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CHECK report for SIMAT on tokay1

This page was generated on 2018-04-12 13:25:54 -0400 (Thu, 12 Apr 2018).

Package 1298/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMAT 1.10.0
Mo R. Nezami Ranjbar
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SIMAT
Branch: RELEASE_3_6
Last Commit: aae6512
Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIMAT
Version: 1.10.0
Command: rm -rf SIMAT.buildbin-libdir SIMAT.Rcheck && mkdir SIMAT.buildbin-libdir SIMAT.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIMAT.buildbin-libdir SIMAT_1.10.0.tar.gz >SIMAT.Rcheck\00install.out 2>&1 && cp SIMAT.Rcheck\00install.out SIMAT-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SIMAT.buildbin-libdir --install="check:SIMAT-install.out" --force-multiarch --no-vignettes --timings SIMAT_1.10.0.tar.gz
StartedAt: 2018-04-12 03:13:16 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:15:02 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:  OK  
CheckDir: SIMAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SIMAT.buildbin-libdir SIMAT.Rcheck && mkdir SIMAT.buildbin-libdir SIMAT.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIMAT.buildbin-libdir SIMAT_1.10.0.tar.gz >SIMAT.Rcheck\00install.out 2>&1 && cp SIMAT.Rcheck\00install.out SIMAT-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SIMAT.buildbin-libdir --install="check:SIMAT-install.out" --force-multiarch --no-vignettes --timings SIMAT_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMAT.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 'SIMAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIMAT' version '1.10.0'
* 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 'SIMAT' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getRIStandard: no visible global function definition for 'read.csv'
plotEIC: no visible global function definition for 'stack'
plotEIC: no visible global function definition for 'dnorm'
plotEIC: no visible global function definition for 'dev.copy'
plotEIC: no visible binding for global variable 'pdf'
plotEIC: no visible global function definition for 'dev.off'
plotTIC: no visible binding for global variable 'rt'
Undefined global functions or variables:
  dev.copy dev.off dnorm pdf read.csv rt stack
Consider adding
  importFrom("grDevices", "dev.copy", "dev.off", "pdf")
  importFrom("stats", "dnorm", "rt")
  importFrom("utils", "read.csv", "stack")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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-3.6-bioc/meat/SIMAT.Rcheck/00check.log'
for details.



Installation output

SIMAT.Rcheck/00install.out


install for i386

* installing *source* package 'SIMAT' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SIMAT'
    finding HTML links ... done
    Library                                 html  
    RItable                                 html  
    Run                                     html  
    SIMAT-package                           html  
    Targets                                 html  
    getEIC                                  html  
    getPeak                                 html  
    getPeakScore                            html  
    getRI                                   html  
    getRIStandard                           html  
    getScore                                html  
    getTarget                               html  
    getTargetTable                          html  
    optFrag                                 html  
    plotEIC                                 html  
    plotTIC                                 html  
    putTargetTable                          html  
    readCDF                                 html  
    readMSL                                 html  
    target.table                            html  
    writeMSL                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SIMAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMAT' as SIMAT_1.10.0.zip
* DONE (SIMAT)
In R CMD INSTALL
In R CMD INSTALL

Tests output

SIMAT.Rcheck/tests_i386/runTests.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.

> ## function for RUnit tests
> 
> BiocGenerics:::testPackage("SIMAT")


RUNIT TEST PROTOCOL -- Thu Apr 12 03:14:53 2018 
*********************************************** 
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SIMAT RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 
Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMAT.buildbin-libdir/SIMAT/data/Targets.MSL': No such file or directory
> 
> proc.time()
   user  system elapsed 
   3.14    0.10    3.23 

SIMAT.Rcheck/tests_x64/runTests.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.

> ## function for RUnit tests
> 
> BiocGenerics:::testPackage("SIMAT")


RUNIT TEST PROTOCOL -- Thu Apr 12 03:14:58 2018 
*********************************************** 
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SIMAT RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15 
Number of errors: 0 
Number of failures: 0 
Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMAT.buildbin-libdir/SIMAT/data/Targets.MSL': No such file or directory
> 
> proc.time()
   user  system elapsed 
   4.64    0.09    4.71 

Example timings

SIMAT.Rcheck/examples_i386/SIMAT-Ex.timings

nameusersystemelapsed
Library0.020.000.01
RItable000
Run0.090.000.09
Targets0.020.000.02
getEIC0.210.000.22
getPeak0.330.040.36
getPeakScore0.290.030.33
getRI000
getRIStandard000
getScore000
getTarget2.110.022.12
getTargetTable000
optFrag2.330.002.33
plotEIC1.940.011.95
plotTIC0.420.020.44
putTargetTable0.000.020.02
readCDF1.700.011.71

SIMAT.Rcheck/examples_x64/SIMAT-Ex.timings

nameusersystemelapsed
Library0.010.000.02
RItable0.020.000.01
Run0.060.020.08
Targets000
getEIC0.170.000.18
getPeak0.470.000.47
getPeakScore0.340.000.34
getRI000
getRIStandard000
getScore000
getTarget3.030.013.05
getTargetTable0.030.000.03
optFrag2.370.002.38
plotEIC2.290.002.28
plotTIC0.780.020.80
putTargetTable0.010.000.01
readCDF3.410.003.41