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CHECK report for BioTIP on merida1

This page was generated on 2020-07-29 12:02:07 -0400 (Wed, 29 Jul 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BioTIP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 178/1879HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioTIP 1.3.0
Zhezhen Wang , X Holly Yang < xyang2@uchicago> and Yuxi (Jennifer) Sun
Snapshot Date: 2020-07-28 14:50:55 -0400 (Tue, 28 Jul 2020)
URL: https://git.bioconductor.org/packages/BioTIP
Branch: master
Last Commit: b00b2f8
Last Changed Date: 2020-07-20 18:48:03 -0400 (Mon, 20 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BioTIP
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioTIP_1.3.0.tar.gz
StartedAt: 2020-07-29 04:54:40 -0400 (Wed, 29 Jul 2020)
EndedAt: 2020-07-29 04:58:18 -0400 (Wed, 29 Jul 2020)
EllapsedTime: 217.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BioTIP.Rcheck
Warnings: 5

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioTIP_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioTIP.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.3.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:40: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:52: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:55: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:58: unexpected section header '\value'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:63: unexpected section header '\description'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:68: unexpected section header '\examples'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:78: unexpected section header '\seealso'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:81: unexpected section header '\author'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT '
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:29: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:41: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:44: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:47: unexpected section header '\value'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:54: unexpected section header '\description'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:61: unexpected section header '\examples'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:71: unexpected section header '\seealso'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:74: unexpected section header '\author'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:77: unexpected END_OF_INPUT '
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioTIP.Rcheck/00install.out’ for details.
* 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: 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 ‘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’
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
  is legend matplot maxMCIms mtext par points queryHits rainbow
  readthrough sd subjectHits text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "matplot", "mtext", "par", "points", "text")
  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
prepare_Rd: man/optimize.sd_selection.Rd:40: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:52: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:55: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:58: unexpected section header '\value'
prepare_Rd: man/optimize.sd_selection.Rd:63: unexpected section header '\description'
prepare_Rd: man/optimize.sd_selection.Rd:68: unexpected section header '\examples'
prepare_Rd: man/optimize.sd_selection.Rd:78: unexpected section header '\seealso'
prepare_Rd: man/optimize.sd_selection.Rd:81: unexpected section header '\author'
prepare_Rd: man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT '
'
checkRd: (5) optimize.sd_selection.Rd:0-85: Must have a \description
prepare_Rd: man/sd_selection.Rd:29: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:41: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:44: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:47: unexpected section header '\value'
prepare_Rd: man/sd_selection.Rd:54: unexpected section header '\description'
prepare_Rd: man/sd_selection.Rd:61: unexpected section header '\examples'
prepare_Rd: man/sd_selection.Rd:71: unexpected section header '\seealso'
prepare_Rd: man/sd_selection.Rd:74: unexpected section header '\author'
prepare_Rd: man/sd_selection.Rd:77: unexpected END_OF_INPUT '
'
checkRd: (5) sd_selection.Rd:0-78: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘TSdist’ in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getTopMCI’
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 '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 '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

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'optimize.sd_selection'
  ‘method’ ‘control_df’ ‘control_samplesL’

Undocumented arguments in documentation object 'plot_Ic_Simulation'
  ‘which2point’

Documented arguments not in \usage in documentation object 'plot_SS_Simulation':
  ‘which2point’

Undocumented arguments in documentation object 'sd_selection'
  ‘method’ ‘control_df’ ‘control_samplesL’

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: 5 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioTIP.Rcheck/00check.log’
for details.



Installation output

BioTIP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioTIP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BioTIP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:40: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:52: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:55: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:58: unexpected section header '\value'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:63: unexpected section header '\description'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:68: unexpected section header '\examples'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:78: unexpected section header '\seealso'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:81: unexpected section header '\author'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT '
'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:29: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:41: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:44: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:47: unexpected section header '\value'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:54: unexpected section header '\description'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:61: unexpected section header '\examples'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:71: unexpected section header '\seealso'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:74: unexpected section header '\author'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/BioTIP/man/sd_selection.Rd:77: unexpected END_OF_INPUT '
'
*** 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.shrink2.0210.2172.240
cor.shrink0.4990.0700.570
getBiotypes0.7020.0860.791
getCTS0.0010.0000.002
getCluster_methods0.0320.0020.034
getIc0.0080.0000.009
getIc.new0.7250.1850.912
getMCI0.0130.0000.014
getMaxMCImember0.0530.0020.055
getMaxStats0.0190.0010.020
getNetwork0.0210.0010.021
getReadthrough3.6730.0873.771
plotBar_MCI0.0390.0020.041
plotIc0.0040.0010.005
plotMaxMCI0.0030.0000.004
plot_Ic_Simulation0.0020.0000.003
plot_MCI_Simulation0.0060.0010.007
plot_SS_Simulation0.0090.0000.011
simulationMCI0.0050.0010.036
simulation_Ic0.0140.0010.054
simulation_Ic_sample0.0070.0000.008