12:40:40 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:07 -0400 (Thu, 12 Apr 2018).
| Package 899/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSGFgui 1.12.0 Thomas Lin Pedersen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: MSGFgui |
| Version: 1.12.0 |
| Command: rm -rf MSGFgui.buildbin-libdir MSGFgui.Rcheck && mkdir MSGFgui.buildbin-libdir MSGFgui.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFgui.buildbin-libdir MSGFgui_1.12.0.tar.gz >MSGFgui.Rcheck\00install.out 2>&1 && cp MSGFgui.Rcheck\00install.out MSGFgui-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSGFgui.buildbin-libdir --install="check:MSGFgui-install.out" --force-multiarch --no-vignettes --timings MSGFgui_1.12.0.tar.gz |
| StartedAt: 2018-04-12 01:38:14 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:40:18 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 124.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSGFgui.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf MSGFgui.buildbin-libdir MSGFgui.Rcheck && mkdir MSGFgui.buildbin-libdir MSGFgui.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFgui.buildbin-libdir MSGFgui_1.12.0.tar.gz >MSGFgui.Rcheck\00install.out 2>&1 && cp MSGFgui.Rcheck\00install.out MSGFgui-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSGFgui.buildbin-libdir --install="check:MSGFgui-install.out" --force-multiarch --no-vignettes --timings MSGFgui_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MSGFgui.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.12.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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-3.6-bioc/meat/MSGFgui.Rcheck/00check.log'
for details.
MSGFgui.Rcheck/00install.out
install for i386
* installing *source* package 'MSGFgui' ...
** R
** inst
** preparing 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_1.12.0.zip
* DONE (MSGFgui)
In R CMD INSTALL
In R CMD INSTALL
|
MSGFgui.Rcheck/tests_i386/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
Loading required package: rJava
Loading required package: xlsxjars
== testthat results ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.85 0.14 3.45
|
MSGFgui.Rcheck/tests_x64/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
Loading required package: rJava
Loading required package: xlsxjars
== testthat results ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
5.26 0.28 5.53
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MSGFgui.Rcheck/examples_i386/MSGFgui-Ex.timings
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MSGFgui.Rcheck/examples_x64/MSGFgui-Ex.timings
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