Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-03 11:05:14 -0500 (Sat, 03 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4152
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BioTIP on nebbiolo1


To the developers/maintainers of the BioTIP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioTIP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 200/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioTIP 1.13.0  (landing page)
Yuxi (Jennifer) Sun , Zhezhen Wang , and X Holly Yang
Snapshot Date: 2022-12-02 14:00:12 -0500 (Fri, 02 Dec 2022)
git_url: https://git.bioconductor.org/packages/BioTIP
git_branch: master
git_last_commit: e763a88
git_last_commit_date: 2022-11-01 11:20:36 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'scran' which is not available

Summary

Package: BioTIP
Version: 1.13.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BioTIP_1.13.0.tar.gz
StartedAt: 2022-12-02 19:22:07 -0500 (Fri, 02 Dec 2022)
EndedAt: 2022-12-02 19:25:11 -0500 (Fri, 02 Dec 2022)
EllapsedTime: 183.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BioTIP.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BioTIP_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BioTIP.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.13.0’
* 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 ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BioTIP.wrap: warning in getMaxMCImember(membersL[["members"]],
  membersL[["MCI"]], min = getTopMCI.gene.minsize, n =
  n.getMaxMCImember): partial argument match of 'min' to 'minsize'
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
  abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
  match of 'weight' to 'weights'
BioTIP.wrap: no visible global function definition for ‘assayNames’
BioTIP.wrap : myplotIc: no visible global function definition for ‘pdf’
BioTIP.wrap : myplotIc: no visible global function definition for ‘par’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘text’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘getTopHVGs’
BioTIP.wrap: no visible global function definition for
  ‘normalized_counts’
BioTIP.wrap: no visible global function definition for ‘logcounts’
BioTIP.wrap: no visible global function definition for ‘pdf’
BioTIP.wrap: no visible global function definition for ‘abline’
BioTIP.wrap: no visible global function definition for ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘par’
BioTIP.wrap: no visible binding for global variable
  ‘getTopMCI.gene.maxsiz’
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: no visible binding for global variable ‘pb’
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 assayNames axis barplot boxplot cor cutree density
  dev.off dist getTopHVGs getTopMCI.gene.maxsiz hclust i is legend
  logcounts matplot maxMCIms mtext normalized_counts par pb pdf points
  queryHits rainbow readthrough sd subjectHits text title
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "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 ... OK
* 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 'avg.cor.shrink':
avg.cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

Codoc mismatches from documentation object 'cor.shrink':
cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

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 = 1)
  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 = 1,
                 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: 'PCC_sample.target' Code: 1 Docs: c("average", "zero", "half")
    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 'plotIc':
plotIc
  Code: function(Ic, las = 0, order = NULL, ylab = "Ic.shrink", col =
                 "black", main = NULL, add = FALSE, ylim = NULL, lty =
                 1:5, lwd = 1)
  Docs: function(Ic, las = 0, order = NULL, ylab = "Ic", col = "black",
                 main = NULL, add = FALSE, ylim = NULL, lty = 1:5, lwd
                 = 1)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

Codoc mismatches from documentation object 'plot_Ic_Simulation':
plot_Ic_Simulation
  Code: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic.shrink", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Docs: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

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 = 1)
  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 = 1)
  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 ... OK
* 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 LazyData ... OK
* 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 ...
  ‘BioTIP.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BioTIP.Rcheck/00check.log’
for details.



Installation output

BioTIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BioTIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BioTIP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BioTIP)

Tests output


Example timings

BioTIP.Rcheck/BioTIP-Ex.timings

nameusersystemelapsed
avg.cor.shrink2.6330.3032.936
cor.shrink0.5230.0190.543
getBiotypes0.4830.0310.515
getCTS0.0020.0000.002
getCluster_methods0.0600.0070.068
getIc0.0070.0000.007
getIc.new0.5130.1120.625
getMCI0.0080.0030.012
getMaxMCImember0.0480.0040.052
getMaxStats0.0110.0000.011
getNetwork0.0160.0000.016
getReadthrough2.8390.0352.875
plotBar_MCI0.0250.0000.025
plotIc0.0020.0000.002
plotMaxMCI0.0020.0000.002
plot_Ic_Simulation0.0020.0000.002
plot_MCI_Simulation0.0050.0000.005
plot_SS_Simulation0.0080.0000.008
sd_selection0.0020.0000.002
simulationMCI0.0050.0000.025
simulation_Ic0.0060.0030.040
simulation_Ic_sample0.0060.0000.006