sigsquared 1.8.0
UnJin Lee
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/sigsquared | | Branch: RELEASE_3_5 | | Last Commit: a526da8 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sigsquared_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/sigsquared.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.8.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
analysisPipeline 11.656 0.012 11.676
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/sigsquared.Rcheck/00check.log’
for details.
* 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
* DONE (sigsquared)