lpNet 2.5.0
Lars Kaderali
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lpNet | | 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 | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lpNet_2.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/lpNet.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lpNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lpNet’ version ‘2.5.0’
* 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 ‘lpNet’ 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
* 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
.calcRangeLambda_steadyState: no visible global function definition for
‘var’
.calcRangeLambda_timeSeries: no visible global function definition for
‘var’
.calculatePredictionValue_Kfold_ts: no visible global function
definition for ‘rnorm’
.calculatePredictionValue_LOOCV_ss: no visible global function
definition for ‘rnorm’
.calculatePredictionValue_LOOCV_ts: no visible global function
definition for ‘rnorm’
.set_per_gene_exp_time_values: no visible global function definition
for ‘rnorm’
.set_per_gene_exp_values: no visible global function definition for
‘rnorm’
.set_per_gene_time_values: no visible global function definition for
‘rnorm’
.set_per_gene_values: no visible global function definition for ‘rnorm’
.set_single_values: no visible global function definition for ‘rnorm’
getSampleAdja: no visible binding for global variable ‘median’
getSampleAdjaMAD: no visible binding for global variable ‘median’
getSampleAdjaMAD: no visible binding for global variable ‘mad’
summarizeRepl: no visible binding for global variable ‘median’
Undefined global functions or variables:
mad median rnorm var
Consider adding
importFrom("stats", "mad", "median", "rnorm", "var")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runitCalcActivation.R’
Running ‘runitCalcPredictionKfoldCV.R’
Running ‘runitCalcPredictionKfoldCV_timeSeries.R’
Running ‘runitCalcPredictionLOOCV.R’
Running ‘runitCalcPredictionLOOCV_timeSeries.R’
Running ‘runitCalcRangeLambda.R’
Running ‘runitDoILP.R’
Running ‘runitDoILP_timeSeries.R’
Running ‘runitGenerateTimeSeriesNetStates.R’
Running ‘runitGetAdja.R’
Running ‘runitGetBaseline.R’
Running ‘runitGetEdgeAnnot.R’
Running ‘runitGetObsMat.R’
Running ‘runitGetSampleAdja.R’
Running ‘runitGetSampleAdjaMAD.R’
Running ‘runitKfoldCV.R’
Running ‘runitKfoldCV_timeSeries.R’
Running ‘runitLOOCV.R’
Running ‘runitLOOCV_timeSeries.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘KEGGgraph’
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/lpNet.Rcheck/00check.log’
for details.