Multiple platform build/check report for BioC 3.9 - CHECK report for MSGFplus on tokay2

Package: MSGFplus

Version: 1.17.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSGFplus_1.17.1.tar.gz

StartedAt: 2019-04-09 04:25:32 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:26:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 72.1 seconds

RetCode: 0

Status: OK

CheckDir: MSGFplus.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSGFplus_1.17.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSGFplus.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSGFplus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSGFplus' version '1.17.1'
* 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 'MSGFplus' 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
Namespace in Imports field not imported from: 'ProtGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSGFplus.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MSGFplus_1.17.1.tar.gz && rm -rf MSGFplus.buildbin-libdir && mkdir MSGFplus.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSGFplus.buildbin-libdir MSGFplus_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MSGFplus_1.17.1.zip && rm MSGFplus_1.17.1.tar.gz MSGFplus_1.17.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 44719  100 44719    0     0   748k      0 --:--:-- --:--:-- --:--:--  856k

install for i386

* installing *source* package 'MSGFplus' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSGFplus'
    finding HTML links ... done
    MSGFplus-package                        html  
    chargeRange                             html  
    db                                      html  
    enzyme                                  html  
    fragmentation                           html  
    getMSGFpar                              html  
    instrument                              html  
    isotopeError                            html  
    lengthRange                             html  
    matches                                 html  
    mods                                    html  
    msgfAsync-class                         html  
    msgfPar-class                           html  
    msgfPar                                 html  
    msgfParChargeRange-class                html  
    msgfParEnzyme-class                     html  
    msgfParFragmentation-class              html  
    msgfParFromID                           html  
    msgfParGUI                              html  
    msgfParInstrument-class                 html  
    msgfParIsotopeError-class               html  
    msgfParLengthRange-class                html  
    msgfParMatches-class                    html  
    msgfParModification-class               html  
    msgfParModificationList-class           html  
    msgfParNtt-class                        html  
    msgfParProtocol-class                   html  
    msgfParTda-class                        html  
    msgfParTolerance-class                  html  
    ntt                                     html  
    protocol                                html  
    runMSGF                                 html  
    tda                                     html  
    tolerance                               html  
** 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

install for x64

* installing *source* package 'MSGFplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSGFplus' as MSGFplus_1.17.1.zip
* DONE (MSGFplus)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MSGFplus' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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('MSGFplus')
Loading required package: MSGFplus

Attaching package: 'MSGFplus'

The following object is masked from 'package:testthat':

    matches

== testthat results  ===========================================================
OK: 169 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   1.46    0.18    2.40


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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('MSGFplus')
Loading required package: MSGFplus

Attaching package: 'MSGFplus'

The following object is masked from 'package:testthat':

    matches

== testthat results  ===========================================================
OK: 169 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   1.51    0.07    2.26

name	user	system	elapsed
chargeRange	0	0	0
db	0	0	0
enzyme	0.02	0.00	0.02
fragmentation	0	0	0
getMSGFpar	0.01	0.00	0.01
instrument	0	0	0
isotopeError	0.02	0.00	0.02
lengthRange	0	0	0
matches	0	0	0
mods	0	0	0
msgfAsync-class	0	0	0
msgfPar-class	0	0	0
msgfPar	0.04	0.00	0.03
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0	0	0
msgfParFragmentation-class	0	0	0
msgfParFromID	0	0	0
msgfParGUI	0	0	0
msgfParInstrument-class	0	0	0
msgfParIsotopeError-class	0	0	0
msgfParLengthRange-class	0	0	0
msgfParMatches-class	0	0	0
msgfParModification-class	0	0	0
msgfParModificationList-class	0.01	0.00	0.02
msgfParNtt-class	0	0	0
msgfParProtocol-class	0.02	0.00	0.01
msgfParTda-class	0	0	0
msgfParTolerance-class	0	0	0
ntt	0	0	0
protocol	0	0	0
runMSGF	0	0	0
tda	0.01	0.00	0.02
tolerance	0	0	0

name	user	system	elapsed
chargeRange	0	0	0
db	0.01	0.00	0.01
enzyme	0	0	0
fragmentation	0	0	0
getMSGFpar	0.01	0.00	0.02
instrument	0	0	0
isotopeError	0.00	0.01	0.02
lengthRange	0	0	0
matches	0	0	0
mods	0.02	0.00	0.01
msgfAsync-class	0	0	0
msgfPar-class	0	0	0
msgfPar	0.02	0.00	0.01
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0	0	0
msgfParFragmentation-class	0	0	0
msgfParFromID	0	0	0
msgfParGUI	0	0	0
msgfParInstrument-class	0.01	0.00	0.01
msgfParIsotopeError-class	0	0	0
msgfParLengthRange-class	0	0	0
msgfParMatches-class	0	0	0
msgfParModification-class	0	0	0
msgfParModificationList-class	0.02	0.00	0.02
msgfParNtt-class	0	0	0
msgfParProtocol-class	0	0	0
msgfParTda-class	0	0	0
msgfParTolerance-class	0	0	0
ntt	0	0	0
protocol	0	0	0
runMSGF	0	0	0
tda	0	0	0
tolerance	0.01	0.00	0.02

CHECK report for MSGFplus on tokay2

Summary

Command output

Installation output

Tests output

Example timings