LowMACA 1.8.0
Stefano de Pretis , Giorgio Melloni
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/LowMACA | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | 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 LowMACA_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/LowMACA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ 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 ‘LowMACA’ 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
.MAD: no visible global function definition for ‘median’
.Trident_Score: no visible global function definition for ‘data’
.alnWeights: no visible global function definition for ‘aggregate’
.clustalOAlign: no visible global function definition for
‘download.file’
.clustalOAlign: no visible global function definition for ‘write.table’
.filterMAlign: no visible binding for global variable ‘median’
.makeNullProfile: no visible binding for global variable ‘median’
.makeNullProfile: no visible binding for global variable ‘sd’
.makeNullProfile: no visible global function definition for ‘qgamma’
.makeNullProfile: no visible global function definition for ‘pgamma’
.makeUniformModel: no visible binding for global variable ‘median’
.makeUniformModel : pn.optim.aic : polyOrderChisq: no visible global
function definition for ‘lm’
.makeUniformModel : pn.optim.aic : polyOrderChisq: no visible global
function definition for ‘AIC’
.makeUniformModel: no visible global function definition for ‘par’
.makeUniformModel: no visible global function definition for ‘plot’
.makeUniformModel: no visible global function definition for ‘lines’
.profileDensity: no visible global function definition for ‘density’
.profileEntropy: no visible global function definition for ‘pgamma’
.sampleUnifEntropyL: no visible binding for global variable ‘median’
.sampleUnifEntropyL.old: no visible binding for global variable
‘median’
.sampleUnifEntropyL.old : <anonymous>: no visible global function
definition for ‘density’
.scoreMatrix: no visible global function definition for ‘read.table’
.scoreMatrix : <anonymous>: no visible global function definition for
‘median’
allPfamAnalysis: no visible global function definition for ‘read.table’
allPfamAnalysis : <anonymous>: no visible global function definition
for ‘capture.output’
allPfamAnalysis : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘pbinom’
showTumorType: no visible global function definition for ‘aggregate’
bpAll,LowMACA: no visible global function definition for
‘colorRampPalette’
bpAll,LowMACA: no visible global function definition for ‘barplot’
bpAll,LowMACA: no visible global function definition for ‘legend’
entropy,LowMACA: no visible global function definition for ‘p.adjust’
lfm,LowMACA: no visible global function definition for ‘p.adjust’
lmPlot,LowMACA: no visible global function definition for ‘par’
lmPlot,LowMACA: no visible global function definition for ‘layout’
lmPlot,LowMACA: no visible global function definition for
‘colorRampPalette’
lmPlot,LowMACA: no visible global function definition for ‘barplot’
lmPlot,LowMACA: no visible global function definition for ‘axis’
lmPlot,LowMACA: no visible global function definition for ‘plot.new’
lmPlot,LowMACA: no visible global function definition for ‘plot.window’
lmPlot,LowMACA: no visible global function definition for ‘topo.colors’
lmPlot,LowMACA: no visible global function definition for ‘rect’
lmPlot,LowMACA: no visible global function definition for ‘text’
nullProfile,LowMACA: no visible global function definition for
‘p.adjust’
nullProfile,LowMACA: no visible global function definition for
‘barplot’
nullProfile,LowMACA: no visible global function definition for ‘axis’
nullProfile,LowMACA: no visible global function definition for ‘lines’
nullProfile,LowMACA: no visible global function definition for ‘text’
protter,LowMACA: no visible global function definition for ‘p.adjust’
protter,LowMACA: no visible global function definition for
‘download.file’
protter,LowMACA : <anonymous>: no visible global function definition
for ‘png’
protter,LowMACA : <anonymous>: no visible global function definition
for ‘par’
protter,LowMACA : <anonymous>: no visible global function definition
for ‘plot’
protter,LowMACA : <anonymous>: no visible global function definition
for ‘text’
protter,LowMACA : <anonymous>: no visible global function definition
for ‘dev.off’
show,LowMACA: no visible global function definition for ‘head’
Undefined global functions or variables:
AIC aggregate axis barplot capture.output colorRampPalette data
density dev.off download.file head layout legend lines lm median
p.adjust par pbinom pgamma plot plot.new plot.window png qgamma
read.table rect sd text topo.colors write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "png",
"topo.colors")
importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
"par", "plot", "plot.new", "plot.window", "rect", "text")
importFrom("stats", "AIC", "aggregate", "density", "lm", "median",
"p.adjust", "pbinom", "pgamma", "qgamma", "sd")
importFrom("utils", "capture.output", "data", "download.file", "head",
"read.table", "write.table")
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 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 ... ERROR
Running examples in ‘LowMACA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMutations
> ### Title: Retrieve mutation data for a LowMACA object
> ### Aliases: getMutations
>
> ### ** Examples
>
> #Create an object of class LowMACA
> lm <- newLowMACA(pfam="PF12906")
> #Change some paramters
> #By default, LowMACA retrieve only missense mutations.
> #We want all mutations
> lmParams(lm)[['mutation_type']] <- 'all'
> #By default, LowMACA takes mutations from all the kinds of tumor
> #We want just prostate cancer samples
> lmParams(lm)[['tumor_type']] <- 'prad'
> lm <- getMutations(lm)
Getting mutations from cancers studies...
Error in `[.data.frame`(getGeneticProfiles(mycgds, i), , c(1:2)) :
undefined columns selected
Calls: getMutations ... .getGeneMutations -> applyfun -> FUN -> [ -> [.data.frame
Execution halted
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/LowMACA.Rcheck/00check.log’
for details.