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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioTIP_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BioTIP.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
vignettes/.RData
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioTIP’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Hmisc’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
match of 'weight' to 'weights'
cor.shrink: no visible binding for global variable ‘sd’
getBiotypes: no visible global function definition for ‘is’
getBiotypes: no visible global function definition for ‘queryHits’
getBiotypes: no visible global function definition for ‘subjectHits’
getBiotypes: no visible global function definition for ‘aggregate’
getCluster_methods : <anonymous>: no visible global function definition
for ‘hclust’
getCluster_methods : <anonymous>: no visible global function definition
for ‘dist’
getCluster_methods: no visible global function definition for ‘par’
getCluster_methods : <anonymous>: no visible global function definition
for ‘cutree’
getIc : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible binding for global variable ‘sd’
getMCI_inner : <anonymous>: no visible global function definition for
‘cor’
getMCI_inner : <anonymous>: no visible binding for global variable ‘sd’
getNextMaxStats: no visible binding for global variable ‘maxMCIms’
getReadthrough: no visible global function definition for ‘subjectHits’
getReadthrough: no visible binding for global variable ‘readthrough’
getReadthrough : <anonymous>: no visible global function definition for
‘queryHits’
getReadthrough : <anonymous>: no visible global function definition for
‘subjectHits’
optimize.sd_selection : <anonymous>: no visible binding for global
variable ‘sd’
optimize.sd_selection : <anonymous> : <anonymous>: no visible global
function definition for ‘sd’
plotBar_MCI: no visible global function definition for ‘par’
plotBar_MCI: no visible global function definition for ‘barplot’
plotBar_MCI: no visible global function definition for ‘rainbow’
plotBar_MCI: no visible global function definition for ‘title’
plotBar_MCI: no visible global function definition for ‘text’
plotIc: no visible global function definition for ‘matplot’
plotIc: no visible global function definition for ‘axis’
plotMaxMCI: no visible global function definition for ‘is’
plotMaxMCI: no visible global function definition for ‘matplot’
plotMaxMCI: no visible global function definition for ‘text’
plotMaxMCI: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘matplot’
plot_Ic_Simulation: no visible global function definition for ‘boxplot’
plot_Ic_Simulation: no visible global function definition for ‘points’
plot_Ic_Simulation: no visible global function definition for ‘mtext’
plot_Ic_Simulation: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘abline’
plot_MCI_Simulation: no visible global function definition for
‘boxplot’
plot_MCI_Simulation: no visible global function definition for ‘axis’
plot_MCI_Simulation: no visible global function definition for ‘points’
plot_MCI_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘density’
plot_SS_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘legend’
sd_selection : <anonymous>: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘i’
simulation_Ic_sample: no visible global function definition for
‘density’
simulation_Ic_sample: no visible global function definition for
‘abline’
simulation_Ic_sample: no visible global function definition for ‘text’
Undefined global functions or variables:
abline aggregate axis barplot boxplot cor cutree density dist hclust
i is legend matplot maxMCIms mtext par points queryHits rainbow
readthrough sd subjectHits text title
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "barplot", "boxplot",
"legend", "matplot", "mtext", "par", "points", "text",
"title")
importFrom("methods", "is")
importFrom("stats", "aggregate", "cor", "cutree", "density", "dist",
"hclust", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: gencode.Rd:19-21: Dropping empty section \description
checkRd: (5) gencode.Rd:0-23: Must have a \description
prepare_Rd: getIc.new.Rd:67-69: Dropping empty section \references
prepare_Rd: getMCI_inner.Rd:40-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘TSdist’
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘getNextMaxStats’ ‘getTopMCI’ ‘membersL’ ‘subcounts’
Undocumented data sets:
‘membersL’ ‘subcounts’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getIc':
getIc
Code: function(counts, sampleL, genes, output = c("Ic", "PCCg",
"PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
= c("everything", "all.obs", "complete.obs",
"na.or.complete", "pairwise.complete.obs"),
PCC_sample.target = c("average", "zero", "half"))
Docs: function(counts, sampleL, genes, output = c("Ic", "PCCg",
"PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
= c("everything", "all.obs", "complete.obs",
"na.or.complete", "pairwise.complete.obs"))
Argument names in code not in docs:
PCC_sample.target
Codoc mismatches from documentation object 'getIc.new':
getIc.new
Code: function(X, method = c("BioTIP", "Ic"), PCC_sample.target =
c("average", "zero", "half"), output = c("Ic", "PCCg",
"PCCs"))
Docs: function(X, method = c("BioTIP", "Ic"), PCC_sample.target =
c("average", "zero", "half"), output = c("IndexScore",
"PCCg", "PCCs"))
Mismatches in argument default values:
Name: 'output' Code: c("Ic", "PCCg", "PCCs") Docs: c("IndexScore", "PCCg", "PCCs")
Codoc mismatches from documentation object 'getMaxMCImember':
getMaxMCImember
Code: function(membersL, MCIl, minsize = 1, n = 1)
Docs: function(membersL, MCIl, minsize = 1)
Argument names in code not in docs:
n
Codoc mismatches from documentation object 'plotBar_MCI':
plotBar_MCI
Code: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
minsize = 3, states = NULL, title.size = 30)
Docs: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
minsize = 3, states = NULL)
Argument names in code not in docs:
title.size
Codoc mismatches from documentation object 'plot_SS_Simulation':
plot_SS_Simulation
Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
order = NULL, main = "1st max - 2nd max", ylab =
"Density")
Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
order = NULL, main = "1st max - 2nd max", ylab = "1st
max - 2nd max")
Mismatches in argument default values:
Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max"
Codoc mismatches from documentation object 'simulationMCI':
simulationMCI
Code: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
= c("cor", "BioTIP"), M = NULL)
Docs: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
= c("cor", "BioTIP"))
Argument names in code not in docs:
M
Codoc mismatches from documentation object 'simulation_Ic':
simulation_Ic
Code: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
"BioTIP"), shrink = TRUE, use = c("everything",
"all.obs", "complete.obs", "na.or.complete",
"pairwise.complete.obs"), output = c("Ic", "PCCg",
"PCCs"), PCC_sample.target = c("average", "zero",
"half"))
Docs: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
"BioTIP"), shrink = TRUE, use = c("everything",
"all.obs", "complete.obs", "na.or.complete",
"pairwise.complete.obs"), output = c("Ic", "PCCg",
"PCCs"))
Argument names in code not in docs:
PCC_sample.target
Codoc mismatches from documentation object 'simulation_Ic_sample':
simulation_Ic_sample
Code: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
NULL, main = "simulation of samples", fun = c("cor",
"BioTIP"), shrink = TRUE, use = c("everything",
"all.obs", "complete.obs", "na.or.complete",
"pairwise.complete.obs"), output = c("Ic", "PCCg",
"PCCs"), plot = FALSE, PCC_sample.target =
c("average", "zero", "half"))
Docs: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
NULL, main = "simulation of samples", fun = c("cor",
"BioTIP"), shrink = TRUE, use = c("everything",
"all.obs", "complete.obs", "na.or.complete",
"pairwise.complete.obs"), output = c("Ic", "PCCg",
"PCCs"), plot = FALSE)
Argument names in code not in docs:
PCC_sample.target
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plot_Ic_Simulation'
‘which2point’
Documented arguments not in \usage in documentation object 'plot_SS_Simulation':
‘which2point’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 15 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/BioTIP.Rcheck/00check.log’
for details.
