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BioC 3.4: CHECK report for sigsquared on moscato1

This page was generated on 2016-09-21 03:46:49 -0700 (Wed, 21 Sep 2016).

Package 1117/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigsquared 1.5.0
UnJin Lee
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sigsquared
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ ERROR ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: sigsquared
Version: 1.5.0
Command: rm -rf sigsquared.buildbin-libdir sigsquared.Rcheck && mkdir sigsquared.buildbin-libdir sigsquared.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigsquared.buildbin-libdir sigsquared_1.5.0.tar.gz >sigsquared.Rcheck\00install.out 2>&1 && cp sigsquared.Rcheck\00install.out sigsquared-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sigsquared.buildbin-libdir --install="check:sigsquared-install.out" --force-multiarch --no-vignettes --timings sigsquared_1.5.0.tar.gz
StartedAt: 2016-09-20 16:38:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:40:44 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 108.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: sigsquared.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sigsquared.buildbin-libdir sigsquared.Rcheck && mkdir sigsquared.buildbin-libdir sigsquared.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigsquared.buildbin-libdir sigsquared_1.5.0.tar.gz >sigsquared.Rcheck\00install.out 2>&1 && cp sigsquared.Rcheck\00install.out sigsquared-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sigsquared.buildbin-libdir --install="check:sigsquared-install.out" --force-multiarch --no-vignettes --timings sigsquared_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/sigsquared.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.5.0'
* 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 '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
** 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: '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'sigsquared-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ensembleAdjustable
> ### Title: Application of geneSignature object
> ### Aliases: ensembleAdjustable
> 
> ### ** Examples
> 
> require(Biobase)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> ## Generate test geneSignature object with 0s for thresholds
> gs <- setGeneSignature(g=new("geneSignature"), direct=c(1,1,1), genes=c("A", "B", "C"), thresholds=c(0, 0, 0))
> 
> ## Generate randomly distributed matrix and ExpressionSet
> mat <- matrix(rnorm(9, 0, 1), nrow=3)
> rownames(mat) <- c("A", "B", "C")
> posmat <- abs(mat)
> expset <- new("ExpressionSet")
> exprs(expset) <- mat
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
Calls: exprs<- ... assayDataElementReplace -> .validate_assayDataElementReplace
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'sigsquared-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ensembleAdjustable
> ### Title: Application of geneSignature object
> ### Aliases: ensembleAdjustable
> 
> ### ** Examples
> 
> require(Biobase)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> ## Generate test geneSignature object with 0s for thresholds
> gs <- setGeneSignature(g=new("geneSignature"), direct=c(1,1,1), genes=c("A", "B", "C"), thresholds=c(0, 0, 0))
> 
> ## Generate randomly distributed matrix and ExpressionSet
> mat <- matrix(rnorm(9, 0, 1), nrow=3)
> rownames(mat) <- c("A", "B", "C")
> posmat <- abs(mat)
> expset <- new("ExpressionSet")
> exprs(expset) <- mat
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
Calls: exprs<- ... assayDataElementReplace -> .validate_assayDataElementReplace
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/sigsquared.Rcheck/00check.log'
for details.

sigsquared.Rcheck/00install.out:


install for i386

* installing *source* package 'sigsquared' ...
** R
** data
** inst
** preparing 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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'sigsquared' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigsquared' as sigsquared_1.5.0.zip
* DONE (sigsquared)

sigsquared.Rcheck/examples_i386/sigsquared-Ex.timings:

nameusersystemelapsed
analysisPipeline11.75 0.0111.76

sigsquared.Rcheck/examples_x64/sigsquared-Ex.timings:

nameusersystemelapsed
analysisPipeline13.37 0.0413.41