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 | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings sigsquared_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/sigsquared.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 ‘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 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/sigsquared.Rcheck/00check.log’
for details.