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CHECK report for StarBioTrek on malbec2

This page was generated on 2020-10-17 11:55:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE StarBioTrek PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1742/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
StarBioTrek 1.14.0
Claudia Cava
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/StarBioTrek
Branch: RELEASE_3_11
Last Commit: 4eddfd1
Last Changed Date: 2020-04-27 15:03:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: StarBioTrek
Version: 1.14.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings StarBioTrek_1.14.0.tar.gz
StartedAt: 2020-10-17 05:50:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:56:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 331.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: StarBioTrek.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings StarBioTrek_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/StarBioTrek.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘StarBioTrek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘StarBioTrek’ version ‘1.14.0’
* 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 ‘StarBioTrek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
* 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: ‘AnnotationDbi’
  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
svm_classification: no visible binding for global variable ‘Target’
Undefined global functions or variables:
  Target
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'svm_classification':
  ‘Target’

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 ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/StarBioTrek.Rcheck/00check.log’
for details.



Installation output

StarBioTrek.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL StarBioTrek
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘StarBioTrek’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (StarBioTrek)

Tests output


Example timings

StarBioTrek.Rcheck/StarBioTrek-Ex.timings

nameusersystemelapsed
ConvertedIDgenes4.2230.0444.267
GE_matrix0.0620.0000.061
GE_matrix_mean0.0640.0000.063
GetData000
GetPathData0.0020.0030.006
GetPathNet0.0040.0000.003
IPPI000
SelectedSample0.1760.0080.185
average1.1970.0801.277
circleplot0.7000.0000.701
dsscorecrtlk0.0240.0000.024
eucdistcrtlk0.0220.0000.022
getNETdata000
listpathnet0.9520.0000.953
pathnet0.2380.0000.239
plotcrosstalk0.0090.0000.008
stdv0.0210.0000.021
svm_classification000