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CHECK report for sigsquared on tokay1

This page was generated on 2019-04-13 11:24:56 -0400 (Sat, 13 Apr 2019).

Package 1447/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigsquared 1.14.0
UnJin Lee
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/sigsquared
Branch: RELEASE_3_8
Last Commit: 689d036
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sigsquared
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sigsquared_1.14.0.tar.gz
StartedAt: 2019-04-13 05:32:51 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:35:36 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 164.6 seconds
RetCode: 0
Status:  OK  
CheckDir: sigsquared.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sigsquared_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sigsquared.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 'sigsquared/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigsquared' version '1.14.0'
* 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 'sigsquared' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
* 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: 'methods'
  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
analysisPipeline,ExpressionSet-geneSignature: no visible binding for
  global variable 'nCores'
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for 'mcparallel'
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for 'mccollect'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable 'mc'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable 'nCores'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for 'mcparallel'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for 'mccollect'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'new'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable 'mc'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable 'nCores'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'rnorm'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'mcparallel'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for 'mccollect'
genGeneDirect,matrix: no visible global function definition for 'sd'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'new'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'rnorm'
optCF,ExpressionSet-geneSignature: no visible global function
  definition for 'optim'
summarizeSolnSpace,solnSpace: no visible global function definition for
  'sd'
Undefined global functions or variables:
  mc mccollect mcparallel nCores new optim rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "optim", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
analysisPipeline 15.35   0.05   15.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
analysisPipeline 16.84   0.05   16.89
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/sigsquared.Rcheck/00check.log'
for details.



Installation output

sigsquared.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sigsquared_1.14.0.tar.gz && rm -rf sigsquared.buildbin-libdir && mkdir sigsquared.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigsquared.buildbin-libdir sigsquared_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sigsquared_1.14.0.zip && rm sigsquared_1.14.0.tar.gz sigsquared_1.14.0.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
  0  150k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  150k  100  150k    0     0  2066k      0 --:--:-- --:--:-- --:--:-- 2144k

install for i386

* installing *source* package 'sigsquared' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'ensembleCostFcn' with signature 'dataSet="ExpressionSet",geneSig="geneSignature",jpdf="solnSpace"': no definition for class "solnSpace"
in method for 'getCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
in method for 'summarizeCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
** help
*** installing help indices
  converting help for package 'sigsquared'
    finding HTML links ... done
    BrCa443                                 html  
    analysisPipeline                        html  
    ensembleAdjustable                      html  
    geneSignature-class                     html  
    setGeneSignature                        html  
    sigsquared                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sigsquared' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigsquared' as sigsquared_1.14.0.zip
* DONE (sigsquared)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sigsquared' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

sigsquared.Rcheck/tests_i386/runTests.Rout


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.

> BiocGenerics:::testPackage("sigsquared")


RUNIT TEST PROTOCOL -- Sat Apr 13 05:35:26 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.45    0.17    1.68 

sigsquared.Rcheck/tests_x64/runTests.Rout


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.

> BiocGenerics:::testPackage("sigsquared")


RUNIT TEST PROTOCOL -- Sat Apr 13 05:35:29 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.50    0.18    1.67 

Example timings

sigsquared.Rcheck/examples_i386/sigsquared-Ex.timings

nameusersystemelapsed
analysisPipeline15.35 0.0515.39
ensembleAdjustable0.080.020.09
geneSignature-class000
setGeneSignature000

sigsquared.Rcheck/examples_x64/sigsquared-Ex.timings

nameusersystemelapsed
analysisPipeline16.84 0.0516.89
ensembleAdjustable0.10.00.1
geneSignature-class000
setGeneSignature000